• This is why it is so difficult for humans to mount an effective immune response and why it is challenging for researchers to develop vaccines targeting the HIV envelope proteins," Dr. Blanchard says. (sciencedaily.com)
  • The 1.9Å crystal structure of the human CA VI catalytic domain reveals a prototypical mammalian CA fold, and a novel dimeric arrangement as compared to previously-reported CA structures. (ox.ac.uk)
  • The structure revealed an active conformation of the catalytic domain that formed canonical interactions with the bound ligand Mg-ADP. (ox.ac.uk)
  • Today's tools are increasingly internet aware, often integrated tightly with structure databases ( Table 1 ), as well as with databases containing sequences and other features (for example, domains, single-nucleotide polymorphisms (SNPs), interactions). (nature.com)
  • 2018). Here, we have performed two RT crystallographic screens of PTP1B using many of the same fragments, representing the largest RT crystallographic screens of a diverse library of ligands to date, and enabling a direct interrogation of the effect of data collection temperature on protein-ligand interactions. (rcsb.org)
  • 3) Protein interactions and enzyme characterization. (manchester.ac.uk)
  • Stability, dynamics and interactions of proteins: packing and electrostatics. (lu.se)
  • Through techniques such as X-ray crystallography, the three-dimensional structure of IL7RA can be determined, which can provide detailed information about the protein's shape, conformation, and interactions. (creativebiomart.net)
  • Moreover, targeting protein functional motions bears a great potential to control and modulate proteins' activities and interactions in physio-pathological contexts. (biorxiv.org)
  • These techniques provide valuable insights on proteins' functioning and interactions with their environment. (biorxiv.org)
  • The structure of the tubular assembly shows, at the three-fold interface 11 , a three-helix bundle with critical hydrophobic interactions. (nature.com)
  • To be able to perform their biological function, proteins fold into one, or more, specific spatial conformations, driven by a number of noncovalent interactions such as hydrogen bonding, ionic interactions, Van Der Waals forces and hydrophobic packing. (phys.org)
  • To increase our understanding about the structural contribution of hydrolysis in the receptor function and its interaction with downstream signalling proteins, I have used X-ray crystallography to examine the structures of two DAD2 mutants, DAD2-N242I and DAD2-D166A, that show WT-like hydrolytic activity but display altered protein-protein interactions with petunia's F-box protein, PhMAX2A. (auckland.ac.nz)
  • Scientists at the Pacific Northwest National Laboratory in Richland, Wash., have used an established technique to observe real-time interactions between single protein molecules for the first time. (the-scientist.com)
  • Proposed by Peter Wolynes at the University of California, San Diego, 2 this theory states that weak interactions between relatively unstructured proteins initiate protein-protein binding. (the-scientist.com)
  • TM84 traps the enzyme-tRNA complex in a novel 'aminoacylation-like' conformation, forming novel interactions with the KMSKS loop and the tRNA 3'-end. (ox.ac.uk)
  • CONCLUSION: In FMDV type C, amino acid substitutions seen in mutants that are resistant to neutralization by monoclonal antibodies (MAbs) map to predominantly surface-oriented residues with solvent-accessible side-chains not involved in interactions with other amino acids, whereas residues which are accessible but not substituted are found to be more frequently involved in protein-protein interactions. (ox.ac.uk)
  • Therefore understanding molecular details of receptor organization and mapping interactions with other membrane proteins that might influence receptor conformation and function, are of key importance. (unideb.hu)
  • Protein stabilization by cosolutes or crowders has been shown to be largely driven by protein-cosolute volume exclusion complemented by chemical and soft interactions. (bvsalud.org)
  • All or other nearby charged groups, the pKa shift of a buried pH-dependent properties of proteins are ultimately governed residue is dominated by the large electrostatic self-energy by the electrostatic interactions of ionizable side chains. (lu.se)
  • 2004). The effect of electrostatic interactions is usually polarization effects in the protein are subsumed in an quantified in terms of the shift, DpKa, of the pKa value of an apparent dielectric constant, eP. (lu.se)
  • You will find out about the experimental techniques, such as X-ray crystallography, nuclear magnetic resonance and electron microscopy, which are used to determine the 3D structure of proteins. (manchester.ac.uk)
