Protein Conformation
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
Erabutoxins
X-Ray Diffraction
The scattering of x-rays by matter, especially crystals, with accompanying variation in intensity due to interference effects. Analysis of the crystal structure of materials is performed by passing x-rays through them and registering the diffraction image of the rays (CRYSTALLOGRAPHY, X-RAY). (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Models, Molecular
Magnetic Resonance Spectroscopy
Structure-Activity Relationship
Amino Acid Sequence
Protein Binding
Crystallography, X-Ray
Protein Structure, Secondary
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Circular Dichroism
Binding Sites
Protein Structure, Tertiary
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
Thermodynamics
A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)
Hydrogen Bonding
Solutions
Nuclear Magnetic Resonance, Biomolecular
Polymorphism, Single-Stranded Conformational
Variation in a population's DNA sequence that is detected by determining alterations in the conformation of denatured DNA fragments. Denatured DNA fragments are allowed to renature under conditions that prevent the formation of double-stranded DNA and allow secondary structure to form in single stranded fragments. These fragments are then run through polyacrylamide gels to detect variations in the secondary structure that is manifested as an alteration in migration through the gels.
Mutation
Models, Chemical
Molecular Dynamics Simulation
Ligands
A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)
Molecular dynamics studies of U1A-RNA complexes. (1/8682)
The U1A protein binds to a hairpin RNA and an internal-loop RNA with picomolar affinities. To probe the molecular basis of U1A binding, we performed state-of-the-art nanosecond molecular dynamics simulations on both complexes. The good agreement with experimental structures supports the protocols used in the simulations. We compare the dynamics, hydrogen-bonding occupancies, and interfacial flexibility of both complexes and also describe a rigid-body motion in the U1A-internal loop complex that is not observed in the U1A-hairpin simulation. We relate these observations to experimental mutational studies and highlight their significance in U1A binding affinity and specificity. (+info)Gangliosides of human kidney. (2/8682)
Five gangliosides isolated from human kidney have been characterized. The two main fractions were shown to be typical extraneural gangliosides in having lactose as their neutral carbohydrate moiety. Their structures were identified as: AcNeu(alpha2-3)Gal(beta1-4)Glc(beta1-1)Cer and AcNeu(alpha2-8)AcNeu(alpha2-3)Gal(beta1-4)Glc(beta1-1)Cer. The two main hexosamine-containing gangliosides are structurally related to human blood group substances of glycosphingolipid nature. The following structures are postulated: AcNeu(alpha2-3)Gal(beta1-4)GlcNAc(beta1-3)Gal(beta1-4)Glc(beta1-1)Cer and AcNeu(alpha2-3)Gal(beta1-4)[Fuc(alpha1-3)]GlcNAc(beta1-3)Gal(beta1-4)Glc(beta1-1) Cer. The third hexosamine-containing ganglioside belongs to a different series of glycolipids and was shown to have the structure of a major ganglioside of human brain: AcNeu(alpha2-3)Gal(beta1-3)GalNAc(beta1-4)[AcNeu(alpha2-3)]Gal(beta1-4)Glc(beta1- 1)Cer. The fatty acid structure of different gangliosides was shown to resemble that of neutral glycolipids of human kidney with the nonhydroxy acids C16:0, C22:0, and C24:0 as major components. (+info)Carbon 13 NMR study of nonenzymatic reactions of pyridoxal 5'-phosphate with selected amino acids and of related reactions. (3/8682)
Carbon 13 nuclear magnetic resonance spectroscopy has been used to monitor the nonenzymatic reactions of pyridoxal 5'-phosphate with glycine, alanine, valine, serine, and with several other model compounds. Isotopically enriched amino acids were employed so that low concentrations could be utilized while still allowing relatively rapid acquisition of spectral data. The results for alanine and serine are particularly noteworthy in that alanine is deaminated to pyruvate and pyruvate is aminated to alanine, but contrary to the enzymatic reactions of various serine dehydratases wherein serine is converted to pyruvate, the nonenzymatic reaction utilizing serine results in hydroxypruvate rather than pyruvate formation. In the reverse reaction, hydroxypyruvate is aminated to serine but very inefficiently relative to the amination of pyruvate to alanine. The experimental results have been formulated into a proposed reaction mechanism for deamination of amino acids by pyridoxal-P. (+info)Voltage sensors in domains III and IV, but not I and II, are immobilized by Na+ channel fast inactivation. (4/8682)
Using site-directed fluorescent labeling, we examined conformational changes in the S4 segment of each domain of the human skeletal muscle sodium channel (hSkM1). The fluorescence signals from S4 segments in domains I and II follow activation and are unaffected as fast inactivation settles. In contrast, the fluorescence signals from S4 segments in domains III and IV show kinetic components during activation and deactivation that correlate with fast inactivation and charge immobilization. These results indicate that in hSkM1, the S4 segments in domains III and IV are responsible for voltage-sensitive conformational changes linked to fast inactivation and are immobilized by fast inactivation, while the S4 segments in domains I and II are unaffected by fast inactivation. (+info)Quantitative study of polymer conformation and dynamics by single-particle tracking. (5/8682)
We present a new method for analyzing the dynamics of conformational fluctuations of individual flexible polymer molecules. In single-particle tracking (SPT), one end of the polymer molecule is tethered to an immobile substratum. A microsphere attached to the other end serves as an optical marker. The conformational fluctuations of the polymer molecule can be measured by optical microscopy via the motion of the microsphere. The bead-and-spring theory for polymer dynamics is further developed to account for the microsphere, and together the measurement and the theory yield quantitative information about molecular conformations and dynamics under nonperturbing conditions. Applying the method to measurements carried out on DNA molecules provides information complementary to recent studies of single DNA molecules under extensional force. Combining high precision measurements with the theoretical analysis presented here creates a powerful tool for studying conformational dynamics of biological and synthetic macromolecules at the single-molecule level. (+info)The structure of human parathyroid hormone-related protein(1-34) in near-physiological solution. (6/8682)
Parathyroid hormone-related protein plays a major role in the pathogenesis of humoral hypercalcemia of malignancy. Under normal physiological conditions, parathyroid hormone-related protein is produced in a wide variety of tissues and acts in an autocrine or paracrine fashion. Parathyroid hormone-related protein and parathyroid hormone bind to and activate the same G-protein-coupled receptor. Here we present the structure of the biologically active NH2-terminal domain of human parathyroid hormone-related protein(1-34) in near-physiological solution in the absence of crowding reagents as determined by two-dimensional proton magnetic resonance spectroscopy. An improved strategy for structure calculation revealed the presence of two helices, His-5-Leu-8 and Gln-16-Leu-27, connected by a flexible linker. The parathyroid hormone-related protein(1-34) structure and the structure of human parathyroid hormone(1-37) as well as human parathyroid hormone(1-34) are highly similar, except for the well defined turn, His-14-Ser-17, present in parathyroid hormone. Thus, the similarity of the binding affinities of parathyroid hormone and parathyroid hormone-related protein to their common receptor may be based on their structural similarity. (+info)Apolipoprotein A-I charge and conformation regulate the clearance of reconstituted high density lipoprotein in vivo. (7/8682)
While low apolipoprotein A-I (apoA-I) levels are primarily associated with increased high density lipoprotein (HDL) fractional catabolic rate (FCR), the factors that regulate the clearance of HDL from the plasma are unclear. In this study, the effect of lipid composition of reconstituted HDL particles (LpA-I) on their rate of clearance from rabbit plasma has been investigated. Sonicated LpA-I containing 1 to 2 molecules of purified human apoA-I and 5 to 120 molecules of palmitoyl-oleoyl phosphatidylcholine (POPC) exhibit similar charge and plasma FCR to that for lipid free apoA-I, 2.8 pools/day. Inclusion of 1 molecule of apoA-II to an LpA-I complex increases the FCR to 3.5 pools/day, a value similar to that observed for exchanged-labeled HDL3. In contrast, addition of 40 molecules of triglyceride, diglyceride, or cholesteryl ester to a sonicated LpA-I containing 120 moles of POPC and 2 molecules of apoA-I increases the negative charge of the particle and reduces the FCR to 1.8 pools/day. Discoidal LpA-I are the most positively charged lipoprotein particles and also have the fastest clearance rates, 4.5 pools/day. Immunochemical characterization of the different LpA-I particles shows that the exposure of an epitope at residues 98 to 121 of the apoA-I molecule is associated with an increased negative particle charge and a slower clearance from the plasma. We conclude that the charge and conformation of apoA-I are sensitive to the lipid composition of LpA-I and play a central role in regulating the clearance of these lipoproteins from plasma. conformation regulate the clearance of reconstituted high density lipoprotein in vivo. (+info)Application of distance geometry to 3D visualization of sequence relationships. (8/8682)
SUMMARY: We describe the application of distance geometry methods to the three-dimensional visualization of sequence relationships, with examples for mumps virus SH gene cDNA and prion protein sequences. Sequence-sequence distance measures may be obtained from either a multiple sequence alignment or from sets of pairwise alignments. AVAILABILITY: C/Perl code and HTML/VRML files from http://www.nibsc.ac.uk/dg3dseq/ (+info)
Language: English / Publisher: American Chemical Society / Subject: Molecular Structure and Molecular Conformation - Linus...
