This paper describes a Bayesian learning based approach to protein secondary structure prediction. Four secondary structure types are considered, including
CiteSeerX - Scientific documents that cite the following paper: 119931, A decision graph explanation of protein secondary structure prediction
A powerful tool used to monitor secondary structure is circular dichroism (CD), which is the differential absorbance of left and right circularly polarized light. Since proteins consist of chiral amino acids, they are CD active and exhibit distinct CD spectra that are sensitive to the proteins secondary structure. This spectra can provide a qualitative snapshot of the protein structure or the secondary structure composition of a protein can be estimated from the far UV CD spectrum using a number of algorithms, several of which are made available in Olis GlobalWorks software.. Protein secondary structure can also be used to monitor protein folding and unfolding. An equilibrium study consists of collection of CD spectra as a function of increasing temperature or chemical denaturant. As the protein unfolds, the CD spectrum reflects this. Fitting data at a single wavelength or the full spectral scans during this denaturation process provides thermodynamic information such as the melting temperature ...
Activation helix orientation of estrogen receptor is mediated by receptor dimerization: evidence from molecular dynamics simulations
Quanta will calculate hydrogen bonds and then analyze the secondary structure in its Protein Design Module, but it seems like a rather large investment if all you want to do is determine the secondary structure......... ........Tom Branham ...
Diatoms and sponges use proteins, long chain polyamines, and other biomolecules to assemble silica structures of controlled morphology. Investigated here are biosilicification peptides. Under mild conditions, these peptides produce silica nanoparticles from solutions of silicic acid, whereas harsh methods are currently employed to produce these nanoparticles commercially. Biomimetic precipitation studies have shown that LKα14 (Ac-LKKLLKLLKKLLKL- C), an amphiphilic lysine/leucine repeat peptide with an α-helical secondary structure at polar/apolar interfaces, co-precipitates with silica to form nanospheres. Previous work con- firmed the α-helical secondary structure in both the neat and silica-complexed states of the peptide and suggested that the tetrameric bundles of peptide that are known to form in solution persisted in the silica-complexed form. To further investigate the peptide aggregation, deuterium solid-state nuclear magnetic resonance (2H ssNMR) was used to establish how the ...
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Designed peptides that fold autonomously to specific conformations in aqueous solution are useful for elucidating protein secondary structural preferences. For example, autonomously folding model systems have been essential for establishing the relationship between alpha-helix length and alpha-helix stability, which would be impossible to probe with alpha-helices embedded in folded proteins. Here, we use designed peptides to examine the effect of strand length on antiparallel beta-sheet stability. alpha-Helices become more stable as they grow longer. Our data show that a two-stranded beta-sheet (beta-hairpin) becomes more stable when the strands are lengthened from five to seven residues, but that further strand lengthening to nine residues does not lead to further beta-hairpin stabilization for several extension sequences examined. (In one case, all-threonine extension, there may be an additional stabilization on strand lengthening from seven to nine residues.) These results suggest that there may be
The following is a list of how-to and tutorial content that matched your search term. ProgrammableWebs how-to content comes from two sources; full-blown tutorials that we publish ourselves and other highly relevant tutorials that we find elsewhere on the Web. This list represents on combination of both tutorial types and if you go to ProgrammableWebs API University, youll not only be able to find more, they are organized based on your role (API providers or developers who consumes APIs). If you know of a tutorial that would be of interest to the ProgrammableWeb community, wed like to know about it. Be sure to check our guidelines for making contributions to ProgrammableWeb ...
jay ananth wrote: , I need one help from u... , , search for best tools for the following : , 1.Secondary Structure prediction in RNA , 2.Protein Secondary Structure Prediction. , 3.Prediction of disordered regions in proteins.. , 4.Case Std on Structure-function relationships in proteins , 5.Prediction of transmembrane regions in proteins , 6.Characterization of antigenecity in polypeptides- epitope mapping , , , , Are you looking for computational tools to do the above ? Can you be more specific ? Autodock, Gromacs are some of the tools that you can use for protein structure prediction. -- Deepan http://codeshepherd.com/ http://codeshepherd.blogspot.com/ http://sudoku-solver.net/ ...
In recent years, the nuclear receptors (NR) dynamics have been studied extensively by various approaches. However, the transition path of helix 12 (H12) to an agonist or an antagonist conformation and the exchange pathway between these states is not clear yet. A number of accelerated molecular dynamics (aMD)
Motivation: Transmembrane beta-barrels exist in the outer membrane of gram-negative bacteria as well as in chloroplast and mitochondria. They are often involved in transport processes and are promising antimicrobial drug targets. Structures of only a few beta-barrel protein families are known. Therefore, a method that could automatically generate such models would be valuable. The symmetrical arrangement of the barrels suggests that an approach based on idealized geometries may be successful. Results: Here, we present tobmodel; a method for generating 3D models of beta-barrel transmembrane proteins. First, alternative topologies are obtained from the BOCTOPUS topology predictor. Thereafter, several 3D models are constructed by using different angles of the beta-sheets. Finally, the best model is selected based on agreement with a novel predictor, ZPRED3, which predicts the distance from the center of the membrane for each residue, i.e. the Z-coordinate. The Z-coordinate prediction has an average ...
The DSSP program works by calculating the most likely secondary structure assignment given the 3D structure of a protein. It does this by reading the position of the atoms in a protein (the ATOM records in a PDB file) followed by calculation of the H-bond energy between all atoms. The best two H-bonds for each atom are then used to determine the most likely class of secondary structure for each residue in the protein.. This means you do need to have a full and valid 3D structure for a protein to be able to calculate the secondary structure. Theres no magic in DSSP, so e.g. it cannot guess the secondary structure for a mutated protein for which you dont have the 3D structure ...