  • This is the topic of the scientific field of structural biology, that employs techniques such as X-ray crystallography or NMR spectroscopy, to determine the structure of proteins. (phys.org)
  • Molecular biologists view RNA structures and complexes with proteins to gain insight into RNA signal and message processing. (nature.com)
  • However, less is understood about how RT crystallography may impact the conformational landscapes of protein-ligand complexes. (rcsb.org)
  • Large macromolecules, including proteins and their complexes, very often adopt multiple conformations. (biorxiv.org)
  • Large macromolecules, including proteins and their complexes, are intrinsically flexible, and this flexibility is often linked with their function. (biorxiv.org)
  • Comparison with the structures of four different RT and non-nucleoside inhibitor complexes reveals that only minor domain rearrangements occur, but there is a significant repositioning of a three-stranded beta-sheet in the p66 subunit (containing the catalytic aspartic acid residues 110, 185 and 186) with respect to the rest of the polymerase site. (ox.ac.uk)
  • Advances in crystallography and new methods of structure determination enabled crystallization and analysis of large macromolecular complexes, such as RNA polymerase II or GroEL, often in different conformations. (molmovdb.org)
  • The availability of several conformations for macromolecular multichain complexes with ten thousands of residues poses a need for new analysis methods and tools capable of extracting useful information from the different conformations. (molmovdb.org)
  • Using X-ray crystallography, we determined the structures of the engineered protein-antibody complexes. (postech.ac.kr)
  • That's why large complexes, such as ribosomes and viruses, have been among the first structures to be solved by cryo-EM. (asbmb.org)
  • Most importantly, cryo-EM can visualize protein complexes and give indications about protein flexibility. (asbmb.org)
  • Small angle neutron scattering (SANS) provides unique insight into biomacromolecular complexes by combining solvent contrast variation (H2O:D2O exchange) with either natural contrast between different classes of biomolecules (proteins, RNA/DNA, lipids/detergents) and/or by applying artificial contrast, i.e. deuteration of specific biomolecules. (lu.se)
  • In a first couple of examples, I will show how distance and shape restraints from SANS have helped to improve the uniqueness of structural models for two multi-protein-RNA complexes, in combination with NMR restraints and building blocks from crystallography [1, 2]. (lu.se)
  • You will learn how proteins are produced, how they fold into their secondary and tertiary structures and how they interact with each other. (manchester.ac.uk)
  • 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)
  • Much of our current understanding of how small-molecule ligands interact with proteins stems from X-ray crystal structures determined at cryogenic (cryo) temperature. (rcsb.org)
  • We show that at RT, fewer ligands bind, and often more weakly - but with a variety of temperature-dependent differences, including unique binding poses, changes in solvation, new binding sites, and distinct protein allosteric conformational responses. (rcsb.org)
  • Bone morphogenetic proteins (BMPs) are secreted ligands of the transforming growth factor-β (TGF-β) family that control embryonic patterning, as well as tissue development and homeostasis. (ox.ac.uk)
  • To better understand how small molecules bind within this domain, we examined the structures and equilibrium and transition-state thermodynamics of HIF2R PAS-B with several artificial ligands using isothermal titration calorimetry, NMR exchange spectroscopy, and X-ray crystallography. (elsevierpure.com)
  • To better understand the relationships between preferred conformations and functional properties of β-homo-amino acids, the synthesis and conformation characterization by X-ray diffraction analysis of peptides containing conformationally constrained Cα,α-dialkylated amino acid residues, such as α-aminoisobutyric acid or 1-aminocyclohexane-1-carboxylic acid and a single β-homo-amino acid, differently displaced along the peptide sequence have been carried out. (cnr.it)
  • In the crystal state, most of the NH groups of β-homo residues of tri- and tetrapeptides are not involved in intramolecular hydrogen bonds, thus failing to achieve helical structures similar to those of peptides exclusively constituted of Cα,α-disubstituted amino acid residues. (cnr.it)
  • Previously, several antibodies have been shown to recognize the alphahelical conformation of antigenic peptides. (postech.ac.kr)
  • Variants produced by substitution of Cys(972) and Cys(353) by Ser using site-directed mutagenesis have distinctly lower specific activities, supporting the crucial role of these highly conserved redox-sensitive amino acid residues for P-protein activity. (nih.gov)
