• The mechanisms of cryoprecipitation are poorly understood, but several factors have been investigated. (medscape.com)
  • They hope their work will shed light on what remain relatively poorly understood neurological diseases. (bbc.co.uk)
  • The relationship between 3D organization of the genome and gene-regulatory networks is poorly understood. (ca.gov)
  • Despite numerous structural studies, the molecular basis for Rab/effector specificity and subsequent biological activity remains poorly understood. (anl.gov)
  • Several HSP70 inhibitors have been reported, but because the majority have poor physicochemical properties and for many the exact mode of action is poorly understood, more detailed mechanistic and structural insight into ligand-binding to HSP70s is urgently needed. (rcsb.org)
  • However, how an array of nucleosomes folds into and switches between different fiber conformations is poorly understood. (nih.gov)
  • Although the serious adverse effects of Hg and Cd have been known for hundreds of years, the mechanisms of their toxicity are still poorly understood. (atlasofscience.org)
  • The molecular mechanism underlying prion-induced neurodegeneration is still poorly understood. (biomedcentral.com)
  • However, the rational design of compounds that target the allosteric site is difficult, as conformations required for receptor activation are poorly understood. (wiley.com)
  • How proteins mediate this curvature generation is a fundamental question that is still poorly understood. (lu.se)
  • How the DNA encoding these selfish elements spreads within and between genomes is poorly understood, particularly in eukaryotes where inteins are scarce. (lu.se)
  • Implementing REST to the entire ligand as opposed to solely the perturbed region, and also some important flexible protein residues (pREST region) in the ligand binding domain (LBD) has considerably improved the FEP+ results in most of the studied cases. (nature.com)
  • BmK M7 crystallizes as a dimer in which the identical non-proline peptide bond between residues 9 and 10 exists either in the cis conformation or as a mixture of cis and trans conformations in either monomer. (rcsb.org)
  • Cis/trans interconversion of the switch residue at position 8 appears to be sequence-dependent as the peptide bond between residues 9 and 10 retains its wild-type cis conformation in the BmK M1 (K8Q) mutant structure. (rcsb.org)
  • α/β-Peptides containing 25-30% β residues, with α → β replacement sites distributed evenly, can adopt an α-helix-like conformation and bind to protein partners that naturally associate with α-helical ligands. (wisc.edu)
  • The conformation of many charged residues is poorly defined by NMR data but mutational studies have indicated that removal of polar side chains decreases binding affinity, while non-polar contacts are malleable. (uzh.ch)
  • Residues in an alpha-helical conformation are marked α , and those in a beta strand conformation, β . (proteopedia.org)
  • Our data confirm that long-range chromatin interactions are primarily associated with the spatial segregation of open and closed chromatin, defining overall chromosome conformation. (ca.gov)
  • Underlining the independence of these networks and their functional relevance for genome organization, loss of the Polycomb protein Eed diminishes interactions between Polycomb-regulated regions without altering overarching chromosome conformation. (ca.gov)
  • Analysis of the three-dimensional maps and known biochemical composition allows determination of capsid protein location, globular shape, stoichiometry, quaternary organization, and interactions with adjacent capsid proteins. (silverchair.com)
  • We have asked how backbone modification affects the informational properties of polypeptides, i.e., how this type of modification affects interactions with partner proteins. (wisc.edu)
  • The anti-viral example illustrates how polypeptides with modified backbones can bind to specific recognition sites on target proteins and thereby block pathogenic protein-protein interactions while resisting proteolytic destruction. (wisc.edu)
  • Knowledge of the three-dimensional structures of the carbo-hydrate molecules is indispensable for a full understanding of the molecular processes in which carbohydrates are involved, such as protein glycosylation or protein-carbohydrate interactions. (iucr.org)
  • As a consequence, other IxI/V containing proteins can bind more to HSPB1, explaining the altered protein-protein interactions. (uantwerpen.be)
  • The simulation identifies protein-DNA interactions that are poorly resolved or only surmised from the NMR ensemble. (uzh.ch)