Secondary structure prediction and consensus sequence of PelD and PleD. A. Secondary structure predication was made using the web-based ProteinPredict program h
This study demonstrates the feasibility of creating structurally complex and catalytically active enzymes by assembling randomized modules that are constructed from a limited set of building blocks and biased toward helical secondary structure by binary patterning. The binary distribution of hydrophilic/hydrophobic residues is inherent in the genetic code (NAN/NTN), and our results support suggestions (9, 26, 27) that modern enzymes could have evolved from primitive precursors constructed from a relatively small number of polar and nonpolar amino acids. There is, nevertheless, a low probability of finding catalysts, even when both position and identity of all critical active site residues are determined in advance. This finding contrasts with the ease of obtaining folded helical proteins through binary patterning (9), underscoring the exacting demands that catalysis places on protein design.. Extrapolating from our data and from modest sequence constraints on interhelical turns (23, 28-30), we ...
... , In parallel beta sheets, the adjacent polypeptide chains run in the same direction. Typically parallel beta sheets are large structures that usually consist of at least five strands. Parallel beta sheets usually have hydrophobic residues on both sides of the sheet.
C. E. N. T. E. R. F. O. R. I. N. T. E. G. R. A. T. I. V. E. B. I. O. I. N. F. O. R. M. A. T. I. C. S. V. U. Lecture 14 Secondary Structure Prediction. Bioinformatics Center IBIVU. Protein structure . Linus Pauling (1951). Slideshow 80412 by LeeJohn
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 ...
Lee, C., L. Kalmar, B. Xue, P. Tompa, G. W. Daughdrill, V. N. Uversky, and K-H. Han, Contribution of proline to the pre-structuring tendency of transient helical secondary structure elements in intrinsically disordered proteins., Biochim Biophys Acta, vol. 1840, issue 3, pp. 993-1003, 2014 Mar. ...
Secondary structure of proteins refers to local and repetitive conformations, such as α‐helices and β‐strands, which occur in protein structures
Synonyms for alpha-helix, alpha-helix in Free Thesaurus. Antonyms for alpha-helix, alpha-helix. 15 synonyms for helix: spiral, twist, curl, loop, coil, corkscrew, gyre, curlicue, volute, spiral, coil, volute, whorl, spiral, genus Helix. What are synonyms for alpha-helix, alpha-helix?
View Notes - Bio 1A Lect 2 Quiz from BIO 1A at Berkeley. Bio 1A Lect 2 Quiz 50% adenine aldose alpha alpha-helix amino Amino acids antiparallel beta beta-pleated sheets blood flow carbonyl cell
Its not true that the Ramachandran plot will determine the secondary structure of an amino acid. Ramachandran plots show the sterically allowed phi/psi angles of an amino acid. As such nearly all non-glycine amino acids are in alpha/beta spaces. Random coil segments of structure consist mostly of alpha and beta conformation amino acids in nonsense ...
As evidenced by a buried core of hydrophobic residues within globular proteins, hydrophobicity provides essential insights into the folding structure of pr
6. "Helix Propensities of Amino Acid Residues via Thioester Exchange." Fisher, B. F.; Hong, S.H.; Gellman, S.H. J. Am. Chem. Soc. DOI: 10.1021/jacs.7b07930. 5. "Detection and analysis of chimeric tertiary structures by backbone thioester exchange: Packing of an alpha helix against an alpha/beta-peptide helix," Price, J. L.;Hadley,E. B.;Steinkruger,J. D. and Gellman,S. H., Angew.Chem.Int.Ed Engl., 2010, 49, 368-371.. 4. "Preferred Side-chain Constellations at Antiparallel Coiled-coil Interfaces," E. B. Hadley, O. D. Testa, D. N. Woolfson and S. H. Gellman Proc. Natl. Acad. Sci. USA 2008, 105, 530.. 3. "An Antiparallel α-Helical Coiled-Coil Model System for Rapid Assessment of Side Chain Recognition at the Hydrophobic Interface," E. B. Hadley an d S. H. Gellman J. Am. Chem. Soc. 2006, 128, 16444.. 2. "Thermodynamic Analysis of β-Sheet Secondary Structure Via Backbone Thioester Exchange," E. B. Hadley, A. M. Witek, F. Friere, A. J. Peoples and S. H. Gellman Angew. Chem. Int. Ed. 2007, 46, ...
On Sun, 13 May 2007, Rolf Kalbermatter wrote: , Changelog , include/winsvc.h , Fix names of structure elements to match PSDK [...] , diff --git a/include/winsvc.h b/include/winsvc.h , index 7a29e8f..af56d29 100644 , --- a/include/winsvc.h , +++ b/include/winsvc.h , @@ -196,13 +196,13 @@ DECL_WINELIB_TYPE_AW(LPENUM_SERVICE_STATUS) , typedef struct _ENUM_SERVICE_STATUS_PROCESSA { , LPSTR lpServiceName; , LPSTR lpDisplayName; , - SERVICE_STATUS_PROCESS ServiceStatusProcess; , + SERVICE_STATUS_PROCESS ServiceStatus; , } ENUM_SERVICE_STATUS_PROCESSA, *LPENUM_SERVICE_STATUS_PROCESSA; [..] This patch is wrong. This field is really called ServiceStatusProcess in the PSDK. -- Francois Gouget ,fgouget at free.fr, http://fgouget.free.fr/ You can have my guns when you pry them from my kids cold, dead hands ...
Scientists have identified where a four-stranded version of DNA exists within the genome of human cells, and suggest that it may hold a key to developing new, targeted therapies for cancer.