  • For chains under 40 residues the term peptide is frequently used instead of protein. (phys.org)
  • Protein sizes range from this lower limit to several thousand residues in multi-functional or structural proteins. (phys.org)
  • However, the current estimate for the average protein length is around 300 residues. (phys.org)
  • Our findings, as well as literature data, strongly indicate that conformations of βH-residues, with the μ torsion angle equal to - 60°, are very unlikely. (cnr.it)
  • Our results may inspire future use of RT crystallography to interrogate the roles of protein-ligand conformational ensembles in biological function. (rcsb.org)
  • While X-ray crystallography captures single stable states, cryo-EM allows observing conformational ensembles in solution. (biorxiv.org)
  • The long-term goals of our research are to understand how protein conformational ensembles are reshaped by chemical, genetic, and physical perturbations. (fraserlab.com)
  • We study proteins as conformational ensembles. (fraserlab.com)
  • These include X-ray crystallography, cryo-electron microscopy (cryo-EM), nuclear magnetic resonance (NMR), small-angle scattering and many others ( 1 ). (biorxiv.org)
  • At present it offers more information about protein-protein interaction dynamics than can be obtained with conventional structural biology techniques such as nuclear magnetic resonance (NMR) and X-ray crystallography. (the-scientist.com)
  • Training in the relevant theoretical and experimental methods described for the study of protein structure and dynamics. (lu.se)
  • Alushin studies how these little-understood physical dynamics act on the cell's cytoskeleton, an internal network of protein filaments that constantly reconfigures itself to help the cell move, change shape, or ferry molecules from one cell compartment to another. (rockefeller.edu)
  • In both larger surveys and isolated mechanistic studies, we have demonstrated the value of room temperature data collection for revealing the structural basis of protein conformational dynamics, leading to new insights into enzymes, and increasing connections to dynamics studies from NMR and simulations. (fraserlab.com)
  • The cryo-electron-microscopy structures enable modelling by large-scale molecular dynamics simulation, resulting in all-atom models for the hexamer-of-hexamer and pentamer-of-hexamer elements as well as for the entire capsid. (nature.com)
  • We have brilliant colleagues who are in the forefront of their respective research and focused on an understanding of protein structure and dynamics, and how we might understand how life actually works by probing these things at an intimate level of detail. (nih.gov)
  • Protein conformation fluctuation dynamics is a stochastic process," says lead investigator H. Peter Lu, a staff scientist at PNNL. (the-scientist.com)
  • Electric Proteins Dr. Stuart Lindsey at Arizona State University is an expert in single-molecule dynamics in biomolecules. (bracemccoy.com)
  • Biophysical/advanced microscopic methods (fluorescence resonance energy transfer (FRET), fluorescence crosscorrelation spectroscopy (FCCS), near-field scanning optical microscopy (NSOM), X-ray crystallography, surface plasmon resonance, NMR spectroscopy) have been instrumental in clarifying the details of receptor structure and organization from the atomic level to the assembly and dynamics of supramolecular clusters. (unideb.hu)
  • Finally, molecular dynamics simulations reveal conversion between open and closed conformations of the protein and pathways of ligand entry into the binding pocket. (elsevierpure.com)
  • As the freezing process captures the molecules in action, cryo-EM permits researchers to look at multiple conformations of molecules within a single field of view and get an appreciation for the dynamics of a protein. (asbmb.org)
  • Subsequently, YTHDF2 increases the interaction between the dynein motor protein and the misfolded polypeptide-associated complex, facilitating the diffusion dynamics of the movement of misfolded polypeptides toward aggresomes. (bvsalud.org)
  • Atomic structure and dynamics link mechanism, phenotype and diseases to a mechanistic chemical explanation. (infn.it)
  • Intrinsically disordered protein mesophases and their regulation are at the center of cellular nano organisation that guide development and cellular dynamics. (infn.it)
  • Proteins are an important class of biological macromolecules present in all biological organisms, made up of such elements as carbon, hydrogen, nitrogen, oxygen, and sulphur. (phys.org)
  • In our present view, these areas are found for systems where several types of macromolecules (proteins, polysaccharides or polyelectrolytes) and/or amphiphiles interact to form a functional or destructive unit. (lu.se)