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Naphthalene
Dieter Cremer; Thomas Schmidt; Charles W. Bock (1985). "Theoretical determination of molecular structure and conformation. 14. ...
Bicyclo(6.2.0)decapentaene
"Theoretical determination of molecular structure and conformation. 14. Is bicyclo[6.2.0]decapentaene aromatic or antiaromatic ...
Neuromuscular-blocking drug
Lee, C.; Jones, T. (2002). "Molecular conformation-activity relationship of decamethonium congeners". British Journal of ... In general, molecular rigidity contributes to potency, while size affects whether a muscle relaxant shows a polarizing or a ... Comparing molecular lengths, the pachycurares dimethyltubocurarine and d-tubocurarine both are very rigid and measure close to ... Mivacurium for example has a molecular length of 3.6 nm when stretched out, far from the 2 to 2.1 nm optimum. Mivacurium, ...
Decamethonium
"Molecular conformation-activity relationship of decamethonium congeners". British Journal of Anaesthesia. 88 (5): 692-9. doi: ...
Aldosterone
Duax, William L.; Hauptman, Herbert (1972). "Crystal structure and molecular conformation of aldosterone". J. Am. Chem. Soc. 94 ... A Cellular And Molecular Approaoch. Elsevier/Saunders. p. 1300. ISBN 1-4160-2328-3. Williams GH, Dluhy RG (November 1972). " ... Molecular and Cellular Endocrinology. 217 (1-2): 1-21. doi:10.1016/j.mce.2003.10.004. PMID 15134795. S2CID 5738857. Williams JS ... "Cellular and Molecular Mechanisms of Chronic Kidney Disease with Diabetes Mellitus and Cardiovascular Diseases as Its ...
Tetrahydrofuran
Cremer, Dieter (1983). "Theoretical Determination of Molecular Structure and Conformation. XI. The Puckering of Oxolanes". ... For example, it can be used to dissolve polymers prior to determining their molecular mass using gel permeation chromatography ... Although THF is traditionally dried by distillation from an aggressive desiccant, molecular sieves are superior. In the ...
Estramustine phosphate
"Molecular conformation of estramustine and two analogues". Mol. Pharmacol. 41 (3): 569-76. PMID 1545778. Hauser AR, Merryman R ... The molecular weight of EMP sodium is 564.3 g/mol, of EMP meglumine is 715.6 g/mol, of EMP is 520.4 g/mol, of estramustine is ... The medication is of about 91% higher molecular weight than estradiol due to the presence of its C3 normustine and C17β ... As a result of these differences in molecular weights, EMP contains about 52%, EMP sodium about 48%, and EMP meglumine about 38 ...
Latha Venkataraman
"Dependence of single-molecule junction conductance on molecular conformation". Nature. 442 (7105): 904-907. doi:10.1038/ ... Her thesis was titled Electronic properties of one-dimensional conductors: A study of molybdenum selenide molecular wires and ... A study of molybdenum selenide molecular wires" - via NASA ADS. "Latha Venkataraman CV" (PDF). www.columbia.edu. 2021. " ... "Single-Molecule Circuits with Well-Defined Molecular Conductance". Nano Letters. 6 (3): 458-462. doi:10.1021/nl052373+. Aradhya ...
Dihedral angle
... s are used to specify the molecular conformation. Stereochemical arrangements corresponding to angles between 0° ... The syn-conformation shown above, with a dihedral angle of 60° is less stable than the anti-conformation with a dihedral angle ... The synperiplanar conformation is also known as the syn- or cis-conformation; antiperiplanar as anti or trans; and synclinal as ... "Side Chain Conformation". Dunbrack, RL Jr.; Karplus, M (20 March 1993). "Backbone-dependent rotamer library for proteins. ...
Accelerando
"A Direct Search Method for the Molecular Conformation Problem" (PDF). Archived from the original (PDF) on 17 October 2004. ...
C3a receptor
Reid RC, Yau MK, Singh R, Lim J, Fairlie DP (August 2014). "Stereoelectronic effects dictate molecular conformation and ... Molecular Immunology. 35 (3): 137-48. doi:10.1016/S0161-5890(98)00021-2. PMID 9694514. Lienenklaus S, Ames RS, Tornetta MA, ... "Molecular cloning and characterization of the human anaphylatoxin C3a receptor". The Journal of Biological Chemistry. 271 (34 ...
Imre Gyula Csizmadia
I.G. Csizmadia (1982). Molecular Structure and Conformation: Recent Advances (Progress in Theoretical Organic Chemistry). ... 6. Ab initio molecular orbital calculations on the thermodynamic and kinetic stability of the oxirene molecule". Journal of the ... In 1985, he founded the Journal of Molecular Structure: THEOCHEM, a computational chemistry journal, and served as its editor ... Imre G. Csizmadia; Botond Penke; Gábor Tóth (2004). The Role of Chemistry in the Evolution of Molecular Medicine. Elsevier ...
Neosaxitoxin
Sheets MF, Fozzard HA, Lipkind GM, Hanck DA (January 2010). "Sodium channel molecular conformations and antiarrhythmic drug ... Molecular Toxicology. 1 (2-3): 209-16. PMID 3130568. Schwartz DM, Duncan KG, Fields HL, Jones MR (October 1998). "Tetrodotoxin ...
Molecular demon
The molecular demon switches mainly between two conformations. The first, or basic state, upon recognizing and binding the ... A Molecular demon or biological molecular machine is a biological macromolecule that resembles and seems to have the same ... Molecular demons or molecular machines either biological or artificially constructed are continuously pushed around by the ... Proteins therefore must be considered essential molecular agents in the teleonomic performances of all living beings. Molecular ...
Polymer stabilizers
Part VI-Relationship between performance and molecular conformation". Polymer Degradation and Stability. 39 (3): 329-343. doi: ... These alkyl radicals react very rapidly with molecular oxygen (rate constants ≈ 107-109 mol-1 s-1) to give peroxy radicals, ... Modern phenolic antioxidants have complex molecular structures, often including a propionate-group at the para position of the ...