Chord diagram. The backbone chain is represented by a circle. Chords (arcs) connect those residues that are in contact. Structure elements can be removed from the above chord diagram by clicking on their symbols. In case of proteins for which it is possible to identify the secondary structure, symbols are given in the Stride classification (e.g. AH stands for "alpha-helix"). {{ pdb }} {{ chain }} ...
Chord diagram. The backbone chain is represented by a circle. Chords (arcs) connect those residues that are in contact. Structure elements can be removed from the above chord diagram by clicking on their symbols. In case of proteins for which it is possible to identify the secondary structure, symbols are given in the Stride classification (e.g. AH stands for "alpha-helix"). {{ pdb }} {{ chain }} ...
contains an N-terminal beta-sheet that forms a beta-triangle structure; the remainder is a multihelical array of long and short helices ...
Mental exercise is one way to help prevent Alzheimers. Another means of prevention is to remain physically fit throughout life....
The amino-terminal extremity of the human immunodeficiency virus type 1 transmembrane protein (gp41) is thought to play a pivotal role in the fusion of virus membranes with the plasma membrane of the target cell and in syncytium formation. Peptides with sequences taken from the human immunodeficiency virus type 1 gp41 fusogenic (synthetic peptides SPwt and SP-2) and nonfusogenic (SP-3 and SP-4) glycoproteins adopt mainly a beta-sheet conformation in the absence of lipid, as determined by attenuated total reflection Fourier transform infrared spectroscopy, and after interaction with large unilamellar liposomes, the beta-sheet is partly converted into an alpha-helical conformation. Peptides SPwt and SP-2 but not SP-3 or SP-4 were able to promote lipid mixing as assessed by fluorescence energy transfer assay and dye leakage in a vesicle leakage assay. By using polarized attenuated total reflection Fourier transform infrared spectroscopy, SPwt and SP-2 were found to adopt an oblique orientation in ...
in Journal of Protein Chemistry (1994), 13(1), 77-88. Peptides corresponding to lipid binding domains of Apo B-100 were synthesized, purified, and incubated with dimyristoylphosphatidylcholine (DMPC) liposomes. The secondary structure of the apo B-100 ... [more ▼]. Peptides corresponding to lipid binding domains of Apo B-100 were synthesized, purified, and incubated with dimyristoylphosphatidylcholine (DMPC) liposomes. The secondary structure of the apo B-100 peptide-lipid complexes was evaluated by attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). Those peptides belonging to the hydrophobic core domain of apo B-100 when associated with phospholipids were rich in beta sheet structure; a predominant alpha helical conformation was shown to be associated with one peptide located in a surface region of apo B-100. IR dichroic spectra revealed, in the case of the core peptides, that the beta sheet component is the only oriented structure with respect to the ...
In this chapter we provide a survey of protein secondary and supersecondary structure prediction using methods from machine learning. Our focus is on machine learning methods applicable to β-hairpin and β-sheet prediction, but we also discuss methods for more general supersecondary structure prediction. We provide background on the secondary and supersecondary structures that we discuss, the features used to describe them, and the basic theory behind the machine learning methods used. We survey the machine learning methods available for secondary and supersecondary structure prediction and compare them where possible.. ...
In this study, hierarchical cluster analysis (HCA) and principal component analysis (PCA) were used to classify blends produced from diesel S500 and different kinds of biodiesel produced by the TDSP methodology. The different kinds of biodiesel studied in this work were produced from three raw materials: soybean oil, waste cooking oil and hydrogenated vegetable oil. Methylic and ethylic routes were employed for the production of biodiesel. HCA and PCA were performed on the data from attenuated total reflectance Fourier transform infrared spectroscopy, showing the separation of the blends into groups according to biodiesel content present in the blends and to the kind of biodiesel used to form the mixtures ...
LmrP is an electrogenic H(+)/drug antiporter that extrudes a broad spectrum of antibiotics. Five carboxylic residues are implicated in drug binding (Asp142 and Glu327) and proton motive force-mediated restructuring (Asp68, Asp128 and Asp235). ATR-FTIR (Attenuated Total Reflection - Fourier Transform Infrared) and tryptophan quenching experiments revealed that phosphatidylethanolamine (PE) is required to generate the structural intermediates induced by ionization of carboxylic residues. Surprisingly, no ionization-induced conformational changes were detectable in the absence of PE, suggesting either that carboxylic acid residues do not ionize or that ionization does not lead to any conformational change. The mean pKa of carboxylic residues evaluated by ATR-FTIR spectroscopy was 6.5 for LmrP reconstituted in PE liposomes, whereas the pKa calculated in the absence of PE was 4.6. Considering that 16 of the 19 carboxylic residues are located in the extramembrane loops, the pKa values obtained in the ...
Abstract This paper proposes a direct and efficient method to discriminate between counterfeit and authentic Cialis and Viagra samples by combining attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy with multivariate techniques. The chemical profile of 53 commercial samples (Viagra®, Cialis®) and 104 counterfeit samples (Viagra and Cialis) from distinct seizures were obtained from ATR-FTIR…. [...] ...
Looking for online definition of alpha helix conformation in the Medical Dictionary? alpha helix conformation explanation free. What is alpha helix conformation? Meaning of alpha helix conformation medical term. What does alpha helix conformation mean?
Research Corridor has published a new research study titled "Circular Dichroism Spectroscopy Market - Growth, Share, Opportunities, Competitive Analysis and Forecast, 2017 - 2025". The Circular Dichroism Spectroscopy Market report studies current as well as future aspects of the Circular Dichroism Spectroscopy Market based upon factors such as market dynamics, key ongoing trends and segmentation analysis. Apart from the above elements, the Circular Dichroism Spectroscopy Market research report provides a 360-degree view of the Lipstick Packing industry with geographic segmentation, statistical forecast and the competitive landscape.. Browse the complete report at http://www.researchcorridor.com/circular-dichroism-spectroscopy-market/. Geographically, the Circular Dichroism Spectroscopy Market report comprises dedicated sections centering on the regional market revenue and trends. The Circular Dichroism Spectroscopy Market has been segmented on the basis of geographic regions into North America, ...
