• Serpins fold to a metastable native state and are susceptible to undergoing spontaneous conformational change to more stable conformers, such as the latent form. (proteopedia.org)
  • NMR spectroscopy as a powerful technique is often used to investigate on structural and conformational studies on proteins and drug compounds. (sharif.edu)
  • Thus, while the adenine site preferences of the spliceosome and of phage GA may be due to protein factors, the preferred adenine is predisposed in the free RNA to conformational rearrangement involved in formation of the active complexes. (rcsb.org)
  • 2.There is a known phenomenon, called "induced fit", whereby a target protein undergoes conformational changes upon ligand binding. (cecam.org)
  • Induced fit phenomenon occurs also when two proteins associate, i.e. both of them undergo conformational changes, so that the structure of the complex is not equivalent to rigid composition of two proteins. (cecam.org)
  • Upon binding, proteins and small-molecule ligands can undergo significant conformational changes, as schematized by the "induced fit" and "conformational selection" paradigms [1]. (cecam.org)
  • The extraordinary biology and transmissibility of these disorders stems from the protean conformational properties of the prion protein (PrP). (cdc.gov)
  • Its six backbone torsion angles and glycosidic bond between base and ribose provide conformational dynamics not afforded by the peptide bond of proteins and more flexibility than the DNA backbone. (datexis.com)
  • Thus, the accuracy of dynamic conformational ensembles should be evaluated differently to that of single conformers. (biomedcentral.com)
  • IDPs can not be described with single-conformer models but only with conformational ensembles capturing the diversity of structures. (biomedcentral.com)
  • Nevertheless, even the conformational heterogeneity of globular proteins due to their internal dynamics requires the use of such representations. (biomedcentral.com)
  • The so-called dynamic conformational ensembles reflecting the flexibility of proteins can be regarded as a novel type of models of protein structure. (biomedcentral.com)
  • These substitutions either create premature termination codons, which lead to truncated proteins, or substitute highly conserved residues in the bHLH region. (biomedcentral.com)
  • For V3L, this observation can be explained by stabilization of the inactive conformation of the loop of residues 181-197, which prevents substrate binding. (rcsb.org)
  • In the crystal structure of V3L, electron density corresponding to a leucine residue is present in a position that stabilizes the loop of residues 181-197 in the inactive conformation. (rcsb.org)
  • To protect it with a gap-free protein shell, 30 Å thick, would require roughly 25,000 amino acid residues-far more than the viral nucleic acid can encode. (basicmedicalkey.com)
  • We have completed a systematical analysis of how temperature, pH, presence of charged residues, but most importantly backbone conformation and dynamics affect isomerization rates as determined by NMR in the case of designed Asn/Asp polypeptide-models. (elte.hu)
  • We concluded that spontaneous deamidation prompted backbone isomerization of Asn/Asp residues resulting in - most cases - the insertion of an extra methylene group into the backbone poses a threat to the structural integrity of proteins. (elte.hu)
  • This paper describes results on the association between protein kinase A and peptides corresponding to wild-type PLN (residues 8-22) and peptides bearing mutations (R9C and A11E) which in the context of full-length PLN (52 residues) result in dilated cardiomyopathy. (elifesciences.org)
  • In proteins, for instance, absorption in the near UV range is mainly due to the aromatic side chain of the tryptophan, tyrosine and phenylalanine amino acids and both spectroscopic and dynamic properties of these chromophores generally depend on their immediate environment, i.e., on the local conformation of the protein. (cea.fr)
  • We show that the geometric descriptors of the initial nucleophilic attack of the isomerization can be used to classify local conformation and contribute to the design of stable protein drugs, antibodies or the assessment of the severity of mutations. (elte.hu)
  • Some functions are performed by disordered protein structural parts. (alzforum.org)