  • Select appropriate experimental techniques for protein purification and characterization (conformation and stability), and describe the relative precision of various approaches and the assumptions implied by each method. (manchester.ac.uk)
  • These data can be used to evaluate its conformation and stability. (creativebiomart.net)
  • Secondary structure formation and stability are essential features in the knowledge of complex folding topology of biomolecules. (cnr.it)
  • Basic knowledge of protein structure: polypeptide conformation. (lu.se)
  • Some eight years later it was discovered that triplets of the base pairs specified each amino acid in the polypeptide chain of each protein [ 11 , 12 ]. (biomedcentral.com)
  • Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. (biorxiv.org)
  • Describe protein folds in terms of secondary structural elements and the restrictions on peptide structure imposed by the planarity of the peptide bond. (manchester.ac.uk)
  • Protein secondary and three-dimensional structure. (lu.se)
  • However, by repeating the structural motifs observed in the molecules investigated, a β-pleated sheet secondary structure, and a new helical structure, named (14/15)-helix, were generated, corresponding to calculated minimum-energy conformations. (cnr.it)
  • There is considerable use of graphs and underlying theory in the description of properties of proteins and how these are studied. (manchester.ac.uk)
  • The course covers both the principles that determine the properties of proteins and the experimental methods that are used to study these properties in modern molecular protein science. (lu.se)
  • Outline methods for 3D structure determination by X-ray crystallography, NMR and electron microscopy. (manchester.ac.uk)
  • Some of them can be seen experimentally, for example with X-ray crystallography or cryo-electron microscopy. (biorxiv.org)
  • He switched to an emerging method in which frozen proteins were visualized with an electron microscope-and while it improved his batting average, it too wasn't easy. (rockefeller.edu)
  • Back then, electron microscopy methods to study structures were in their infancy, so one of the things we had to do was to take pictures of proteins using photographic film," he says. (rockefeller.edu)
  • We are expanding, this direction to include modeling and validating protein structural data generated by cryo-electron microscopy (using EMRinger and ensemble modeling) and through integrative approaches to discover cryptic ligand binding sites. (fraserlab.com)
  • Here we report the cryo-electron microscopy structure of a tubular HIV-1 capsid-protein assembly at 8 Å resolution and the three-dimensional structure of a native HIV-1 core by cryo-electron tomography. (nature.com)
  • Our method is simple and efficient, and it will have applications in protein X-ray crystallography, electron microscopy, and nanotechnology. (postech.ac.kr)
  • With the rapid progress and improvements in the fields of macromolecular crystallography, Cryo-EM, small angle scattering, electron diffraction and use of XFELs, the new LINXS theme INTEGRATIVE STRUCTURAL BIOLOGY is formed to advance cutting-edge research and to encourage new users to utilize integrative structure biology to address key scientific questions. (lu.se)
  • The first symposium, which is the kick-off event for the new LINXS theme, will focus on advanced, cutting-edge research in the fields of macromolecular crystallography, Cryo-EM, small angle scattering, electron diffraction, mass-spectroscopy, NMR, and use of XFELs etc. (lu.se)
  • Distinguish between various modes of protein-protein interaction and catalysis. (manchester.ac.uk)
  • The researchers found that the two proteins fluctuated between bound and loosely associated states, in support of the so-called fly-casting mechanism of protein-protein interaction. (the-scientist.com)
  • The circadian clock found in Synechococcus elongatus, the most ancient circadian clock, is regulated by the interaction of three proteins, KaiA, KaiB, and KaiC. (ox.ac.uk)
  • Thus the results imply that compound PCF functions as an inhibitior of SOD1 misfolding/aggregation through direct interaction with the protein SOD1 at the W32 binding site. (bvsalud.org)
  • However, TAP is likely to act as an inhibitor through a different mechanism rather than direct interaction with the protein SOD1. (bvsalud.org)
  • Traditionally, X-ray crystallography was dominating the interaction of large facilities with life sciences. (infn.it)
  • a - d , f ) A simple way to gain insight into function is to use ribbon representation colored by sequence features: for example, domains ( a ), SNPs ( b ), exons ( c ), protein binding sites ( d ) and sequence conservation ( f ). ( e ) An effective way to show overall shape is with nonphotorealistic rendering using flat colors and outlines. (nature.com)