Calponin 1
Jin JP, Walsh MP, Sutherland C, Chen W (September 2000). "A role for serine-175 in modulating the molecular conformation of ... Ser175 phosphorylation alters the molecular conformation of calponin and dissociates calponin from F-actin. The consequence is ... Masuda H, Tanaka K, Takagi M, Ohgami K, Sakamaki T, Shibata N, Takahashi K (August 1996). "Molecular cloning and ... Burgstaller G, Kranewitter WJ, Gimona M (May 2002). "The molecular basis for the autoregulation of calponin by isoform-specific ...
I-TASSER
"Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling". Structure. 19 (12): ... Atomic-level structure refinement by fragment-guided molecular dynamics simulation (FG-MD) or ModRefiner 6, Structure-based ...
CHELPG
It should be remembered that atomic charges depend on the molecular conformation. The representative atomic charges for ... While CHELPG is restricted to non-periodic (e.g., molecular) systems, the DDEC methods can be applied to both non-periodic and ... flexible molecules hence should be computed as average values over several molecular conformations. A number of alternative ... The charge calculation methods based on fitting of molecular electrostatic potential (MESP) (including CHELPG) are not well- ...
Edgar Heilbronner
E. Heilbronner (1964). "Hückel molecular orbitals of Möbius-type conformations of annulenes". Tetrahedron Letters. 5 (29): 1923 ... On Molecular Orbital Correlation Diagrams, the Occurrence of Möbius Systems in Cyclization Reactions, and Factors Controlling ...
Möbius aromaticity
Heilbronner, E. (1964). "Hückel molecular orbitals of Möbius-type conformations of annulenes". Tetrahedron Letters. 5 (29): ... In terms of molecular orbital theory these compounds have in common a monocyclic array of molecular orbitals in which there is ... Möbius molecular systems were considered in 1964 by Edgar Heilbronner by application of the Hückel method, but the first such ... One of them was found to have a C2 molecular symmetry corresponding to a Möbius aromatic and another Hückel isomer was found ...
Judith Frydman
"POSTPONED - Knowing right from wrong (protein conformation): the challenging choices of (molecular) chaperones , NIH Office of ... In 2017, she was given the American Society for Biochemistry and Molecular Biology-Merck Award. She is an editor of the Journal ... Her laboratory discovered the molecular chaperone TRiC/CCT and determined its mechanism and function for protein folding. She ...
1,5-Cyclooctadiene
The molecular conformation of (E,E)-COD is twisted rather than chair-like. The compound has been investigated as a click ... Boeckh, Dieter; Huisgen, Rolf; Noeth, Heinrich (1987). "Preparation and conformation of (E,E)-1,5-cyclooctadiene". J. Am. Chem ...
Heparin
"N.M.R. and molecular-modeling studies of the solution conformation of heparin". Shaya D, Tocilj A, Li Y, et al. (June 2006). " ... Mulloy B, Forster MJ, Jones C, Davies DB (August 1993). "N.m.r. and molecular-modelling studies of the solution conformation of ... Native heparin is a polymer with a molecular weight ranging from 3 to 30 kDa, although the average molecular weight of most ... Two models were constructed, one in which all IdoA(2S) were in the 2S0 conformation (A and B below), and one in which they are ...
Robert Charles Hider
Hider RC, Drake AF, Inagaki F, Williams RJP, Endo T and Miyatawa T. The molecular conformation of α-cobratoxin as studied by ... Molecular conformation of α- bungarotoxin as studied by nuclear magnetic resonance and circular dichroism. J. Mol. Biol., 1985 ...
Poly(A)-binding protein
The polyadenylate RNA adopts an extended conformation running the length of the molecular trough. Adenine recognition is ...
Dendrotoxin
However, the molecular architecture and folding conformation of these proteins are all very similar. Dendrotoxins possess a ... and Structure-Activity Studies of Dendrotoxin and Its Homologues Using Molecular Mechanics and Molecular Dynamics Techniques. ... Journal of Molecular Biology 296:1283-1294 Harvey AL, Rowan EG, Vatanpour H, Engstrom A, Westerlund B, Karlsson E (1997). ... A two-stranded antiparallel β-sheet occupies the central part of the molecular structure. These two β-strands are connected by ...
Cyclooctane
"The molecular structure and conformation of cyclooctane as determined by electron diffraction and molecular mechanics ... Hendrickson, James B. (1967). "Molecular Geometry V. Evaluation of Functions and Conformations of Medium Rings". Journal of the ... This conformation was confirmed by Allinger and co-workers. The crown conformation (below) is slightly less stable. Among the ... Cyclooctane is a cycloalkane with the molecular formula (CH2)8. It is a simple colourless hydrocarbon, but it is often a ...
Knotted polymers
Circuit topology and knot theory formalise and classify such molecular conformations. A simple modification to atom transfer ... Of note, 85% of elasticity in natural rubber is due to knot-like structures within its molecular chain. An intramolecular ... Erman, James E. Mark ; Burak (2007). Rubberlike elasticity : a molecular primer (2. ed.). Cambridge [u.a.]: Cambridge Univ. ...
Pharmacophore
Molecular superimposition - Superimpose ("fit") all combinations of the low-energy conformations of the molecules. Similar ( ... Kier LB (September 1967). "Molecular orbital calculation of preferred conformations of acetylcholine, muscarine, and muscarone ... A pharmacophore is an abstract description of molecular features that are necessary for molecular recognition of a ligand by a ... Conformational analysis - Generate a set of low energy conformations that is likely to contain the bioactive conformation for ...
Perfluorocyclohexane
The molecule predominantly exists in its chair conformation, in which it possesses D3d molecular symmetry. Sander, M.; Blöchl, ...
Uridine monophosphate synthase
Suchi M, Mizuno H, Kawai Y, Tsuboi T, Sumi S, Okajima K, Hodgson ME, Ogawa H, Wada Y (Mar 1997). "Molecular cloning of the ... Traut TW, Payne RC (Dec 1980). "Dependence of the catalytic activities on the aggregation and conformation states of uridine 5 ... Suchi M, Harada N, Tsuboi T, Asai K, Okajima K, Wada Y, Takagi Y (1990). "Molecular cloning of human UMP synthase". Purine and ... Suttle DP, Bugg BY, Winkler JK, Kanalas JJ (Mar 1988). "Molecular cloning and nucleotide sequence for the complete coding ...
Gamma-aminobutyric acid receptor subunit gamma-2
Coyle JE, Qamar S, Rajashankar KR, Nikolov DB (January 2002). "Structure of GABARAP in two conformations: implications for GABA ... alpha 1 beta 3 gamma 2 receptors determined by molecular modeling". Biochimica et Biophysica Acta (BBA) - Biomembranes. 1565 (1 ...
Abietane
The conformation of the GGPP molecule dictates the stereochemistry of the CPP intermediate after cyclization. The ... Because polar functional groups reduce molecular volatility and make separation by gas chromatography difficult, abietane ... conformation, although some abietanes with alternative stereochemistry may be cyclized from CCP isomers containing alternative ...
Prokaryotic DNA replication
Journal of Molecular Biology. 106 (4): 963-81. doi:10.1016/0022-2836(76)90346-6. PMID 789903. Drake JW (1970) The Molecular ... Filling of the sites changes origin conformation from its native state. It is hypothesized that DNA stretching by DnaA bound to ... Bussiere DE, Bastia D (March 1999). "Termination of DNA replication of bacterial and plasmid chromosomes". Molecular ... Journal of Molecular Biology. 31 (3): 519-540. doi:10.1016/0022-2836(68)90425-7. PMID 4866337. Leonard, Alan C.; Grimwade, ...