  • In this work, conformations and structural properties of drug compounds and some nucleoside derivations have been studied using advanced NMR techniques including H-H COSY, HMQC, HMBC and NOESY and quantum based calculations.Experimental analysis on Valsartan show that there are two simultaneous conformers (M and m) with unequal population in M-m type solvents and two stable conformers (N and n) in the N-n type solvents. (sharif.edu)
  • Large polypeptides that form a-helix or ß-sheet structures are currently beyond the reach of rotational spectroscopists, but the recent ion-drift experiments [13-15] on acetyl-(alanine)7-lysine suggest that the first direct observations of the structural motifs found in protein and peptide secondary structure using high resolution spectroscopy may not be far off. (kent.edu)
  • MARV assembles and buds from the host cell plasma where MARV matrix protein (mVP40) dimers associate with anionic lipids at the plasma membrane inner leaflet and undergo a dynamic and extensive self-oligomerization into the structural matrix layer. (uci.edu)
  • MolView started out as 2D to 3D structure converter where the user can draw a structural formula and view a generated 3D conformer that was generated using the Chemical Identifier Resolver (e) . (divched.org)
  • The ability to detect structural and dynamic information about folding intermediates in vitro provides an excellent opportunity to gain new insights into the energetic aspects of the energy landscape of protein folding. (elte.hu)
  • In this paper, we will discuss about the component of supramolecular protein assembly and classify their conformation according to structural dimensionality. (springeropen.com)
  • In conjunction with the recognition of the functional role of internal dynamics of proteins at various timescales, there is an emerging use of dynamic structural ensembles instead of individual conformers. (biomedcentral.com)
  • Chemoproteomics (also known as chemical proteomics) entails a broad array of techniques used to identify and interrogate protein-small molecule interactions. (wikipedia.org)
  • Chemoproteomics also attempts to address the inherent challenge of drug promiscuity in small molecule drug discovery by analyzing protein-small molecule interactions on a proteome-wide scale. (wikipedia.org)
  • Derivatization-free approaches aim to infer drug-target interactions by observing changes in protein stability or drug chromatography upon binding. (wikipedia.org)
  • A clear understanding of protein-protein interactions, both for stable complexes and for transient ones, would therefore mark a major step forward, and it would have enormous consequences for designing new strategies of therapeutic intervention in diseases like cancer. (cecam.org)
  • FLIM-FRET analysis of protein-protein interactions showed that PLIN5 S155 phosphorylation regulates PLIN5 interaction with adipose triglyceride lipase at the lipid droplet, but not with α-β hydrolase domain-containing 5. (uci.edu)
  • We propose that the resulting disruption of native TM interactions disrupts the conformation of the kinase domain, inhibiting EGFR's ability to send migratory cell signals. (biorxiv.org)
  • Alternative holoenzyme conformations reveal important functional interactions that maintain PCNA orientation during synthesis. (nature.com)
  • Furthermore, alternative conformations or overlapping entries that might be annotated in the original protein structure are removed, as they could disturb the analysis of molecular interactions. (proteins.plus)
  • chemically we view some relationships and serial simulations about the protein of design in talented items, looking and playing dose-dependent chat interactions for the paint of financial strategies and conducting a business for a practical shape of such counter. (bob-fernsehdienst.de)
  • Our structures, combined with the results from other biophysical and biochemical assays, reveal a common disease mechanism: the mutations in PLN reduce its phosphorylation level by changing its conformation and weakening its interactions with PKA. (elifesciences.org)
  • Functional interactions perturb this state by shifting the equilibrium towards 'active conformations' that are present but are low-populated in the apo state. (biomedcentral.com)
  • Our data show that the stable knockdown of HIPK2 led to wtp53 misfolding, as detected by p53 immunoprecipitation with conformation-specific antibodies, and that p53 protein misfolding impaired p53 DNA binding and transcription of target genes. (aacrjournals.org)