  • Single water molecules and water clusters dynamically optimize the complementarity of polar interactions at the "wet" protein-DNA interface. (uzh.ch)
  • Also, they share a similar protein architecture based on an N-terminal ssDNA binding domain of ~180 amino acids and a C-terminal extension that in the case of RAD52 is required for homologous recombination (HR) through specific protein-protein interactions 6 . (nature.com)
  • 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)
  • Interactions with other proteins or molecules are another feature of cysteines that can affect protein activity. (hindawi.com)
  • 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)
  • Although the majority of VWA-containing proteins are extracellular, the most ancient ones present in all eukaryotes are all intracellular proteins involved in functions such as transcription, DNA repair, ribosomal and membrane transport and the proteasome. (embl.de)
  • Three of the intracellular proteins (a G-protein and two β-arresins) that sense the receptor's binding to the hormone and initiate signaling cascades are indicated. (wisc.edu)
  • Receptor conformational changes induced GPCR engagement with an agonist are detected by intracellular proteins, such G proteins and β-arrestins, which then initiate distinct signaling processes. (wisc.edu)
  • G protein-coupled receptors are transmembrane proteins that help to regulate a wide array of biological processes, which makes them important drug targets. (elifesciences.org)
  • A ) G protein-coupled receptors (GPCRs) are transmembrane proteins (bottom) that can be regulated by orthosteric ligands (such as acetylcholine or iperoxo) and positive allosteric modulators (PAMs). (elifesciences.org)
  • For the PIV5 fusion protein, the fusion peptide (FP) and the transmembrane domain (TMD) show striking membrane-dependent conformations. (lu.se)
  • VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). (embl.de)
  • They mediate spatial and temporal recruitment of effector proteins to distinct cellular compartments through GTP-induced changes in their conformation. (anl.gov)
  • Among the range of proteins shown to co-localize to WPB is angiopoietin-2 (Angpt-2), a ligand of the receptor tyrosine kinase Tie-2. (imperial.ac.uk)
  • The Anaeramoeba inteins reside in a wide range of proteins, only some of which correspond to intein-containing proteins in other eukaryotes, prokaryotes, and viruses. (lu.se)
  • Introduced into healthy cells, the misfolded proteins made contact with molecules identical to the proteins from which they were originally made, and caused them to warp into exactly the same shape. (bbc.co.uk)
  • We are interested in relationships between biopolymer structure and function, with an emphasis on proteins and protein-inspired molecules. (wisc.edu)
  • Our intein dataset greatly expands the spectrum of intein-containing proteins and provides insights into the evolution of inteins in eukaryotes. (lu.se)
  • Many aspects regarding the molecular mechanisms of small heat shock proteins, both in health and disease, remain to be unraveled. (uantwerpen.be)
  • Cargo that can be delivered or by cytoskeleton-dependent intracellular transport mechanisms can include other proteins and complex components. (mechanobio.info)
  • Despite R406 (freebase) considerable research in the area of sepsis severe sepsis and septic shock the pathophysiological mechanisms of this disease state remains poorly recognized as evinced by continued new strategies proposed for sepsis treatment [25] [26]. (ecolowood.com)
  • The main causes of this destabilization are related to mutations or cellular stress, which is higher in the elderly, since the mechanisms of protein homeostasis are more obsolete. (zientzia.eus)
  • I will present our recent structural studies, using solid-state NMR spectroscopy, of three membrane proteins that give insights into the mechanisms of virus-cell membrane fusion and virus budding. (lu.se)
  • We further identified top 5 compounds including cynarine, stigmasterin, kushenol, β -sitosterol, and (24S)-24-propylcholesta-5-ene-3 β -ol as putative key active compounds on the basis of their molecular docking scores with identified hub target proteins. (hindawi.com)
  • 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)
  • Proteins evolve naturally via side chain modification (mutation of one α-amino acid residue to another), and engineered side chain modification has become a standard strategy in protein science. (wisc.edu)
  • X: any amino acid except Pro) present in newly synthesized protein in yeast and mammalian cells. (elifesciences.org)