Halobacterium salinarum
Upon absorption of a photon, retinal changes its conformation, causing a conformational change in the bacterioopsin protein, as ... Graur, Dan; Pupko, Tal (2001-02-15). "The Permian Bacterium that Isn't". Molecular Biology and Evolution. Oxford Journals. 18 ( ... Journal of Molecular Biology. 6: 34-8. doi:10.1016/s0022-2836(63)80079-0. PMID 13964964. Peck, R. F.; Dassarma, S; Krebs, M. P ... Molecular Microbiology. 35 (3): 667-76. doi:10.1046/j.1365-2958.2000.01739.x. PMID 10672188. Brijesh Rajanandam, K S; Siva ...
Multiple system atrophy
Burn DJ, Jaros E (December 2001). "Multiple system atrophy: cellular and molecular pathology". Molecular Pathology. 54 (6): 419 ... The conformation of the alpha-synuclein is different from that of alpha-synuclein in Lewy bodies. The disease probably starts ... Burn DJ, Jaros E (December 2001). "Multiple system atrophy: cellular and molecular pathology". Molecular Pathology. 54 (6): 419 ... Waxman EA, Giasson BI (July 2009). "Molecular mechanisms of alpha-synuclein neurodegeneration". Biochimica et Biophysica Acta ( ...
LILRA3
Arm JP, Nwankwo C, Austen KF (September 1997). "Molecular identification of a novel family of human Ig superfamily members that ... "HLA class I allelic sequence and conformation regulate leukocyte Ig-like receptor binding". Journal of Immunology. 186 (5): ... Norman PJ, Carey BS, Stephens HA, Vaughan RW (June 2003). "DNA sequence variation and molecular genotyping of natural killer ...
Catenin
Nature Reviews Molecular Cell Biology. 10 (4): 276-86. doi:10.1038/nrm2654. PMID 19305417. S2CID 7602580. MacDonald BT, Tamai K ... "An ensemble of flexible conformations underlies mechanotransduction by the cadherin-catenin adhesion complex". Proc Natl Acad ...
HSPA1B
June 2021). "DNAJC9 integrates heat shock molecular chaperones into the histone chaperone network". Molecular Cell. 81 (12): ... with other heat shock proteins and chaperone systems to maintain proteostasis by stabilizing the structural conformation of ... Molecular Cell Biology. 20 (11): 665-680. doi:10.1038/s41580-019-0133-3. PMID 31253954. S2CID 195739183. Kishor A, White EJ, ... Mohanan V, Grimes CL (July 2014). "The molecular chaperone HSP70 binds to and stabilizes NOD2, an important protein involved in ...
Voltage-gated ion channel
Bénitah JP, Chen Z, Balser JR, Tomaselli GF, Marbán E (March 1999). "Molecular dynamics of the sodium channel pore vary with ... The membrane potential alters the conformation of the channel proteins, regulating their opening and closing. Cell membranes ... Lodish H, Berk A, Zipursky SL, Matsudaira P, Baltimore D, Darnell J (2000). "Section 21.3, Molecular Properties of Voltage- ... ISBN 978-0-87893-742-4. Catterall WA (April 2000). "From ionic currents to molecular mechanisms: the structure and function of ...
Promoter (genetics)
A promoter is induced in response to changes in abundance or conformation of regulatory proteins in a cell, which enable ... Molecular Cell Biology. 16 (3): 155-166. doi:10.1038/nrm3951. PMC 4963239. PMID 25693131. Mikhaylichenko O, Bondarenko V, ... Journal of Molecular Biology. 346 (2): 399-409. doi:10.1016/j.jmb.2004.11.075. PMID 15670592. Martins L, Mäkelä J, Häkkinen A, ...
Mitochondrial DNA
Xu, X.; Arnason, U. (1 May 1996). "A complete sequence of the mitochondrial genome of the western lowland gorilla". Molecular ... Deletion breakpoints frequently occur within or near regions showing non-canonical (non-B) conformations, namely hairpins, ... Liu Z, Zhou T, Ziegler AC, Dimitrion P, Zuo L (2017). "Oxidative Stress in Neurodegenerative Diseases: From Molecular ... Delsuc F, Stanhope MJ, Douzery EJ (August 2003). "Molecular systematics of armadillos (Xenarthra, Dasypodidae): contribution of ...
Oligosaccharyltransferase
Move these two large substrates into their proper locations and conformations. Activate the Asn amide nitrogen atom for the ... Karaoglu D, Kelleher DJ, Gilmore R (October 2001). "Allosteric regulation provides a molecular mechanism for preferential ... Marquardt T, Denecke J (June 2003). "Congenital disorders of glycosylation: review of their molecular bases, clinical ...
Padmanabhan Balaram
He has been a major contributor to the evaluation of factors influencing the folding and conformations of designed peptides, ... where he has been ever since as a faculty member in the Molecular Biophysics Unit. He presently holds a Chaired Professorship ... Balaram's main area of research has been the investigation of the structure, conformation, and biological activity of designed ... he has also pioneered the use of alpha-amino isobutyric acid to induce and retain helicity and constrain peptide conformations ...
Peptide bond
Methods in Molecular Biology. Vol. 1401. pp. 3-29. doi:10.1007/978-1-4939-3375-4_1. ISBN 978-1-4939-3373-0. PMC 4760355. PMID ... antiperiplanar conformation). Amide groups can isomerize about the C'-N bond between the cis and trans forms, albeit slowly ( τ ... Journal of Molecular Biology. 377 (4): 1117-1129. doi:10.1016/j.jmb.2008.01.051. PMID 18308334.{{cite journal}}: CS1 maint: ... synperiplanar conformation), and ω = 180 ∘ {\displaystyle \omega =180^{\circ }} for the trans isomer ( ...
Ramakrishnan Nagaraj
Nagaraj joined the Centre for Cellular and Molecular Biology (CCMB) in 1980 as a scientist where he heads a team of scientists ... Mandal, M.; Jagannadham, M.V.; Nagaraj, R. (March 2002). "Antibacterial activities and conformations of bovine β-defensin BNBD- ... Ramakrishnan Nagaraj (born 1953) is an Indian biochemist, molecular biologist and the leader of a team of scientists working in ... Arthropod defensin Padmanabhan Balaram India portal Biology portal "Our People". Centre for Cellular and Molecular Biology. ...
Glass electrode
and chalcogenide matrix based on a molecular network of AsS, AsSe, AsTe. Because of the ion-exchange nature of the glass ... The silica glass structure (that is, the conformation of its atomic structure) is shaped so that it allows Na+ ions some ... There are two main glass-forming systems: silicate matrix based on a molecular network of silicon dioxide (SiO2) with additions ...
Histamine H3 receptor
Nakamura T, Itadani H, Hidaka Y, Ohta M, Tanaka K (Dec 2000). "Molecular cloning and characterization of a new human histamine ... evidence for heterogeneous active state receptor conformations". J. Pharmacol. Exp. Ther. 314 (1): 271-81. doi:10.1124/jpet. ... Wellendorph P, Goodman MW, Burstein ES, Nash NR, Brann MR, Weiner DM (Jun 2002). "Molecular cloning and pharmacology of ... Molecular Interventions. 6 (2): 77-88, 59. doi:10.1124/mi.6.2.5. PMID 16565470. Lovenberg TW, Roland BL, Wilson SJ, Jiang X, ...
Oxymercuration reaction
The electrons in the highest occupied molecular orbital of the double bond are donated to mercury's empty 6s orbital and the ... A bulky group like t-butyl locks the ring in a chair conformation and prevents ring flips. With 4-t-butylcyclohexene, ... electrons in mercury's dxz (or dyz) orbital are donated in the lowest unoccupied molecular orbital of the double bond. In the ...