  • Such an approach has been developed by a collaboration between the SBM team of LFP (CEA-CNRS URA2453), a theoretical team of the Ruđer Bošković Institut (Zagreb, Croatia) and two experimentalists of CLUPS (Paris Sud University, Orsay) in order to characterize the excited states of the stable conformers of a model peptide and establish the nonradiative relaxation mechanisms. (cea.fr)
  • See also David Thirumalai's Emerging Ideas on the Molecular Basis of Protein and Peptide Aggregation ' (.pdf). (alzforum.org)
  • There are specific problems of protein-protein docking, protein-peptide docking and protein-drug docking with corresponding areas of applications. (cecam.org)
  • A major plaque component, β amyloid peptide (Aβ), derives from the amyloid precursor protein (APP). (jneurosci.org)
  • Homeodomain-interacting protein kinase-2 (HIPK2) is a positive regulator of p53 oncosuppressor function. (aacrjournals.org)
  • Perilipin 5 (PLIN5) is a lipid-droplet-associated protein that coordinates intracellular lipolysis in highly oxidative tissues and is thought to regulate lipid metabolism in response to phosphorylation by protein kinase A (PKA). (uci.edu)
  • PLN interacts with sarco/endoplasmic reticulum Ca 2+ -ATPase (SERCA) and regulates calcium uptake, which is modulated by the protein kinase A (PKA)-dependent phosphorylation of PLN during the fight-or-flight response. (elifesciences.org)
  • As part of the "flight or fight" response, protein kinase A phosphorylates phospholamban (PLN), thereby relieving a tonic inhibition of the endo/sarco-plasmic reticulum calcium pump, which results in an increased force of cardiac contraction. (elifesciences.org)
  • In this context, synergetic theoretical/experimental studies of gas phase model peptides as proteins building blocks should lead to better understanding the photophysical phenomena involved in the relaxation mechanisms of proteins. (cea.fr)
  • The reason why Peter Lansbury and others used the term 'natively unfolded' for a-synuclein and other proteins, especially peptides, is that they do not exist, to a significant degree, in the same kind of stable structure that larger native proteins like myoglobin do. (alzforum.org)
  • Here we demonstrate that RNA-targeting CRISPR effector proteins, a programmable class of gene silencing agents that includes the Cas13 family of enzymes and Cas7-11, can be used to mitigate TDP-43 pathology when programmed to target ataxin-2, a modifier of TDP-43-associated toxicity. (bvsalud.org)
  • Effector proteins are then recruited to activate various cellular signaling pathways, including RAS/RAF/MEK, PI3K/AKT/mTOR, and JAK/STAT ( 1 ). (biorxiv.org)
  • I agree with you that we also want to examine the earlier, less stable structures. (alzforum.org)
  • For the first time crystal structures of wild-type bovine pancreatic ribonuclease A and its markedly less stable variant modified at position Ile106 were determined at different pressures. (udg.edu)
  • MolView offers a simple search interface to find small molecules, proteins and crystal structures in these databases. (divched.org)
  • It adds missing hydrogen atoms to protein structures (PDB-format) and detects reasonable protonation states, tautomers, and hydrogen coordinates of both protein and ligand molecules. (proteins.plus)
  • In contrast, one protein forms various structures and implements other biological phenomena depending on the situation. (springeropen.com)
  • The basic principle that forms these hierarchical structures is protein self-assembly. (springeropen.com)
  • Supramolecular assembly is a very common phenomena in nature and these natural supramolecular proteins have various structures, from simple structures to complex structures [ 1 , 2 ]. (springeropen.com)
  • however, more protein structures have been identified by advanced technology (Fig. 1 ). (springeropen.com)
  • A better understanding of the proteins contributes to designing new supramolecular structures from rational design to de novo design. (springeropen.com)
  • Recently, the de novo design of proteins that start from scratch can create a new topology beyond experimentally determined structures. (springeropen.com)
  • Protein NMR is the method of choice for determining protein structures at the atomic level in solution. (biomedcentral.com)
  • It should be kept in mind that all representations of protein structures are actually models of the 'real' ones and thus can have different types of errors. (biomedcentral.com)