Transmembrane helix-helix interactions may have at least two major functions: 1) intramolecular helix-helix interactions would serve to stabilize the tertiary structure of the protein in the membrane bilayer, and 2) helix-helix interactions between two or more integral membrane proteins appear to regulate ligand-initiated response systems. X-Ray crystallography of the α1-subunit of Na/K-ATPase (Figure 6) indicates that 5 of the 10 helices (M4, M5, M6, M7 and M8) lie largely within the core of the α1-subunit, whereas the remaining 5 helices (M1, M2, M3 M9 and M10)) are on the periphery. Computer-generated projections of each helix (Figure 7) indicate that helices within the core are disordered whereas peripheral helices are largely ordered. This suggests that the disordered helices contribute to and/or maintain the tertiary structure of the α1-subunit, whereas the peripheral ordered helices are available for interaction with ordered helices of neighboring integral membrane proteins.. In our ...
The model six-residue linear peptide AAGDYY-NH2 from TEM-1 beta -lactamase inhibitor protein and BLIP was predicted to adopt a beta -turn conformation and synthesized in order to elucidate the mechanism of beta -turn formation and stability. Its structural preferences in solution were comprehensively characterized using CD (circular dichroism), FT-IR and H-1-NMR spectroscopy. The set of observed short- and medium-range NOEs, the restrained molecular dynamics simulation, CD and FT-IR spectroscopy were consistent with the formation of beta -turn in solution by the model peptide. The results implicate beta -turn playing an important role in the process of protein folding. ...
To maintain genome integrity, segmented double-stranded RNA viruses of the Reoviridae family must accurately select and package a complete set of up to a dozen distinct genomic RNAs. It is thought that the high fidelity segmented genome assembly involves multiple sequence-specific RNA-RNA interactions between single-stranded RNA segment precursors. These are mediated by virus-encoded non-structural proteins with RNA chaperone-like activities, such as rotavirus (RV) NSP2 and avian reovirus sigma NS. Here, we compared the abilities of NSP2 and sigma NS to mediate sequence-specific interactions between RV genomic segment precursors. Despite their similar activities, NSP2 successfully promotes inter-segment association, while sigma NS fails to do so. To understand the mechanisms underlying such selectivity in promoting inter-molecular duplex formation, we compared RNA-binding and helix-unwinding activities of both proteins. We demonstrate that octameric NSP2 binds structured RNAs with high affinity, ...
The cpssp package ------------------------------------------------------------------------------ This package is released under the LaTeX Project Public License v1.3c or later (see http://www.latex-project.org/lppl.txt). The cpssp package allows you to draw a two-dimensional representation of a proteins secondary structure in LaTeX. Besides, it is possible to graphically compare protein secondary structure predictions. One can both compare predictions from a single program for several protein sequences (which have been aligned using any appropriate algorithm) and predictions from several programs for a single protein sequence. Installation: Run cpssp.ins through LaTeX and follow the instructions. -- Wolfgang Skala June 6th, 2009 ...
For the current problem we define a neural network with one input layer, one hidden layer and one output layer. The input layer encodes a sliding window in each input amino acid sequence, and a prediction is made on the structural state of the central residue in the window. We choose a window of size 17 based on the statistical correlation found between the secondary structure of a given residue position and the eight residues on either side of the prediction point [2]. Each window position is encoded using a binary array of size 20, having one element for each amino acid type. In each group of 20 inputs, the element corresponding to the amino acid type in the given position is set to 1, while all other inputs are set to 0. Thus, the input layer consists of R = 17x20 input units, i.e. 17 groups of 20 inputs each.. In the following code, we first determine for each protein sequence all the possible subsequences corresponding to a sliding window of size W by creating a Hankel matrix, where the ith ...
An alpha helix (α-helix) is a twisted part of a protein. It is one of the two most common parts of the secondary structure, or shape, of a protein. The other is the beta sheet. An alpha helix is created by alternating groups of atoms. There is a carbonyl group, created by a carbon atom double bonded to an oxygen atom, and an amine group, created by a nitrogen atom bonded to a hydrogen atom. Each section containing one of each of these groups is called a residue, a general term for a small part of a molecule. Each amine group forms a hydrogen bond with the carbonyl group four residues earlier. A prion is a protein that causes disease by changing the shape of another protein. It does this by changing some of the alpha helices, which are more common in normal cells, to beta sheets, which are more common in prions. The alpha helix consists of 3.6 residues per turn. All hydrogen bonds face in the same direction. If two or more alpha helices come together, they become a tertiary structure. (Ex. Five ...
Synonyms for a-helix in Free Thesaurus. Antonyms for a-helix. 15 synonyms for helix: spiral, twist, curl, loop, coil, corkscrew, gyre, curlicue, volute, spiral, coil, volute, whorl, spiral, genus Helix. What are synonyms for a-helix?
Autotransporter of N-terminal protease passenger domain that cleaves surface-localized virulence factors. The 3-d structure is known (Oomen et al., 2004). The crystal structure of the NalP translocator domain revealed a 12 β-stranded transmembrane beta-barrel containing a central alpha-helix. The transmembrane beta-barrel is stable even in the absence of the alpha-helix. Removal of the helix results in an influx of water into the pore region, suggesting the helix acts as a plug (Khalid and Sansom 2006). The dimensions of the pore fluctuate, but the NalP monomer is sufficient for the transport of the passenger domain in an unfolded or extended conformation (Khalid and Sansom 2006). NalP is subject to phase variation (Oldfield et al. 2013). ...