LDL receptor
After dissociation, the receptor folds back on itself to obtain a closed conformation and recycles to the cell surface. The ... Hobbs HH, Brown MS, Goldstein JL (1993). "Molecular genetics of the LDL receptor gene in familial hypercholesterolemia". Human ... Gent J, Braakman I (October 2004). "Low-density lipoprotein receptor structure and folding". Cellular and Molecular Life ... Gent J, Braakman I (October 2004). "Low-density lipoprotein receptor structure and folding". Cellular and Molecular Life ...
Sucrose-phosphate synthase
In the open conformation of H. orenii SPS, fructose 6-phosphate forms hydrogen bonds with Gly-33 and Gln-35 residues in the A ... Annual Review of Plant Physiology and Plant Molecular Biology. 47: 431-444. CiteSeerX 10.1.1.473.6911. doi:10.1146/annurev. ... In this closed conformation, the Gly-34 residue of the A domain interacts with UDP-glucose and forces the substrate to adapt a ...
Structural genomics
This method may help identify distantly related proteins and can be used to infer molecular functions. There are currently a ... which divides the protein into short segments and arranges short polypeptide chain into a low-energy local conformation. ...
Histone H2B
These are highly involved in condensing chromatin from the beads-on-a-string conformation to a 30-nm fiber. Similar to other ... Lodish HF, Berk A, Kaiser C, Krieger M, Bretscher A, Ploegh HL, Amon A, Scott MP (2013). Molecular Cell Biology (Seventh ed.). ... Golebiowski F, Kasprzak KS (November 2005). "Inhibition of core histones acetylation by carcinogenic nickel(II)". Molecular and ...
Polyproline helix
This PPII conformation is also common in proteins and polypeptides with other amino acids apart from proline. Similarly, a more ... Traditionally, PPII has been considered to be relatively rigid and used as a "molecular ruler" in structural biology, e.g., to ... It is also rarer than the PPII conformation because the cis isomer is higher in energy than the trans. Its typical dihedral ... Journal of Molecular Biology. 229 (2): 472-493. doi:10.1006/jmbi.1993.1047. ISSN 0022-2836. PMID 8429558. Davies, Peter L.; ...
Arrestin
February 2017). "Distinct conformations of GPCR-β-arrestin complexes mediate desensitization, signaling, and endocytosis". ... Arrestins are elongated molecules, in which several intra-molecular interactions hold the relative orientation of the two ... Arrestins also bind microtubules (part of the cellular "skeleton"), where they assume yet another conformation, different from ... Unstimulated cell arrestins are localized in the cytoplasm in a basal "inactive" conformation. Active phosphorylated GPCRs ...
Aerolysin
In molecular biology, aerolysin is a cytolytic pore-forming toxin exported by Aeromonas hydrophila, a Gram-negative bacterium ... oligomer derived from electron microscopy have helped to construct a model of the protein in its heptameric conformation, and ... "Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism. The gene for aerolysin have been ...
NE-tag
This synthetic NE peptide adopts random coil conformation and showing strong immunogenicity (computational prediction). This is ... Human Molecular Genetics. 22 (7): 1395-1403. doi:10.1093/hmg/dds556. PMID 23300193. Xu, EG.; Ho, Philip WL.; Tse, Zero HM.; Ho ...
Collagen, type IV, alpha 2
Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another ... Ständer M, Naumann U, Wick W, Weller M (1999). "Transforming growth factor-beta and p-21: multiple molecular targets of decorin ...
Expected progeny difference
Drennan M. J., McGee M. (2008). "Effect of beef sire expected progeny difference for carcass conformation on live animal ... Molecular biology). ...
O-Xylene
... methyl conformation, and dipole moment of ortho-xylene". Journal of Molecular Spectroscopy. 47 (2): 314. Bibcode:1973JMoSp..47 ...
Controlling the SARS-CoV-2 spike glycoprotein conformation | Nature Structural & Molecular Biology
... state conformations more readily than the wild-type S-protein. These results demonstrate that the conformation of the S-protein ... Mutations engineered into the spike ectodomain either lock the RBD in the down state or make it adopt the up conformation more ... 1: Vector-based analysis of the CoV S-protein demonstrates remarkable variability in the S-protein conformation within up and ... state conformations more readily than the wild-type S-protein. These results demonstrate that the conformation of the S-protein ...
Study of Molecular Conformation and Activity-Related Properties of Lipase Immobilized onto Core-Shell Structured Polyacrylic...
Study of Molecular Conformation and Activity-Related Properties of Lipase Immobilized onto Core-Shell Structured Polyacrylic ... Study of Molecular Conformation and Activity-Related Properties of Lipase Immobilized onto Core-Shell Structured Polyacrylic ... Home / KnowledgeBase Articles / Study of Molecular Conformation and Activity-Related Properties of Lipase Immobilized onto Core ... Low- or high-molecular-weight (1800 and 100 000, respectively) PAA molecules were covalently attached onto the surface of amine ...
"Parallel graph algorithms for molecular conformation and tree codes" by Paulius Micikevicius
Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in DNA/RNA aggregates (Journal Article) ...
Molecular dynamics simulations and cluster analysis have been used to select the molecular conformations, reducing the ... Molecular dynamics simulations and cluster analysis have been used to select the molecular conformations, reducing the ... Title: Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in DNA/RNA aggregates ... 2DES maps reveal the spectral fingerprints associated with specific molecular conformations, and are thus a promising option to ...
Molecular Conformation - McMaster Experts
Molecular physiology of adrenoreceptors]. Academic Article * [Predisposition of the optimal conformations of adrenergic ... Conformation of a tethered polymer in a leaky nanocavity Academic Article * Conformation transitions of a polyelectrolyte chain ... Molecular diagnostics in follicular non-Hodgkins lymphoma: a review. Academic Article * Molecular interactions in the model ... Productive conformations of ligands and topography of the alpha1-adrenoreceptor active site based on theoretical conformation ...
A small angle neutron scattering study of the effect of molecular weight on the conformation of side chain liquid crystal...
Godinho, M. H. F. (1999). A small angle neutron scattering study of the effect of molecular weight on the conformation of side ... Godinho, MHF 1999, A small angle neutron scattering study of the effect of molecular weight on the conformation of side chain ... T1 - A small angle neutron scattering study of the effect of molecular weight on the conformation of side chain liquid crystal ... A small angle neutron scattering study of the effect of molecular weight on the conformation of side chain liquid crystal ...
Fluorescence study of the molecular conformation of human haemopexin - Fingerprint
- Albert Einstein College of Medicine
An abasic site in DNA. Solution conformation determined by proton NMR and molecular mechanics calculations
GeoDiff: A Geometric Diffusion Model for Molecular Conformation Generation | appliedAI - TransferLab
GeoDiff: A Geometric Diffusion Model for Molecular Conformation Generation, Minkai Xu, Lantao Yu, Yang Song, Chence Shi, ... Given the 2d graph of a molecule, the goal is to predict all of its stable conformations, i.e. all the stable 3d positions of ... Given the full molecule conformation C, the authors progressively add noise until the 3d structure is lost and only the 2d ... The problem of predicting molecular 3d structure is of fundamental importance in computational chemistry and drug discovery. ...
Predicting new protein conformations from molecular dynamics simulation conformational landscapes and machine learning. |...
Predicting new protein conformations from molecular dynamics simulation conformational lan Predicting new protein conformations ... Molecular dynamics (MD) simulations are a popular method of studying protein structure and function, but are unable to reliably ... conformations that are not present in the training data. This method offers a new approach to the prediction of new low energy/ ... from molecular dynamics simulation conformational landscapes and machine learning. Jin, Yiming; Johannissen, Linus O; Hay, Sam ...
β,γ-CHF- and β,γ-CHCl-dGTP diastereomers: synthesis, discrete 31P NMR signatures, and absolute configurations of new...