  • That's another big problem-huge, very challenging-is to predict which structures can be made and which just might exist on paper, and they may look stable, but nobody can make them, so what is the point looking into them? (nih.gov)
  • Many complex molecular systems absorb light in the UV spectral range, including those of paramount biological importance, like DNA bases or proteins. (cea.fr)
  • In most docking schemes, first an ensemble of conformations which may be relevant for docking is obtained, e.g. from experimentally solved multiple conformers, from molecular dynamics snapshots, from normal modes analysis, essential dynamics, or rigidity theory. (cecam.org)
  • Ongoing efforts to develop functional peptoids will necessitate improved capability for control of peptoid structure, particularly of the backbone amide conformation. (nextbigfuture.com)
  • Available online 25 January 2010 peaks have been linked to a dipolar flip-flop polarization transfer from 1H nuclei to rapidly relaxing amide 14N nuclei in rotationally immobilized proteins. (lu.se)
  • Two small molecules, a tertiary amine pyrazolone (TAP) and a pyrano coumarin ferulate (PCF) were suggested to be ALS drug candidates following experimental observation of their ability to inhibit SOD1 protein misfolding and aggregation. (bvsalud.org)
  • 1 In the King lab, I focused on the aggregation pathways of oxidation-mimicking Trp variants of human γD-crystallin, 2 revealing another unusual phenomenon: the highly stable, aggregation-resistant WT protein drove a destabilized but still well folded variant into an aggregated state without itself aggregating 3 ( Figure 1 ). (mit.edu)
  • In subsequent studies, 4,5 we showed that this effect is mediated by transfer of disulfide bonds from a redox-active site on the WT protein to a non-native site in the W42Q variant, which locked a misfolded conformer prone to non-amyloid aggregation. (mit.edu)
  • PFG-NMR is used to better understand protein unfolding and to quantitatively characterize the degree of denaturation and aggregation. (elte.hu)
  • These ensembles are usually substantially more diverse than conventional NMR ensembles and eliminate the expectation that a single conformer should fulfill all NMR parameters originating from 10 16 - 10 17 molecules in the sample tube. (biomedcentral.com)
  • Entry of HIV-1 into human lymphoid requires activities of viral envelope glycoproteins gp120 and gp41, and two host-cell proteins, the primary receptor CD4 and a chemokine co-receptor. (biomedcentral.com)
  • I suggest a consensus effect of each neuromodulatory molecule on Drosophila aggression, as well as effects of receptor proteins where relevant data are available. (deepdyve.com)
  • DEC-205 (CD205), a member of the macrophage mannose receptor protein family, is the prototypic endocytic receptor of dendritic cells, whose ligands include phosphorothioated cytosine-guanosine (CpG) oligonucleotides, a motif often seen in bacterial or viral DNA. (uci.edu)
  • Here we describe the 3.2 Å cryo-EM structure of human DEC-205, thereby illuminating the structure of the mannose receptor protein family. (uci.edu)
  • In the crystal structure of a V3F.FdUMP binary complex, the nucleotide is bound in an alternative mode to that proposed for the catalytic complex, indicating that the high K(m,app) value is caused not by stabilization of the inactive conformer but by substrate binding in a nonproductive, inhibitory site. (rcsb.org)
  • The work will be of interest to investigators of mechanisms of substrate recruitment by protein kinases, and particularly to those who are trying to understand the mechanisms of familial dilated cardiomyopathy. (elifesciences.org)
  • The applicability of Hα detected spectral approach was probed for proteins to characterize them under physiological conditions. (elte.hu)
  • We detected and characterized different intermediate states by T-dependent NMR of the 15N and 13C/15N labeled (mini)proteins, at different pHs and developed a NMR spectra deconvolution technique to characterize the "invisible" intermediate (I-) state(s), beside the fully folded (F-state) and unfolded (U-) state, all in fast exchange. (elte.hu)
  • Drug discovery has made use of animal knock-out models that highlight the impact of a protein's absence, particularly in the development of disease, and medicinal chemists have leveraged computational chemistry to generate high affinity compounds against disease-causing proteins. (wikipedia.org)