Autotransporter of N-terminal protease passenger domain that cleaves surface-localized virulence factors. The 3-d structure is known (Oomen et al., 2004). The crystal structure of the NalP translocator domain revealed a 12 β-stranded transmembrane beta-barrel containing a central alpha-helix. The transmembrane beta-barrel is stable even in the absence of the alpha-helix. Removal of the helix results in an influx of water into the pore region, suggesting the helix acts as a plug (Khalid and Sansom 2006). The dimensions of the pore fluctuate, but the NalP monomer is sufficient for the transport of the passenger domain in an unfolded or extended conformation (Khalid and Sansom 2006). NalP is subject to phase variation (Oldfield et al. 2013). ...
Secondary structure formation of FRA16B DNA following denaturation and re-annealing (reduplexing) reaction. (A) Gel electrophoresis analysis of re-annealed FRA1
This presentation is designed as an aid in teaching material on the secondary structures of proteins. Buttons are intended for the instructors use and are labeled with key words only. "Movies" are timed so as to allow for explanations between the movements and views of the molecule. To obtain the greatest benefit from the presentation, it is helpful to become fully familiar with the buttons ...
Helix-helix interactions are crucial in the structure assembly, stability and function of helix-rich proteins including many membrane proteins.
Circular Dichroism (CD) analysis from SGS - meet regulatory requirements with class-leading CD spectroscopic analysis, alpha helix beta sheet analysis, and secondary and tertiary structure analysis. Learn more.
Major Professor: Dr. Tim Cross. "Structure determination of M. Tuberculosis small helical membrane proteins in lipid by solid state nuclear magnetic resonance". ...
A regular stress test helps to assess coronary blockages by monitoring EKG changes during treadmill exercise protocols. Although helpful in making a diagnosis, a regular stress test lacks the sensitivity and specificity of nuclear stress tests.. For more information on regular stress tests, please visit our Heart Center.. ...
The surface of beta-sheet proteins contains amphiphilic regions which may provide clues about protein folding.s profile, publications, research topics, and co-authors
Magainin and melittin are 2 members of a class of small amphipathic helical peptides which act as potent antibiotics or toxins. It has been shown that the peptides in this class interact directly with the lipid bilayer ...
Online resource for oligonucleotide and primer design, calculting melting temperature, secondary structure determination, PCR resource and primer databases
The secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids. Secondary structure was predicted by using the programs PSIPRED and ALB. The residues predicted as helical are marked by H by PSIPRED and by H and & by ALB, and those predicted as -structural are marked by E by PSIPRED and by S and B by ALB ...
1qkx: Thermodynamic and structural characterization of Asn and Ala residues in the disallowed II region of the Ramachandran plot.
The level of protein structure in which combinations of secondary protein structures (ALPHA HELICES; BETA SHEETS; loop regions, and AMINO ACID MOTIFS) pack together to form folded shapes. 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. . ...
The publication AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. is placed in the Top 10000 of the best publications in CiteWeb. Also in the category Chemistry it is included to the Top 1000. Additionally, the publicaiton AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. is placed in the Top 1000 among other scientific works published in 1996 ...
1EM7: Structure of a protein G helix variant suggests the importance of helix propensity and helix dipole interactions in protein design.
Buy OUTLOOK II by mc27 as a Poster, Throw Pillow, Tote Bag, Art Print, Canvas Print, Framed Print, Photographic Print, Metal Print, or Greeting Card
1JTN: Crystal Structures of a T4-lysozyme Duplication-extension Mutant Demonstrate that the Highly Conserved beta-Sheet Region has Low Intrinsic Folding Propensity
The behavior of nested sequences as it relates to the Show Dialogs option has always been poorly documented and confusing to many users. The Helix Reference, prior to this amendment mentions only one combination of nested options.. In addition, sequence related bugs in earlier versions of Helix resulted in other areas of the code that did not function according to documentation. Changes were made (in Helix 4.5.3) that resulted in problems for users who had built nested sequences and were accustomed to the previous behavior. Furthermore, in an attempt to address another longstanding bug, the Helix 5.0 team went too far, not only fixing the bug, but also breaking an intended (but never documented) function of conditional sequences.. Changes in Helix 5.3 correct incorrect behaviors and implements the originally intended behavior, while providing a mechanism for avoiding problems for collections that rely on one of the prior behaviors.. We have also attempted to document the correct behavior of ...
Dr. A. Ramachandran, M.D.,Ph.D.,D.Sc.,FRCP.(Lond).(Edin)., an internationally acknowledged pivotal figure in the field of contemporary Diabetes Health Care and Researc..
chronic abuse of alcohol or drugs can place significant stress on many bodily systems. Learn how drugs influence the immune system.
It.txpondroilt de ICUl .I cs,,:tt:S*Ct ,112 C-Y:U 1 : j 1.2C I .. .C k. ..0.1. 112:(I VC:IU- .10 1! Intr ICS. t ILSSLCII I ilCit. C t(82 t1 .1 d.L( I i ii lKtie 8jU t.e.,L III jugemn nti rC~iJu ...
We have used three dimensional (3D) extrusion printing to manufacture a multi-active solid dosage form or so called polypill. This contains five compartmentalised drugs with two independently controlled and well-defined release profiles. This polypill demonstrates that complex medication regimes can be combined in a single personalised tablet. This could potentially improve adherence for those patients currently taking many separate tablets and also allow ready tailoring of a particular drug combination/drug release for the needs of an individual. The polypill here represents a cardiovascular treatment regime with the incorporation of an immediate release compartment with aspirin and hydrochlorothiazide and three sustained release compartments containing pravastatin, atenolol, and ramipril. X-ray powder diffraction (XRPD) and Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (ATR-FTIR) were used to assess drug-excipient interaction. The printed polypills were evaluated for ...