Molecular structure vibrational spectral investigation and the conformation analysis of methyl 4 4 formylphenyl benzoate |...
Heterogeneous pattern of DNA methylation in developmentally important genes correlates with its chromatin conformation | BMC...
... thereby resulting in the modulation of chromatin conformation. These findings illustrate that various patterns of DNA ... BMC Molecular Biology volume 18, Article number: 1 (2017) Cite this article ... Curradi M, Izzo A, Badaracco G, Landsberger N. Molecular mechanisms of gene silencing mediated by DNA methylation. Mol Cell ... Heterogeneous pattern of DNA methylation in developmentally important genes correlates with its chromatin conformation. *Puja ...
Molecular phylogeny of the tropical wandering spiders (Ctenidae) and the evolution of the eye conformation in the RTA clade |...
Dissipative particle dynamics simulations in colloid and Interface science: a review. | Semantic Scholar
Mesoscale Modeling of Agglomeration of Molecular Bottlebrushes: Focus on Conformations and Clustering Criteria. *Sidong Tu, C. ... A novel method of investigating the link between molecular features of polymer molecules and the rheological properties of ... Using dissipative particle dynamics, we characterize dynamics of aggregation of molecular bottlebrushes in solvents of various ...
Jason M. Key, Ph.D. | Harvard Catalyst Profiles | Harvard Catalyst
Nuclear Magnetic Resonance Platform Applications - Faculty of Science - About
Author: 'Pang, Z.' / Subject: indoles and metabolites / Text Availability: Citation in PubAg - PubAg Search Results
Table of Contents page: Journal of Biological Chemistry
Frontiers | Dynamics Rationalize Proteolytic Susceptibility of the Major Birch Pollen Allergen Bet v 1
Here, we perform classic and enhanced molecular dynamics (MD) simulations to quantify fold dynamics on extended timescales of ... Here, we perform classic and enhanced molecular dynamics (MD) simulations to quantify fold dynamics on extended timescales of ... dissecting the relationship between molecular conformation and allergenic potency. Biochim. Biophys. Acta 1864, 1548-1557. doi ... classic molecular dynamics; MDMD, metadynamics molecular dynamics; PDB, protein data bank; MSM, Markov state model; PCA, ...
Inter Research » MEPS » v300 » p91-103
Molecular variation was assessed with the single-strand conformation polymorphism (SSCP) method. In total, 32 different ... Analysis of molecular variance (AMOVA) indicated a strong genetic differentiation among populations. The Lake Grevelingen ... KEY WORDS: Pellioditis marina · Single-strand conformation polymorphism · Cryptic species · Population genetic structure ...
Gelation of |i|Antheraea pernyi|/i| Silk Fibroin Accelerated by Shearing
The Molecular Conformation of SF. CD is generally used to test different protein conformations in dilute aqueous solutions. ... The percentages of molecular conformations in SF solutions after shearing for 90 min at various rates were calculated based on ... There was no significant difference in the molecular conformation of the SF gels, all of which were mainly composed of β-sheets ... After incubating for 24 h, the molecular conformations of both the ASF and the BSF solutions changed significantly. The α-helix ...
Browsing public research data by Author "Haddow, Sarah L."
Transition path times of coupled folding and binding reveal the formation of an encounter complex - Research Collection
Volume 39 Issue 4 | Journal of Medical Entomology
Rapid Identification of Mitochondrial Cytochrome B Haplotypes by Single Strand Conformation Polymorphism in Lutzomyia ... and aid in the discovery of resistance mechanisms through synergist studies and verification of molecular techniques. ... KEYWORDS: Lutzomyia longipalpis, cytochrome b, single strand conformation polymorphism, population genetics, sand fly, ... Single strand conformation polymorphism (SSCP) was used to recognize the presence of L. longipalpis haplotypes; these were ...
Heat shock proteins and hormesis in the diagnosis and treatment of neurodegenerative diseases | SpringerLink
... a large number of proteins need the help of molecular chaperones to maintain their activation-competent conformation. ... Hormetic prevention of molecular damage during cellular aging of human skin fibroblasts and keratinocytes. Ann N Y Acad Sci. ... The molecular mechanisms regulating the NO-induced activation of heat-shock signal seems to involve cellular oxidant/ ... How hsp70 molecular machines interact with their substrates to mediate diverse physiological functions. J Mol Biol. 2015;427(7 ...
Words of the day -- idiopathic | The Spokesman-Review
OpenAGRICOLA
MeSH Browser
CARB CONFORMATION. Entry Term(s). Carbohydrate Linkage NLM Classification #. QU 75. Previous Indexing. Molecular Conformation ( ... Molecular Structure [G02.111.570] * Molecular Conformation [G02.111.570.820] * Bay-Region, Polycyclic Aromatic Hydrocarbon [ ... Carbohydrate Conformation Preferred Term Term UI T006421. Date01/01/1999. LexicalTag NON. ThesaurusID NLM (1980). ... Carbohydrate Conformation Preferred Concept UI. M0003353. Scope Note. The characteristic 3-dimensional shape of a carbohydrate. ...
SimulationsProtein ConformationContaining an intra-molecularIntra-molecularOpen conformationProteinsInteractionsStructuralSpectralConformationalPhosphorylationBiologyPrionsStructuresActaSimulationOxidationDiscreteStructure20172018AdoptsMoleculesCompoundsChemistryDifferent conformationsBackboneInteractionMechanicsInfrared radiationAssembliesModelsGeneFoldSpectroscopyPolymersFunctionalCellularGenesJournalCloningModelingPrion strainAnalysesAnalysisInvestigationReplica-exchange
Simulations10
- Molecular dynamics simulations and cluster analysis have been used to select the molecular conformations, reducing the complexity of the flexible ApA conformational space. (nsf.gov)
- Molecular dynamics (MD) simulations are a popular method of studying protein structure and function, but are unable to reliably sample all relevant conformational space in reasonable computational timescales. (bvsalud.org)
- An autoencoder is used to map snapshots from MD simulations onto a user-defined conformational landscape defined by principal components analysis or specific structural features, and we show that we can predict, with useful accuracy, conformations that are not present in the training data. (bvsalud.org)
- Here, we perform classic and enhanced molecular dynamics (MD) simulations to quantify fold dynamics on extended timescales of Bet v 1a and two variants with higher and lower cleavage rates. (frontiersin.org)
- Molecular dynamic simulations of the vesicles were used to establish the relationship between membrane morphology and averaged cryo-EM images. (osti.gov)
- Sanbonmatsu, K.Y. (2014) Dynamics of Riboswitches: Molecular Simulations. (lanl.gov)
- For simulations: replica-exchange discrete molecular dynamics (rxDMD) provided an independent view of the energy landscape. (elifesciences.org)
- We present a combined computational-experimental study on the incorporation of water in lactose molecular crystals, and show how simulations can be used to associate spectral features in the THz region to crystal conformations and phases. (dannyvanpoucke.be)
- Using periodic DFT simulations of lactose molecular crystals, the role of water in the observed lactose THz spectrum is clarified, presenting both direct and indirect contributions. (dannyvanpoucke.be)
- Molecular dynamics simulations of stretch-induced crystallization in layered polyethylene ( Nikolaos Romanos, Grigorios Megariotis, Doros N. Theodorou ), In Polym. (grnet.gr)
Protein Conformation2
- Fig. 1: Vector-based analysis of the CoV S-protein demonstrates remarkable variability in the S-protein conformation within 'up' and 'down' states between CoV strains. (nature.com)
- Finally, the interactions of cytochrome C and carbon monoxides were simulated using molecular dynamics (MD), and the effect of protein conformation changes on the electrochemical signal was thoroughly examined. (marquette.edu)
Containing an intra-molecular1
- On the other hand, in (II), the penta-fluoro-phen-oxy moiety inter-acts closely with the Cl atom to form a folded conformation containing an intra-molecular halogen-π inter-action. (elsevier.com)