  • j , k ) Increasingly many tools have an integrated, interactive sequence viewer, which helps users understand the relationship between sequence and three-dimensional structure. (nature.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)
  • This was the important clue to the structure of the DNA double helix modeled by Watson and Crick in 1953, and based on the X-ray diffraction studies of Rosalind Franklin [ 10 ]. (biomedcentral.com)
  • In this review, we focus on key biological questions where visualizing three-dimensional structures can provide insight and describe available methods and tools. (nature.com)
  • Proteins are involved in virtually all biological processes and their structure is key to their function. (manchester.ac.uk)
  • To provide core knowledge of the form, function and role of protein molecules in biological processes and further enable an understanding of biological phenomena at the molecular level. (manchester.ac.uk)
  • The course aims to provide a deeper understanding of some of the most important experimental methods used to determine the three-dimensional structures of proteins, as a basis for understanding their biological functions. (lu.se)
  • Significance Statement Proteins perform their biological functions by changing their shapes and interacting with each other. (biorxiv.org)
  • Identifying the molecular states relevant to protein functioning is necessary for our understanding of biological processes. (biorxiv.org)
  • Our group integrates high resolution structural biology (X-ray, EM, NMR), functional studies (deep mutational scanning, enzymology), and computation to study biological mechanisms and to improve protein engineering and small molecule discovery. (fraserlab.com)
  • Crystal structure of the secretory isozyme of mammalian carbonic anhydrases CA VI: implications for biological assembly and inhibitor development. (ox.ac.uk)
  • The general aim of the course is to enable students to acquire an advanced understanding of proteins with an emphasis on their three-dimensional structures, the connection of structures to biological function and how these structures are produced. (lu.se)
  • Here, I present results from different biological projects where SANS has played a crucial role by providing unique restraints for structural refinement and interpretation, complementary to other techniques (NMR, EM, crystallography). (lu.se)
  • EU Marie Curie Training Site on Surface and colloid technology-self-assembled structures of biological and technological relevance. (lu.se)
  • In order to understand the functions of proteins at a molecular level, it is often necessary to determine the three dimensional structure of proteins. (phys.org)
  • The ensemble nature of proteins highlighted by this work feeds into all of our mechanistic studies that interpret the functional effects of mutations, that characterize designed and artificially-evolved proteins, or that seek to modulate protein function with small molecules. (fraserlab.com)
  • Furthermore, we showed that binding of these antihelix antibodies to the engineered target proteins can modulate their catalytic activities by trapping them in selected functional states. (postech.ac.kr)
  • Very large aggregates can be formed from protein subunits, for example many thousand actin molecules assemble into a microfilament. (phys.org)
  • With two of these special beacons in place, smFRET imaging can be used to visualize how the molecules move over time, when the virus proteins change conformation. (sciencedaily.com)
  • These structures provide clues as to how CD1 molecules load glycolipids as well as data to guide the design of new therapeutic agents. (ox.ac.uk)
  • By looking at the frozen action shots of the molecules, researchers can discern their structures and functions. (asbmb.org)
  • Overall, this work suggests that the vast body of existing cryo-temperature protein-ligand structures may provide an incomplete picture, and highlights the potential of RT crystallography to help complete this picture by revealing distinct conformational modes of protein-ligand systems. (rcsb.org)
  • Ligand binding and structure-based drug design. (lu.se)
  • Includes protein crystallization, data collection at MAX IV, data processing, structure determination and modelling, as well as a simple exercise in ligand docking. (lu.se)
  • A previously unobserved conformation for the human Pex5p receptor suggests roles for intrinsic flexibility and rigid domain motions in ligand binding. (ox.ac.uk)
  • The domain movements between various apo conformations are distinct from those involved in ligand binding, although the differences between all observed conformations so far can be characterised by the movement of the two halves of Pex5p(C) as near-rigid bodies with respect to each other. (ox.ac.uk)