  • Cysteine is the most important redox-responsive amino acid within proteins largely due to the wide range of oxidation states that sulfur can occupy-so called, "sulfur switches" [ 4 ]. (hindawi.com)
  • Most of the identified proteins are connected with the initial events of foreign body reaction towards biomaterial (coagulation cascade proteins, complement component, and inflammatory proteins). (ibecbarcelona.eu)
  • In the course of diabetes, complement components, including the central complement protein C3, are deregulated. (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)
  • The interconversion between protein conformations, occurring at multiple timescales, is fundamental for the biological function of proteins. (lu.se)
  • The underlying structural changes, associated to the formation of these large mutant oligomers, were so far poorly characterized. (uantwerpen.be)
  • However, to date FEP has typically been helpful mainly when (1) high-quality X-ray data is available and (2) the target protein does not undergo significant conformational changes. (nature.com)
  • The substitution of Pro182 with Leu allows the IxI/V peptide to sample a larger conformational space and the peptide therefore finds itself less frequently in the required conformation to bind the hydrophobic cleft. (uantwerpen.be)
  • The protein undergoes a subtle conformational transition and is slightly unfolded in the protein-DNA complex. (uzh.ch)
  • Conformational adaptation linked to partial unfolding appears to be induced by protein-DNA contacts. (uzh.ch)
  • A complex interplay between structure, conformational dynamics and pharmacology defines distant regulation of G protein-coupled receptors. (elifesciences.org)
  • in fact, the success of commonly used protein force fields probably depends on their use in a restricted region of conformational space near the crystallographically determined geometry. (lu.se)
  • Protein conformational fluctuations occur on multiple time scales ranging from picoseconds to days. (lu.se)
  • They find that only if the open form is a relatively low energy conformation can the molecule readily adopt the closed conformation with a hydrogen bond. (fieldofscience.com)
  • The Ramachandran Principle says that alpha helices, beta strands, and turns are the most likely conformations for a polypeptide chain to adopt, because most other conformations are impossible due to steric collisions between atoms. (proteopedia.org)
  • We recommend using this workflow before setting up and executing FEP+ calculations, especially for flexible protein structures. (nature.com)
  • Non-proline cis peptide bonds have been observed in numerous protein crystal structures even though the energetic barrier to this conformation is significant and no non-prolyl-cis/trans-isomerase has been identified to date. (rcsb.org)
  • Comparisons of the virion, ISVP and core structures and examination of difference maps reveal dramatic changes in supra-molecular structure and protein conformation that are related to the early steps of reovirus infection. (silverchair.com)
  • The cytoskeleton is a highly dynamic network of filamentous proteins that enables the active transport of cellular cargo, transduces force, and when assembled into higher-order structures, forms the basis for motile cellular structures that promote cell movement. (mechanobio.info)
  • Finally, the co-chaperone BAG3 forms a protein scaffold which binds both small heat proteins and Hsp70. (uantwerpen.be)
  • To avoid the aggregation of proteins that cause neurodegenerative diseases, one of the most important is the Hsp70 system, essential in a healthy and more pathological state, where there will be more damaged proteins. (zientzia.eus)
  • Thus, reversible cysteine modifications can influence protein activity and the relative quantification of the status of the thiol can potentially provide valuable insights into protein activity where the protein exists in a range of redox states. (hindawi.com)
  • In von Willebrand factor, the type A domain (vWF) is the prototype for a protein superfamily. (embl.de)
  • Specific members of the Myosin superfamily of motor proteins are known to transport cargo along actin filaments. (mechanobio.info)
  • Allosterically regulated proteins that require an activator are sometimes based on a thiol exchange interaction involving cysteines, for example, pyruvate kinase uses fructose bisphosphate (FBPs) as a heterotrophic activator and it contains a cysteine in its FBP binding site [ 8 ]. (hindawi.com)
  • Drugs that allosterically modulate G protein-coupled receptor (GPCR) activity display higher specificity and may improve disease treatment. (wiley.com)