Intra-molecular1
- Our research group developed an intra-molecular FRET sensor to detect the interaction between Gα subunits and GPCRs in live cells following agonist stimulation. (umn.edu)
Open conformation1
- In (I), the phen-oxy and phthalonitrile (benzene-1,2- dicarbonitrile) moieties are well separated in an open conformation and inter-molecular C - H⋯π inter-actions are observed in the crystal packing. (elsevier.com)
Proteins4
- These results demonstrate that the conformation of the S-protein can be controlled via rational design and can provide a framework for the development of engineered CoV S-proteins for vaccine applications. (nature.com)
- Research has mostly been limited to applying environmental triggers such as acidification, organic solvents and shear force during the assembly process with the aim of influencing the microstructures that form during the fabrication of fibers and films," says Sun. However, she adds that this still allows very little control over how the proteins fold and the molecular assembly that both critically determine the end material's properties. (phys.org)
- We now show that lysine-specific molecular tweezers bind to a 14-3-3 adapter protein and modulate its interaction with partner proteins. (tue.nl)
- Amyloid-forming proteins can aggregate under different structural conformations known as strains, which can exhibit a prion-like behavior and distinct pathophenotypes. (archives-ouvertes.fr)
Interactions8
- Most mechanistic information of how the interactions between binding partners form or break is, however, hidden in the transition paths, the very short parts of the molecular trajectories from the encounter of the two molecules to the formation of a stable complex. (ethz.ch)
- Computationally, we are using molecular simulation to to understand the interplay between ligand binding, folding and magnesium interactions on riboswitch conformation. (lanl.gov)
- Yet, important fresh perspectives on surface interactions and molecular conformations are gained from adsorption heights that remain largely inaccessible to SPM, but can be precisely measured with both elemental and chemical sensitivity by Normal-Incidence X-ray Standing Wave (NIXSW) analysis. (lancs.ac.uk)
- The interpretation of experimental results is informed by Density Functional Theory (DFT) calculations, providing a consistent picture of adsorption heights and molecular deformations in the networks that result from the interplay between steric hindrance and surface interactions. (lancs.ac.uk)
- We will further explore the next frontier, namely diagnostic analyzers exploiting single-molecule sensitivity to provide detailed information on conformation and interactions at the molecular scale. (tue.nl)
- Hori, A , Inoue, Y & Yuge, H 2011, ' The effect of Cl⋯π interactions on the conformations of 4-chloro-5-(2-phenoxyethoxy)phthalonitrile and 4-chloro-5-[2- (pentafluorophenoxy)ethoxy]phthalonitrile ', Acta Crystallographica Section C: Crystal Structure Communications , vol. 67, no. 5, pp. o154-o156. (elsevier.com)
- In keeping with the rapidly developing fields of mechanobiology and regenerative medicine, Biorheology aims to include studies of the rheological aspects of these fields by focusing on the dynamics of mechanical stress formation and the response of biological materials at the molecular and cellular level resulting from fluid-solid interactions. (semcs.net)
- Precise molecular determinants defining strain specificity and cross-strain interactions (cross-seeding) are currently unknown. (archives-ouvertes.fr)
Structural4
- These conformations can vary significantly in terms of their structural characteristics, resulting in a broad distribution of localized dynamics. (ubc.ca)
- Stereo Isomerism : Two or more than two compounds having same molecular formula, same structural formula but different arrangements of atoms or groups in space. (ybstudy.com)
- Optical isomers : Two or more than two compound have same molecular formula, same structural formula but different behaviour towards PPL (plane polarised light). (ybstudy.com)
- The predicted conformation of ranatuerin-1 (SMLSVLKNLG 10 KVGLGFVACK 20 INK QC), an antimicrobial peptide first isolated from the skin of the bullfrog Rana catesbeiana, comprises three structural domains: α-helix (residues 1-8), β-sheet (residues 11-16) and β-turn (residues 20-25). (elsevier.com)
Spectral3
- 2DES maps reveal the spectral fingerprints associated with specific molecular conformations, and are thus a promising option to enable their quantitative spectroscopic detection beyond standard 1D pump-probe techniques. (nsf.gov)
- The collective vibrations in such molecular crystals can be probed using terahertz spectroscopy, providing unique characteristic spectral fingerprints. (dannyvanpoucke.be)
- However, the association of the spectral features to the crystal conformation, crystal phase and its environment is a difficult task. (dannyvanpoucke.be)
Conformational2
- Predicting new protein conformations from molecular dynamics simulation conformational landscapes and machine learning. (bvsalud.org)
- Conformational Isomerism : The different arrangement of atoms in space that result from the free rotation around single bond, are called conformations. (ybstudy.com)
Phosphorylation1
- Deletion of the leucine zipper motif or PKC phosphorylation affected AFAP-110's conformation, which correlated with changes in multimerization and increased the capability of rAFAP-110 to cross-link actin filaments. (cdc.gov)
Biology1
- Molecular Biology and Evolution. (upmc.fr)
Prions1
- Tau Prions: Conformation-based Classification of Tauopathies" "Neurodegenerative. (houstonmethodist.org)
Structures5
- The figure depicts three different molecular structures of estrogen found in mammals' that differ by the arrangement of bonds and side groups. (asu.edu)
- The molecular structures of the three estrogen molecules differ by the arrangement of chemical bonds and side groups attached to the core steroid structure, cholesterol, which contains three cyclohexane rings and one cyclopentane ring. (asu.edu)
- GAGSGAGAGSGA forms nanowhisker-like structures of highly ordered β sheet molecular conformations. (phys.org)
- Here we show tertiary structures of SPH1118 with six different conformations as determined by X-ray crystallography. (nih.gov)
- This biorheological approach applies in particular to molecular studies where changes of physical properties and conformation are investigated without reference to how the process actually takes place, how the forces generated are matched to the properties of the structures and environment concerned, proper time scales, or what structures or strength of structures are required. (semcs.net)
Acta1
- Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy, 76 (1). (lincoln.ac.uk)
Simulation2
Oxidation1
- Metal-free activation of molecular oxygen by covalent triazine frameworks for selective aerobic oxidation. (mpg.de)
Discrete1
- Self-assembly is a powerful method to obtain large discrete functional molecular architectures. (nature.com)
Structure10
- The problem of predicting molecular 3d structure is of fundamental importance in computational chemistry and drug discovery. (appliedai.de)
- Given the full molecule conformation C, the authors progressively add noise until the 3d structure is lost and only the 2d structure remains. (appliedai.de)
- Molecular structure vibrational spectra. (gazi.edu.tr)
- and 'idiotype,' meaning 'the molecular structure and conformation of an antibody that confers its antigenic specificity. (spokesman.com)
- During material assembly, the localized interaction with different peptides yields a silk film that exhibits topographical control over molecular structure and mechanical properties imparted by the templated crystallization process. (phys.org)
- Four main topics have been covered: (i) the impact of molecular orientation on the energy levels, (ii) energy level tuning with strong electron acceptors, (iii) the role of thermodynamic equilibrium at organic/organic homo-interfaces and (iv) the correlation of interfacial electronic structure and bonding distance. (hu-berlin.de)
- The process can also be templated by a guest molecule that itself has an asymmetrical structure, which paves the way to molecular imprinting techniques at the level of single polymer chains. (nature.com)