  • Rapid association rates reveal that ligand binding is not dependent upon a slow conformational change in the protein to permit ligand access, despite the closed conformation observed in the NMR and crystal structures. (elsevierpure.com)
  • We also present the CD1d structure without lipid, which has a more open conformation of the binding groove, suggesting a dual conformation of CD1d in which the 'open' conformation is more able to load lipids. (ox.ac.uk)
  • Structural biology is rapidly accumulating a wealth of detailed information about protein function, binding sites, RNA, large assemblies and molecular motions. (nature.com)
  • Decades ago, when structural biology was still in its infancy, structures were rare and structural biologists often dedicated years of their life to studying just one structure at atomic detail. (nature.com)
  • We work on many different systems and proteins as we find ourselves drawn, again and again, to the tension of high resolution data in structural biology: as resolution gets better, modeling becomes easier… until the resolution gets too good… and then the ensemble begins to reveal itself and the fun challenges begin. (fraserlab.com)
  • Antibodies are indispensable tools in protein engineering and structural biology. (postech.ac.kr)
  • The once-fringe method is now beating the usual darling of structural biology, X-ray crystallography, at its own game, thanks to advancements in technology. (asbmb.org)
  • We think - and this has been supported by many researchers in structural biology - that cryo-EM most likely will overtake or equal crystallography in the coming decade," says Jon Lorsch , the director of the National Institute of General Medical Sciences. (asbmb.org)
  • Although often presented as taking single `snapshots' of the conformation of a protein, X-ray crystallography provides an averaged structure over time and space within the crystal. (du.edu)
  • Older methods of observing protein structure, such as X-ray crystallography, only gave single snapshots of the highly dynamic world, he says, where proteins rapidly change conformations and interact in complex ways. (bracemccoy.com)
  • This contrasts with a previous cryogenic crystal structure of the V66E mutant, but is consis- tent with the room-temperature crystal structure reported here. (lu.se)
  • L. Cao, O. Caldararu & U. Ryde (2020) "Does the crystal structure of vanadium nitrogenase contain a reaction intermediate? (lu.se)
  • The chaperones also can change the conformation of the nucleosome as a whole. (wikipedia.org)
  • The two first methods allow obtaining large macromolecular structures at high resolution. (biorxiv.org)
  • The team used the technology to study motions of proteins on the surface of the HIV virus (called envelope proteins) that are key to the virus's ability to infect human immune cells carrying CD4 receptor proteins. (sciencedaily.com)
  • CD4 receptor proteins help HIV bind to a cell. (sciencedaily.com)
  • Spike conformation plays an essential role in SARS-CoV-2 evolution via changes in receptor binding domain (RBD) and neutralizing antibody epitope presentation affecting virus transmissibility and immune evasion. (biorxiv.org)
  • In petunia, SL is perceived by its receptor, DAD2, an α/β hydrolase fold protein. (auckland.ac.nz)
  • The hydrolytic function of the receptor is essential for SL signalling and enables the receptor to interact with the downstream signalling proteins, such as the Skp-Cullin-F-box (SCF) E3 ligase complex and target protein(s) to relay the signal. (auckland.ac.nz)
  • At present, it is unclear how the hydrolytic activity of the receptor enables it to interact with the downstream signalling protein to transduce the signal. (auckland.ac.nz)
  • Based on biochemical characterisations, the DAD2-N242I mutant was predicted to exist in a conformation similar to that proposed for the WT receptor in the presence of SL, whereas the DAD2-D166A mutant was predicted to display an altered conformation, specifically in the region where PhMAX2A protein interacts with the receptor. (auckland.ac.nz)
  • The structural examination of the mutants showed that SL increases the flexibility of the receptor without changing the overall conformation of the protein. (auckland.ac.nz)
  • The structure implies that a substantial conformational change involving C epsilon 2 must accompany binding to the mast cell receptor Fc epsilon RI. (ox.ac.uk)
  • Nevertheless, experimental protein structure determination remains a time consuming and costly process. (biorxiv.org)
  • X-ray structure determination of three 11H-indolo[3,2-c]quinoline-6-carboxylic acids cocrystallized with DYRK1A confirmed the predicted binding mode within the ATP binding site. (ox.ac.uk)