  • A crucial problem that advanced computational approaches could solve is that of specificity: how are biologically unique connections made between proteins taken from a wealth of thousands of possible partners? (cecam.org)
  • Moreover, with advances in the computational design of protein folding and protein-protein interfaces, considerable progress has recently been made in the de novo design of protein assemblies. (springeropen.com)
  • De novo design generates a building block based on the basic physical principle of protein by using computational power. (springeropen.com)
  • The development of computational power and increased protein structure databases has expanded our knowledge to understand and design folding units. (springeropen.com)
  • Hydrostatic pressure in range 0.1-1.5 GPa is used to modify biological system behaviour mostly in biophysical studies of proteins in solution. (udg.edu)
  • Our review presents a description of the components of supramolecular protein assembly and their application in understanding biological phenomena to therapeutics. (springeropen.com)
  • For biological systems, Q peaks were first observed in protein from different perspectives [3,7,9,13,15,21-23] , the detailed molec- powders and attributed to 1H-14N spin pairs [9], which were also ular mechanism of the ubiquitous 1H-14N Q peaks in biological sys- thought to be of critical importance for the background 1H relaxa- tems has not been established. (lu.se)
  • Methods for engineering biomolecular systems based on DNA and protein are advancing rapidly, building a technology platform for engineering increasingly large and complex self-assembled nanosystems. (nextbigfuture.com)
  • The same is true for the problem of interpreting the dynamics of macromolecular aggregates from NMR spectroscopy, especially in the presence of natively unstructured proteins. (cecam.org)
  • Broad proteomic and transcriptomic profiling has led to innumerable advances in the biomedical space, but the characterization of RNA and protein expression is limited in its ability to inform on the functional characteristics of proteins. (wikipedia.org)
  • Developments in DNA, protein, and inorganic nanotechnologies are converging to provide a technology platform for the design and fabrication of complex, functional, atomically precise nanosystems. (nextbigfuture.com)
  • Specific modifications commonly found at the junction of the stems of the cloverleaf structure (Figure 1), referred to as the core, elbow or hinge in the three-dimensional structure of most tRNAs, are often associated with functional folding, allowing tRNAs to fold into the common L-shape form critical to ribosomal protein synthesis. (datexis.com)
  • We focus on the dynamics of the pseudorotation process, in particular, the lifetime of the THF conformations and their mutual rearrangements. (researchgate.net)
  • A standard procedure begins with sample lysis, in which proteins are extracted into a denaturing buffer containing salts, an agent that reduces disulfide bonds, such as dithiothreitol, and an alkylating agent that caps thiol groups, such as iodoacetamide. (wikipedia.org)
  • In addition, a third cell-surface protein called protein disulfide isomerase (PDI) is found to play a major role in HIV-1 entry. (biomedcentral.com)
  • It is present mostly in the endoplasmic reticulum and act as oxidase to forms disulfide bonds in nascent proteins and assists in protein folding [ 4 ]. (biomedcentral.com)
  • Most recently, as a postdoc in the Shakhnovich group at Harvard, I drew inspiration from the disulfide chemistry of the lens crystallins to devise a high-throughput disulfide scanning (HTDS) methodology that aims to systematically discover protein conformations, including non-native conformations, and link them to phenotypic effects. (mit.edu)
  • Solution-based approaches involve the use of drug analogs that chemically modify target proteins in solution, tagging them for identification. (wikipedia.org)
  • The autosomal dominant monogenetic disease neurofibromatosis type 1 (NF1) affects approximately one in 3,000 individuals and is caused by mutations in the NF1 tumour suppressor gene, leading to dysfunction in the protein neurofibromin (Nf1) 1 , 2 . (nature.com)
  • To address the first problem, we need scientists who develop methods for estimating changes in protein stability of binding upon mutations. (cecam.org)