- The nanoscale structure of molecular assemblies plays a major role in many (µ)-biological mechanisms. (dannyvanpoucke.be)
- The results suggest that the molecular chains in the materials tested are primarily randomly coiled and lacking in regular structure, and are able to easily change between many transient conformations. (ubc.ca)
- conformation nres: 628 fold_tree nres: 639 When I comment out the native complex structure, there is no more error. (rosettacommons.org)
20171
- 2017). Characterizing the molecular composition of organics in SOA and precursor gases is crucial for understanding the chemical fate, removal, and ultimately the impact on human and environmental health. (copernicus.org)
20182
Adopts2
- Based on this analysis, we developed two soluble ectodomain constructs for the SARS-CoV-2 S-protein, in which the highly immunogenic and mobile receptor binding domain (RBD) is either locked in the all-RBDs 'down' position or adopts 'up' state conformations more readily than the wild-type S-protein. (nature.com)
- The cyclotrithiazene ring adopts a chair conformation with equal bond distances and the norbornadiene is fused in an exo, exo fashion to the heterocycle. (typeset.io)
Molecules2
- Low- or high-molecular-weight (1800 and 100 000, respectively) PAA molecules were covalently attached onto the surface of amine-functionalized magnetic silica nanoacomposite particles. (jascoinc.com)
- 1997. " Search For Native Conformations Of Organic Molecules By Genetic Algorithms " . (uni-heidelberg.de)
Compounds3
- Two or more than two compounds having the same molecular formula but different physical/chemical or both properties are called isomers and the phenomenon is called isomerism. (ybstudy.com)
- Chain Isomerism (C.I.) : The compounds which have same molecular formula, same functional group but different arrangement of carbon chain (Parental or side chain) show chain isomerism. (ybstudy.com)
- Position Isomerism (P.I.) : The compounds which have same molecular formula, same functional group, same parent carbon chain but different position of functional group or multiple bond or substituents, show position isomerism. (ybstudy.com)
Chemistry1
- Nitschke, J. R. Systems chemistry: molecular networks come of age. (nature.com)
Different conformations2
- A computational strategy to simulate two-dimensional electronic spectra (2DES) is introduced, which allows us to analyse ground state dynamics and to sample and measure different conformations attained by flexible molecular systems in solution. (nsf.gov)
- Substrate-free SPH1118 adopted three different conformations in the open form. (nih.gov)
Backbone1
- There is strong anisotropy of the backbone conformation and it becomes stronger as the molecular weight increases. (unl.pt)
Interaction1
- 2019. Interaction mechanism between the focused ultrasound and lipid membrane at the molecular level . (ibpc.fr)
Mechanics1
- An explicit mixed quantum mechanics/molecular mechanics (QM/MM) approach is employed for the evaluation of the necessary electronic excited state energies and transition dipole moments. (nsf.gov)
Infrared radiation1
- After that point, the energy of infrared radiation in too low to produce the molecular conformation change needed to trigger a signal. (thoughtco.com)
Assemblies3
- i) A novel approach is presented to explain the phenomenon that the ionization energy in molecular assemblies is orientation dependent. (hu-berlin.de)
- It is demonstrated that this is due to an impact of intramolecular dipoles on the ionization energy in molecular assemblies. (hu-berlin.de)
- Molecular crystals are one of the most simple of these assemblies and are widely used in a variety of applications from pharmaceuticals and agrochemicals, to nutraceuticals and cosmetics. (dannyvanpoucke.be)
Models2
- The paper [ Xu22G ] describes one implementation of diffusion models for molecular 3d reconstruction. (appliedai.de)
- Development and application of QM/continuum models to describe the effects of the environment of different complexities on molecular systems. (gaussian.com)
Gene2
- These findings illustrate that inconsistent DNA methylation patterns (sporadic, mosaic and heterogeneous) may also influence gene regulation, thereby resulting in the modulation of chromatin conformation. (biomedcentral.com)
- In most cases, addition of acetyl groups to histone tails causes gene activation by inducing and recruiting a euchromatin conformation and bromodomain containing transcription factors respectively for genes in close closeness to the acetylated histone [ 7,8 ]. (avensonline.org)
Fold1
- Also, sometimes when I run docking from unbound components of the complex, I get this error message: ERROR: Conformation: fold_tree nres should match conformation nres. (rosettacommons.org)
Spectroscopy1
- Single-molecule imaging, spectroscopy, and manipulation have uncovered how molecular systems effect function in living cells. (grc.org)
Polymers3
- This means that the tendency for the chains to be confined between the smectic layers is stronger for larger molecular weight polymers. (unl.pt)
- Godinho, MHF 1999, ' A small angle neutron scattering study of the effect of molecular weight on the conformation of side chain liquid crystal polymers in a smectic phase ', Molecular Crystals And Liquid Crystals , vol. 330, no. 1, pp. 285-292. (unl.pt)
- For FimA from Escherichia coli , it has been previously shown that the protein can also adopt a monomeric, self-complemented conformation in which the donor strand is inserted intramolecularly in the opposite orientation relative to that observed for FimA polymers. (jbc.org)
Functional3
- Functional Isomerism : Same molecular formula but different functional groups. (ybstudy.com)
- Metamerism : Same molecular formula, same polyvalent Functional group but different alkyl groups attached to polyvalent Functional group. (ybstudy.com)
- These dynamic conformations can act as functional genomic elements involved in DNA replication and transcription, chromatin organization and genome stability. (utexas.edu)
Cellular1
- if immediate recombination does not occur, these can manifest as some type of molecular, cellular, or organic system alteration. (cdc.gov)
Genes1
- Advantage of high-resolution melting curve analysis over conformation-sensitive gel electrophoresis for mutational screening of BRCA1 and BRCA2 genes. (cdc.gov)
Journal3
- Journal of Molecular Catalysis A: Chemical, 319 (1-2). (lincoln.ac.uk)
- Semack, A, Malik, RU & Sivaramakrishnan, S 2016, ' G protein-selective GPCR conformations measured using FRET sensors in a live cell suspension fluorometer assay ', Journal of Visualized Experiments , vol. 2016, no. 115, e54696. (umn.edu)
- The Journal of molecular diagnostics : JMD 2013 Nov 15 (6): 796-809. (cdc.gov)
Cloning1
- 2011) Molecular cloning and analysis of the UDP-glucose pyrophosphorylase in Streptococcus equi subsp. (jenabioscience.com)
Modeling1
- B. Mennucci, C. Curutchet, "The role of the environment in electronic energy transfer: a molecular modeling perspective", Phys. (gaussian.com)
Prion strain2
- Molecular analysis of prion strain variation and the aetiology of `new vari- ant' CJD. (cdc.gov)
- Our work redefines the conceptual boundaries of prion strain and sheds light on key molecular features concerning an important class of pathogenic agents. (archives-ouvertes.fr)
Analyses2
- Porcine Epidemic Diarrhea in Europe: In-Detail Analyses of Disease Dynamics and Molecular Epidemiology. (cdc.gov)
- Molecular docking analyses of these lysosomotropic agents were performed, namely of fluoxetine, imipramine, chloroquine, verapamil, tamoxifen, amitriptyline, and chlorpromazine against important targets for the pathogenesis of SARS-CoV-2. (bvsalud.org)
Analysis1
- Analysis of molecular variance (AMOVA) indicated a strong genetic differentiation among populations. (int-res.com)
Investigation1
- Investigation of water desalination/purification with molecular dynamics and machine learning techniques ( Christos Stavrogiannis, Filippos Sofos, Theodoros. (grnet.gr)
Replica-exchange1
- Impact of A2T and D23N Mutations on Tetrameric Aβ42 Barrel within a Dipalmitoylphosphatidylcholine Lipid Bilayer Membrane by Replica Exchange Molecular Dynamics. (ibpc.fr)