  • Application of antihelix antibodies in protein structure determination. (postech.ac.kr)
  • Although NIH-funded facilities won't be springing up like Starbucks, the NIH, through a Common Fund initiative, is hoping to start off with three national service centers and eventually expand to having more around the U.S. The initiative aims to give researchers more opportunities to do molecular structure determination by high-resolution cryo-EM. (asbmb.org)
  • Since 2010, Luger has done significant studies of histones, researching the connection between their chaperone proteins and acetylation, as well as variant structures. (wikipedia.org)
  • Histones are important in the process of gene expression, and their positioning as determined by chaperone proteins is essential to that role. (wikipedia.org)
  • In previous apo room-temperature structures, the active site and allosteric sites adopted alternate conformations, including open and closed conformations of the active-site WPD loop and of a distal allosteric site. (iucr.org)
  • By contrast, in our SSX structure the active site is best fitted with a single conformation, but the distal allosteric site is best fitted with alternate conformations. (iucr.org)
  • Structure of the EGL-1/CED-9 complex revealed that EGL-1 adopts an extended alpha-helical conformation and induces substantial structural rearrangements in CED-9 upon binding. (nih.gov)
  • This protein activates T cells and B cells by binding to IL-7 receptors, promoting the enhancement of immune response. (creativebiomart.net)
  • The systematic description of the variety of shapes a protein adopts under particular environmental conditions, upon post-translational modifications and/or partner binding still remains out of reach. (biorxiv.org)
  • 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)
  • The unliganded structure was produced by soaking out a weak binding non-nucleoside inhibitor, HEPT, from pregrown crystals. (ox.ac.uk)
  • Structure of the HIV-1 full-length capsid protein in a conformationally trapped unassembled state induced by small-molecule binding. (nature.com)
  • Binding and crystallography revealed increased flexibility at the functionally critical fusion peptide site in the Omicron spike. (biorxiv.org)
  • Whereas most fluorescent labels require genetic modification of target proteins, I-SO attaches covalently to the protein of interest and changes its fluorescence during a binding event. (the-scientist.com)
  • Here we report the crystal structure of human CD1d in complex with synthetic alpha-galactosylceramide at a resolution of 3.0 A. The structure shows a tightly fit lipid in the CD1d binding groove, with the sphingosine chain bound in the C' pocket and the longer acyl chain anchored in the A' pocket. (ox.ac.uk)
  • The structure suggests that the KaiB binding site is covered in the dimer interface of the KaiA "closed" conformation, observed in the crystal structure, which suggests an allosteric regulation mechanism. (ox.ac.uk)
  • Previously, structural data have been obtained from the TPR domain of Pex5p in both the liganded and unliganded states, indicating a conformational change taking place upon cargo protein binding. (ox.ac.uk)
  • The bound Sr2+ ion changes the dynamic properties of Pex5p(C) affecting its conformation, possibly by making the Sr2+-binding loop - located near the hinge region for the observed domain motions - more rigid. (ox.ac.uk)
  • YTHDF2 has been extensively studied and typified as an RNA-binding protein that specifically recognizes and destabilizes RNAs harboring N6-methyladenosine (m6A), the most prevalent internal modification found in eukaryotic RNAs. (bvsalud.org)
  • This study shows that a long-wavelength beamline results in easily validated anomalous signals that are strong enough to be used to detect and characterize highly disordered sections of crystal structures. (du.edu)
  • This work opens the way to the systematic description of protein motions, whatever their degree of collectivity. (biorxiv.org)
  • In this work, we present a method that generates plausible physics-based protein motions and conformations. (biorxiv.org)
  • This allows us to produce a wide range of motions, some of them previously inaccessible, and to preserve the structure of the protein during the motion. (biorxiv.org)
  • The researchers were able to study proteins from two different strains of HIV, which contained beacons that did not alter the biology of the particles. (sciencedaily.com)
  • Overall, our results illustrate the promise of serial methods for room-temperature crystallography, as well as future avant-garde crystallography experiments, for PTP1B and other proteins. (iucr.org)
  • Perform X-ray crystallography experiments at a basic level, from which the participant can further develop the skills on his/her own. (lu.se)