  • Over 160 TWIST mutations have been described in SCS patients, a majority of which are present in the bHLH domains, mediating protein dimerization, and involving a single base pair substitution (54% of mutations). (biomedcentral.com)
  • Additionally, the interaction of PCNA with Pol δ is critical for coordinating its transient replacement by other PCNA partner proteins. (nature.com)
  • Chemoproteomic tools offer a solution to bridge the gap between a genetic understanding of disease and a pharmacological understanding of drug action by identifying the many proteins involved in therapeutic success. (wikipedia.org)
  • Controlling the biodistribution of protein- and nanoparticle-based therapeutic formulations remains challenging. (uw.edu)
  • TWIST1 proteins can form either homodimeric (TWIST1/TWIST1) or heterodimeric complexes, mainly in association with E2A proteins. (biomedcentral.com)
  • Protoss is a fully automated hydrogen prediction tool for protein-ligand complexes. (proteins.plus)
  • Rarey, M., Fast automated placement of polar hydrogen atoms in protein-ligand complexes. (proteins.plus)
  • Rarey, M., Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes. (proteins.plus)
  • Specifically, the TM of unliganded (inactive) EGFR dimerizes at the C-terminus (C t ), while the ligand bound form dimerizes N-terminally (N t ), and the two helices are also rotated by 180° between the conformations ( 4 , 5 ). (biorxiv.org)
  • The redox inhibitory conformations were energetically and statistically favored and supported the evidence from wet laboratory experiments reported in the literature. (biomedcentral.com)
  • Integrin allosteric changes, clustering, and trafficking cooperate to regulate cell adhesion and motility on extracellular matrix proteins via mechanisms that are partly defined. (life-science-alliance.org)
  • As the results show, different intramolecular hydrogen bond is the reason for stability af all available conformers. (sharif.edu)
  • Protein Folding and Neurodegeneration: Biophysics to the Rescue? (alzforum.org)
  • We define the components of protein assembly in three aspects: folding structure unit, protein-protein interface, and assembly symmetry (Fig. 2 ). (springeropen.com)
  • These building blocks are mostly composed of α-helices, β-sheets, or a mixture of them (Fig. 3 A). The symmetry of the units and dimensions of the supramolecular protein are determined, depending on how the folding unit is configured. (springeropen.com)
  • Low energy difference between the envelope (Cs symmetry) and twisted (C2 symmetry) conformations of the THF molecule leads to the interconversion between the two conformers. (researchgate.net)
  • We observe a different ratio between envelope (Cs) and twisted (C2) conformations with respect to a change of the temperature. (researchgate.net)
  • Our previous studies using gene-targeted mouse models of chronic wasting disease (CWD) demonstrated that Norway and North America cervids are infected with distinct prion strains that respond differently to naturally occurring amino acid variation at residue 226 of the prion protein. (cdc.gov)
  • Here, we show, by microarray analysis, that wtp53 lost the target gene activation following stable knockdown of HIPK2 (HIPK2i) in colon cancer cell line. (aacrjournals.org)
  • The shell of a nonenveloped virus with even a very small genome must therefore contain a large number of identical protein subunits-at least 60, if the coat-protein gene is to use up less than 25% of the coding capacity in the enclosed nucleic acid. (basicmedicalkey.com)
  • higher electropositive substituents like a naphthalene group at the C3-position can enhance the activity of the drug by providing hydrogen bond interaction with the protein target. (fdocument.org)
  • When the structure of the interacting proteins is known, either from experiments or from modeling, several docking algorithms are available which attempt to predict the geometry of the complex. (cecam.org)
  • The TWIST1 protein is highly conserved from Drosophila to humans, where it plays a key role during embryonic morphogenesis, mesoderm patterning and development. (biomedcentral.com)
  • Not only does RNA translate the genetic code decoding it into protein, but it also has various catalytic and regulatory functions yet to be completely elucidated. (datexis.com)