Cellulose nanocrystals (CNC) were successfully obtained and modified with 1,6-hexamethylene diisocyanate (HE)!) by means of in situ polymerization varying the CNC/HDI molar ratio to evaluate the number of anchored chains to the CNC. The modification was examined by elemental analysis, nuclear magnetic resonance ((13)C NMR) and attenuated total reflection Fourier transform infrared spectroscopy (IR-ATR). Nanocomposites containing 1.5 wt% CNC, modified and unmodified, were prepared by solvent casting. Thermal and mechanical properties of the resulting films were evaluated from the viewpoint of polyurethane microphase separated structure, soft and hard domains. CNC were effectively dispersed in the polyurethane matrix and depending on surface chemistry, the nanoreinforcement interacts selectively with matrix nanodomains. This interpretation is supported by differences in thermal and mechanical properties of the nanocomposites and also confirmed by AFM images. Isocyanate rich cellulose nanocrystals ...
Long-term occupational exposure to low level of fluoride can induce oxidative stress and apoptosis in many cells, including lymphocyte. However, the underlying mechanism remains unclear. Hence, this study was designed to explore the potential oxidative stress and apoptosis of long-term occupational exposure to low level of fluoride in aluminum smelter workers. A total of 120 aluminum smelter workers were recruited in control, low-, middle-, and high-fluoride exposure groups with 30 workers for each group. The peripheral blood samples were collected, centrifuged, and isolated to obtain serum and lymphocyte suspensions. The air and serum fluoride concentrations were detected by fluoride ion-selective electrode method. The lymphocytic apoptosis rate, DNA damage, oxidative stress, and mRNA levels of p53, Bcl-2, and Bax were assessed by Annexin V/PI staining, comet assay, attenuated total reflectance Fourier transform infrared spectroscopy and real-time polymerase chain reaction, respectively. ...
On the molecular level, injectable fillers are designed to last different lengths of time, and can be categorized as short (0-3 months), medium (3-12 months), or long-term (12 months to indefinitely) [3]. Collagen, hyaluronic acid, and silicone are examples of commonly used short, medium, and long-term fillers, respectively. Generally speaking, shorter-term products have greater biocompatibility [4]. Depending on the type of filler used, complication rates range from 3 % to 52 % [5]. In the short term, adverse events can include bleeding, infections, edema, and migration. In the long term, there is a risk of lump formation, granulomas, abscesses, more diffuse edema, and skin discoloration [2]. In these cases, having a reliable way to identify unknown substances prior to surgical treatment would be of great value both medically and legally [6]. Attenuated total reflectance/Fourier transform infrared spectroscopy can accurately identify unknown injectable fillers [6]. However, this method requires ...
Iron, an essential nutrient, is primarily present in soils in the form of iron-bearing minerals characterized with low solubilities. Under iron deficient conditions, some plants and microorganisms exude a mixture of iron-complexing agents, including carboxylates and siderophores, that can cause minerals to dissolve and increase iron solubility. Siderophores are chelating agents with functional groups such as hydroxamate, catecholate, or α-hydroxycarboxylate, that have high selectivity and specificity for Fe(III). This thesis is focused on adsorption/dissolution processes at the surface of a common soil mineral, goethite(α-FeOOH), in the presence of oxalate and a trihydroxamate siderophore, desferrioxamine-B (DFOB) at pH 4 and/or 6 in the absence of visible light. In order to characterize these processes at a molecular level and to understand the reaction mechanisms, a combination of attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy, extended X-ray absorption fine ...
Site-directed mutagenesis and other molecular biology-based techniques are now available for probing the amphipathic alpha-helix structural motif in the exchangeable apolipoproteins. Here we survey the published literature on lipid-binding and functional domains in apolipoproteins A-I, A-II, A-IV, C-I, C-II, C-III, and E and compare these results with recently developed computer methods for analysis of the location and properties of amphipathic helixes. This comparison suggests that there are at least three distinct classes of amphipathic helixes (classes A, Y, and G*) in the exchangeable apolipoproteins whose distribution varies within and between the seven apolipoproteins. This comparison further suggests that lipid affinity resides largely in class A amphipathic helixes (Segrest, J. P., et al. 1990. Proteins. 8: 103) and that variations in structure and/or numbers of class A domains in individual apolipoproteins allow a range of lipid affinities from high to low. The positions of the four a ...
A Fourier transform infrared spectrometer equipped with a cylindrical internal reflection element was used to sample the solidâ€"liquid interface of a metallic copper film submerged in an aqueous acidic polysaccharide solution. The presence of a polysaccharide absorption band at 1050 cmâˆ1 in a water-subtracted spectrum supported previous spectroscopic data indicating polymer accumulation at the surface of the film. Firm binding of the polysaccharide to the surface after a 17-day exposure period was demonstrated by the retention of the 1050-cmâˆ1 absorption band in spectra obtained after gentle rinsing of the film surface with polymer-free water. The sampling technique also provided evidence which suggests that acidic polysaccharides, including the firmly bound exopolymers produced by adherent cells of a freshwater sediment bacterium, promoted deterioration of the copper film. Internal reflection Fourier transform infrared spectroscopy appeared to be a useful, nondestructive method to ...
Protein folding is a complex process involving van der Waals and hydrophobic interactions, electrostatics, and hydrogen bonding networks. One approach to understanding protein folding is to design from scratch a particular protein fold, thoroughly characterize its solution properties, and determine its three-dimensional structure. The field of de novo protein design (1, 2) has experienced some recent exciting successes in the redesign of natural proteins to incorporate novel, functional metal-binding sites (3, 4). Also, the redesign of proteins patterned after the sequence or three-dimensional structural motifs such as the zinc finger (5-8), coiled coils (9), or other small protein domains (10, 11) has progressed quite significantly. Unnatural right-handed coiled coils have been successfully designed (12), and small, marginally stable models for protein secondary (13, 14) and supersecondary structures, including helix-loop-helix (15, 16) and three-stranded β-hairpin motifs (17-20), have been ...