  • Combined, these experiments provide an integrated vista of the molecular mechanisms-and their associated kinetics-underpinning the mechanical unfolding and refolding of individual proteins when exposed to mechanical load. (bvsalud.org)
  • Antibodies suitable for structural studies should recognize the 3-dimensional (3D) conformations of target proteins. (postech.ac.kr)
  • We demonstrate that these antibodies can be made to bind to a variety of unrelated "off-target" proteins by modifying amino acids in the preexisting alpha helices of such proteins. (postech.ac.kr)
  • Modelling revealed that the mutations will destabilize the protein structure by varying extents consistent with their previously reported functional heterogeneity. (ox.ac.uk)
  • Such buried ionizable groups destabilize the protein and may trigger conformational changes in response to pH variations. (lu.se)
  • The first tools used for visualizing macromolecular structures were tools for specialists. (nature.com)
  • ComQum-X or quantum refinement is a method to combine X-ray crystallographic refinement with QM/MM calculations to obtain an optimum compromise between crystallography and quantum chemistry. (lu.se)
  • In 2005, Luger and Kenneth Kaye used X-ray crystallography to determine the mechanism that the virus causing Kaposi's sarcoma, a cancer that affects subdermal connective tissue, uses to spread. (wikipedia.org)
  • The mechanism of action for many of these proteins remains mysterious. (fraserlab.com)
  • The envelope consists of three gp120 and gp41 proteins positioned close together, and referred to as "trimers," that open up like a flower in the presence of CD4, exposing the gp41 subunit that is essential for subsequent aspects of the mechanism that causes infection. (sciencedaily.com)
  • Here we show using crystal structure, thermodynamic and kinetic analyses, that this natural antibiotic employs a unique and previously undescribed mechanism to inhibit LeuRS. (ox.ac.uk)
  • Karolin Luger is an Austrian-American biochemist and biophysicist known for her work with nucleosomes and discovery of the three-dimensional structure of chromatin. (wikipedia.org)
  • The nucleosome, a building block of the chromatin genetic material that makes up chromosomes, consists of DNA wrapped around a disk of proteins. (wikipedia.org)
  • She and her research group have also developed various assays for examining chromatin structure, to augment traditional X-ray crystallography. (wikipedia.org)
  • The gene codes for a protein that binds to methyl groups on chromatin, altering its conformation. (wikipedia.org)
  • Over 200 different proteins are associated with chromatin [ 15 ]. (biomedcentral.com)
  • Glycine decarboxylase, or P-protein, is a pyridoxal 5'-phosphate (PLP)-dependent enzyme in one-carbon metabolism of all organisms, in the glycine and serine catabolism of vertebrates, and in the photorespiratory pathway of oxygenic phototrophs. (nih.gov)
  • Room-temperature X-ray crystallography provides unique insights into protein conformational heterogeneity, but obtaining sufficiently large protein crystals is a common hurdle. (iucr.org)
  • For proteins alone, room-temperature (RT) crystallography can reveal previously hidden, biologically relevant alternate conformations. (rcsb.org)
  • Cryo-EM structural data have been deposited in the EMDataBank under accession codesEMD-5582 andEMD-5639, and the MDFF atomic model of the CA HOH and models of HIV-1 capsid have been deposited in the Protein Data Bank under accession numbers 3J34 , 3J3Q , 3J3Y . (nature.com)
  • Structure of the amino-terminal core domain of the HIV-1 capsid protein. (nature.com)
  • Crystal structure of dimeric HIV-1 capsid protein. (nature.com)
  • The resolution attained by cryo-EM is very often lower than that of X-ray structures, mainly due to the structural heterogeneity of the measured samples. (biorxiv.org)
  • However, the ongoing revolution in cryo-EM instrumentation ( 2 ) has supplied an exponentially growing body of near-atomic resolution structures. (biorxiv.org)
  • With this platform, we are also pushing on cryo-EM data processing and refinement methods to enable structure-based drug design, now achieving resolutions better than 2.0 Å. (fraserlab.com)
  • In recent work, we are collaborating with the Bondy-Denomy lab to define the structural basis of anti-CRISPR proteins using a combination of X-ray crystallography, cryo-EM, and NMR. (fraserlab.com)
  • Here, we determine cryo-EM structures of the Omicron and Delta spikes to understand the conformational impacts of mutations in each. (biorxiv.org)
  • Cryo-EM doesn't require the protein to be forced into a crystal, which is a bottleneck in X-ray crystallography. (asbmb.org)
  • For example, the structure of the Zika virus was solved in 2016 by two independent groups using cryo-EM. (asbmb.org)