  • Spatially and temporally conditional knock-out/knock-in systems have improved the level of nuance in in vivo analysis of protein function, but still fail to completely parallel the systemic breadth of pharmacological action. (wikipedia.org)
  • Denatured proteins are proteolysed, often with trypsin, and then separated from other mixture components prior to analysis via LC-MS/MS. For more accurate quantification, different samples can be reacted with isobaric tandem mass tags (TMTs), a form of chemical barcode that allows for sample multiplexing, and then pooled. (wikipedia.org)
  • Clustering analysis allowed identifying the most populated conformers present during the MD simulation, which were used as starting models to perform docking calculations with five DD2-HDAC6 inhibitors: Cay10603 (CAY), Rocilinostat (RCT), Tubastatin A (TBA), Tubacin (TBC) and Nexturastat (NXT), and then were also submitted to 100 ns-long MD simulations. (barbascoinhibitor.com)
  • Gascón, J. A. Finite Temperature Analysis of Inter-Chromophore Electronic Couplings in Different Forms of the Peridinin-Chlorophyll a Protein, POSTER 643, 2020 Biophysical Society Meeting, San Diego, CA, February 15-19, 2020. (uconn.edu)
  • The coat protein can bind helices with bulged adenines at either position, but the 3'-proximal site binds with greater affinity. (rcsb.org)
  • When bound to phage GA coat protein, the bulged adenine loops out of the helix and occupies a binding pocket on the surface of the protein, forming a nucleation complex for phage assembly. (rcsb.org)
  • We have studied this RNA motif in a 21 nucleotide hairpin containing a GA coat protein-binding site whose four nucleotide loop has been replaced by a more stable loop from the related phage Ms2. (rcsb.org)
  • This would fundamentally change our conventional thinking about protein structure-function relationship, no? (alzforum.org)
  • I do not think there is a contradiction to the conventional thinking of protein structure-function relation. (alzforum.org)
  • Using heteronuclear NMR spectroscopy, we have determined the structure of this hairpin to an overall precision of 2.0 A. Both adenine bases stack into the helix, and while all available NOE and coupling constant data are consistent with both possible A.U base pairs, the base pair involving the 5'-proximal adenine appears to be the major conformation. (rcsb.org)
  • DoGSiteScorer is a grid-based method that uses a Difference of Gaussian filter to detect potential binding pockets 1 - solely based on the 3D structure of the protein - and splits them into subpockets. (proteins.plus)
  • Various proteins form one complex structure to control detailed reactions. (springeropen.com)
  • Each components determine the overall structure of supramolecular protein structure and their functions. (springeropen.com)
  • Dynamical studies of the past decade led to the emerging paradigm that the so-called 'native structure' of a protein can be better viewed as a number of more or less similar conformers interconverting on different time scales. (biomedcentral.com)
  • Due to specific influence on the system equilibrium high pressure can act as a filter that enables to identify and investigate higher energy protein conformers. (udg.edu)
  • Deletion of this domain creates a variant--tengpinDelta51--which folds past the native state and readily adopts the latent conformation. (proteopedia.org)
  • The design and synthesis of protein-like polymers is a fundamental challenge in materials science. (nextbigfuture.com)
  • We present evidence that zinc supplementation to HIPK2i cells increased p53 reactivity to conformation-sensitive PAb1620 (wild-type conformation) antibody and restored p53 sequence-specific DNA binding in vivo and transcription of target genes in response to Adriamycin treatment. (aacrjournals.org)
  • Telomerase is an RNA-protein complex (RNP) that comprises 30 ends of linear chromosomes which give rise to generation of the small telomere-repeat sequence (TTGGGG in ciliates and TTAGGG in humans) by using RNA prototype. (springeropen.com)
  • Several agents have been developed to target these key regulatory proteins that are essential for HIV replication. (biomedcentral.com)
  • The 2'-OH of the bulged adenine adopts a regular A-form helical geometry, suggesting that in order to participate in the splicing reaction, the conformation of the branch-point helix in the active spliceosome may change from the conformation described here. (rcsb.org)
  • form, usually the most stable one. (equimount.com)