Results of protein secondary structure analysis are shown in Table 5. The protein internal structure α-helix and β-sheet were modeled and identified using secondary derivative function based on amide I component peaks centered at ca. 1,650 and 1,625 cm−1, respectively. We found the absorbance peak height and area intensities of protein amide I, amide II, α-helix and β-sheet height as well as their ratio in SBM, CM, and RSM. All parameters of protein secondary structure were significantly different (p,0.05) among SBM, CM, and RSM except amide I to amide II area ratio (p = 0.53). Amide I area, Amide I peak height, Amide II area, α-helix and β-sheet height in RSM were significantly lower than those in SBM and in CM (p,0.05). Reports showed that amide I region mainly resulted from C=O stretching vibration and C-N stretching vibration. The region of amide II was primarily associated with NH in-plane bending and C-N stretching, also related to C=O stretching, C-C stretching and N-C stretching ...
Some work on this problem has been done. A fairly recent reference (with abstract) is given below. Authors Thanaraj TA. Argos P. Title Protein secondary structural types are differentially coded on messenger RNA. Source Protein Science. Vol 5(10) (pp 1973-1983), 1996. Abstract Tricodon regions on messenger RNAs corresponding to a set of proteins from Escherichia coli were scrutinized for their translation speed. The fractional frequency values of the individual codons as they occur in mRNAs of highly expressed genes from Escherichia coli were taken as an indicative measure of the translation speed. The tricodons were classified by the sum of the frequency values of the constituent codons. Examination of the conformation of the encoded amino acid residues in the corresponding protein tertiary structures revealed a correlation between codon usage in mRNA and topological features of the encoded proteins. Alpha helices on proteins tend to be preferentially coded by translationally fast mRNA regions ...
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In geometry, a triple helix (plural triple helices) is a set of three congruent geometrical helices with the same axis, differing by a translation along the axis. As with a single helix, a triple helix may be characterized by its pitch and diameter. Structures in the form of a triple helix include: Collagen helix Triple-stranded DNA Triple-threaded worm gears and screws Engel, Jürgen; Bächinger, Hans Peter (2005), "Structure, Stability and Folding of the Collagen Triple Helix", in Brinckmann, Jürgen; Notbohm, Holger; Müller, P. K., Collagen: Primer in Structure, Processing and Assembly, Topics in Current Chemistry, 247, pp. 7-33, doi:10.1007/b103818 (inactive 2017-08-12), ISBN 978-3-540-23272-8 Bernués, J.; Azorín, F. (1995), "Triple-stranded DNA", Nucleic Acids and Molecular Biology, Nucleic Acids and Molecular Biology, 9: 1-21, doi:10.1007/978-3-642-79488-9_1, ISBN 978-3-642-79490-2 . Rattan, S. S. (2009), Theory of Machines (3rd ed.), Tata McGraw-Hill Education, p. 370, ISBN ...
A series of polypeptides with well-defined sequences, (Asp3Phe1)n, (Asp2Phe1)n, (Asp1Phe1)n, (Asp1Phe2)n, and (Asp1Phe3)n, containing the hydrophilic amino acid, aspartic acid (Asp) and the hydrophobic amino acid, phenylalanine (Phe), were synthesized. Their behaviour in aqueous solution was investigated by performing fluorescence quenching and non-radiative energy transfer (NRET) experiments which were complemented by dynamic (DLS) and static (SLS) light scattering. The photophysical properties of the polypeptides were dependent on their Phe content. An increase in the Phe content led to an increase in the extinction coefficient, fluorescence quantum yield, and fluorescence average lifetime of the polypeptides. Circular dichroism experiments revealed that except for the (Asp1Phe3)n polypeptide, which adopts an alpha-helical conformation in aqueous solution, the other polypeptides did not adopt any known conformation in solution. The fluorescence quenching studies performed using molecular ...
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Synchrotron FT-IR micro-spectroscopy was used to determine thermally induced structural changes in thermoplastic protein produced from bloodmeal after mixing with sodium sulphite, sodium dodecyl sulphate, urea, tri-ethylene glycol and water. Changes in protein secondary structure at elevated temperature were assessed using second derivative peak height ratios in the amide III region (1,200-1,330 cm⁻¹) and compared with DSC and DMA results over the same temperature range. The results show an increase in ordered β-sheet structures with temperature at the expense of random coils, and that these β-sheets do not melt in the temperature range up to extrusion temperature of 120 °C. The implication of this is that during melt processing, β-sheet clusters may remain intact, similar to dispersed particulate fillers ...
Certain repetitive structures like to fit together, like beta sheets. But theres an additional mechanism to facilitate the evolution of protein-protein interfaces: domain swapping. Suppose a protein domain has an alpha helix (lets say) on its outside. It must fit into an alpha-helix shaped hole, assuming there are no gaps in the hydrophobic core of the domain. But protein molecules are floppy and vibrate in solution. One change of an amino acid facing into the core can destabilize it a little, so now that alpha helix flops around a bit and spends part of its time not fitting into its hole. If another protein of the same type comes along, they both have the same problem, a flopping alpha helix and a hole that fits it. So copy As alpha helix can fit into the helix-shaped hole on copy B, and copy Bs alpha helix can fit into the helix-shaped hole on copy A. Bango, instant binding of two protein molecules. This has been observed, so its not hypothetical ...
Certain repetitive structures like to fit together, like beta sheets. But theres an additional mechanism to facilitate the evolution of protein-protein interfaces: domain swapping. Suppose a protein domain has an alpha helix (lets say) on its outside. It must fit into an alpha-helix shaped hole, assuming there are no gaps in the hydrophobic core of the domain. But protein molecules are floppy and vibrate in solution. One change of an amino acid facing into the core can destabilize it a little, so now that alpha helix flops around a bit and spends part of its time not fitting into its hole. If another protein of the same type comes along, they both have the same problem, a flopping alpha helix and a hole that fits it. So copy As alpha helix can fit into the helix-shaped hole on copy B, and copy Bs alpha helix can fit into the helix-shaped hole on copy A. Bango, instant binding of two protein molecules. This has been observed, so its not hypothetical ...
Transitions in amino-acid conformation angles tend to accompany various structural modifications in protein structures. Thus, to benefit the modeling of protein structures, the Conformation Angles DataBase (CADB-3.0) has been updated to visualize the conformational angles in varied regions (fully, generously, additionally and disallowed regions). In addition, options are provided to display the angles in the secondary structural elements (α-helix, β-sheet and 310-helix) of the Ramachandran plot. The database is being updated periodically and can be accessed over the World Wide Web at the following URL: http://cluster.physics.iisc.ernet.in/cadb ...
Notice that the helix content rises and falls several times without any trace of it appearing on the RMSD curve. This is because large RMSD values such as 20 Å can result from completely unstructured chains as well as "unbundled" folded helices. Notice also that the hydrogen bond energy is related almost trivially with the helix content. The most probable hydrogen bonds in this system are those associated with the α-helices. Notice that the hydrophobicity energy only reaches its optimum values when the RMSD reaches the native-like values, whereas hydrogen bond (in the left figure) saturates a little before that. Taken together, these plots point towards a folding process in which the helices form independently, before being assembled into a 3-helix bundle. The helix formation is driven mainly by hydrogen bonds where as arrangement of the folded helices is driven by hydrophobicity. ...
Pro)tein (B)ilayer (L)ipid (M)embrane (ProBLM) is a webserver that creates a combined protein-membrane complex when given a membrane protein (helical or beta-barrel) and bilayer lipid membrane (POPC, POPE or artificial). The artificial membrane is generated with ProNOI software (BMC Struct Biol. 2012 Dec 5;12:31) as a parallelepiped made of dummy atoms and has user specified dimensions. By using geometric features within alpha-helical and beta-barrel membrane proteins, ProBLM predict a proteins orientation and position when placed within a membrane environment. If the topology of the protein does not allow for correct orientation within the membrane, the protein is placed in the membrane without being oriented and the user is given the option to manually reorient it using sliders. ...
There might be another problem with the scoring function, along the same lines as the issue with design puzzles favoring the large aromatic side chains.. From what Ive read, serine is considered a structure-breaking amino acids and does not normally show up in sheets or helices. So, if serine doesnt belong in a beta sheet in nature, I wouldnt expect the mutate function to be substituting it into beta sheets very often. However, Ive noticed that in freestyle design Im often getting serine in my beta sheets. If it were just one or two, that would be realistic, but Im looking at a ten-segment beta strand with four serines, and in one case recently I had a sheet that was almost entirely serines. That cant be right.. ...
Given some similarity in sequence between two proteins, a molecular model can be constructed for one sequence provided that the tertiary structure of the other is known. This approach, which is often...
Madine, J., Jack, E., Stockley, P. G., Radford, S. E., Serpell, L. C., & Middleton, D. A. (2008). Structural Insights into the Polymorphism of Amyloid-Like Fibrils Formed by Region 20-29 of Amylin Revealed by Solid-State NMR and X-ray Fiber Diffraction. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130(45), 14990-15001. doi:10.1021/ ...
What is the difference between Alpha helix and Beta Pleated Sheet? Alpha Helix is a right-handed coiled rod-like structure. Beta pleated sheet is a sheet-
Jagadeeswaran, P and Cherayil, Joseph D (1986) A general model for the conformational switch in 5S RNA during protein synthesis. In: Journal of Theoretical Biology, 83 (2). pp. 369-375. Jagadeeswaran , P and Cherayil , JD and Pattabiraman , N and Sasisekharan , V (1978) Computer Method for Predicting Sequence of Transfer-RNA from its Enzymatic Digestion Products Based on Secondary Structure of Transfer-RNA. In: Indian Journal of Biochemistry & Biophysics, 15 (2). 47-48 . ...
More than half of Americans with debt say owing money has had a negative impact on their lives, according to a recent AICPA survey. Nearly a third of people with debt say they worry about it, while about a fifth say it has caused friction with a spouse or partner.
Since the first three-dimensional structures of proteins were elucidated the problem of how proteins fold to such complicated structures has been debated. The subject of this debate is called the protein folding problem which is one of he major challenges in contemporary molecular biology.
Lee, B. and Richards, F.M. (1971). The interpretation of protein structures: estimation of static accesibility. J. Mol. Biol. 55, 379-400
New class PhiPsiAverager to get consensus of phi/psi angles from a TemplateList and an Alignment. Tested with a few examples and seems to work. The wrapping of angles at 180/-180 is not yet taking into account, i.e. if an interval falls in the region just below 180 and just above -180, no consensus will be found. Pdb: added some checks to methods getPhi/Psi so that it doesnt fail when theres no coordinates. Changed yet again the design of TemplateList/Template. Now loading of PDB data happens upon call of the loadPDBdata method. Changed dependencies accordingly ...
HTML 5 makes a leap forward in defining page content with several new structure elements that are designed to give web pages more structure. In this article, we add content specific elements of article, aside, figure, figcaption, hgroup and iframe.