  • The histone H2A.F/Z (H2AZ) variant is a functionally distinct, highly conserved histone subgroup that likely represents a separate evolutionary lineage of histone H2A proteins. (sdbonline.org)
  • These functionally inappropriate proteins are somehow detected in the ER lumen and then transferred to the retrotranslocational channel embedded within the ER membrane, termed the retrotranslocon, followed by ubiquitin-dependent degradation by the proteasome in the cytoplasm. (elifesciences.org)
  • Under inflammatory conditions disturbances to the blood-brain barrier can alter the conformation of limited junctions leading to a functionally jeopardized barrier. (ecolowood.com)
  • The newly synthesized protein must assimilate an adequate three-dimensional structure to be functionally active, but in cells this process is not always spontaneous. (zientzia.eus)
  • In mammalian infections, prions trigger protein clumping that can kill brain cells, whereas yeast prions merely alter a cell's metabolism and are not deadly. (bbc.co.uk)
  • Productive folding of the protein moiety is facilitated during this period by the calnexin/calreticulin cycle in mammalian cells, which relies on G1M9-specific lectin-type chaperones (calnexin and calreticulin) associated with the oxidoreductase ERp57, and UDP-glucose:glycoprotein glucosyltransferases 1 and 2, which are capable of re-adding glucose to M9 if the protein moiety is not yet folded. (elifesciences.org)
  • In this thesis we found that mammalian small heat shock proteins are targeted to the mitochondrial intermembrane space. (uantwerpen.be)
  • While small heat shock proteins of plants are targeted to virtually every membrane-enclosed compartment, this is the first example of mammalian small heat shock proteins to have an organelle-localization. (uantwerpen.be)
  • The causative agent is or is closely related to a pathogenic isoform of the cellular prion protein (PrP c ). (biomedcentral.com)
  • Adequate cellular and protein renewal is essential to ensure the proper functioning of an organism. (zientzia.eus)
  • In these circumstances, the presence of molecular txaperones is lower to deal with the problems of protein flexion (due to its lower expression or the saturation of the system to counteract cellular stress), increasing the amount of damaged and poorly folded proteins7. (zientzia.eus)
  • Scheme of cellular aggregation of proteins]. (zientzia.eus)
  • Molecular analysis suggested that Esc2p contributed to silencing in a manner similar to Sir1p and probably helped recruit or stabilize the other Sir proteins, while Htz1p present at HMR assembled a specialized chromatin structure necessary for silencing (Dhillon, 2000). (sdbonline.org)
  • Long-Range Chromatin Contacts in Embryonic Stem Cells Reveal a Role for Pluripotency Factors and Polycomb Proteins in Genome Organization. (ca.gov)
  • Additionally, the structural data revealed a potential functional role for the ATP ribose moiety in priming the protein for the formation of the ATP-bound pre-hydrolysis complex by influencing the conformation of one of the phosphate binding loops. (rcsb.org)
  • These shared biochemical, protein sequence and functional similarities suggest the existence of an ancestral annealing mechanism involved in HR. (nature.com)
  • One of many important properties for a functional cell membrane is its fluidity, which reflects the movement of lipids and greatly affects the mobility, conformation and activity of some proteins. (atlasofscience.org)
  • Indeed, it has been demonstrated that cysteines are characterized by the most extreme conservation pattern, being highly conserved in functional positions of proteins but poorly conserved otherwise [ 5 ]. (hindawi.com)
  • The vertex-associated cell attachment protein, sigma 1, also undergoes a striking change from a poorly visualized, more compact form, to an extended, flexible fiber. (silverchair.com)
  • We are able to simulate the opening or closing of a protein and the changes it undergoes to adapt to a partner. (biorxiv.org)
  • BACKGROUND: Despite the sharp increase in mpox (formerly monkeypox) incidence and the wide geographic spread of mpox during the 2022 outbreak, the community prevalence of infection remains poorly characterized. (bvsalud.org)
  • 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)
  • Additionally, we identified two further levels of genome organization in ESCs characterized by colocalization of regions with high pluripotency factor occupancy and strong enrichment for Polycomb proteins/H3K27me3, respectively. (ca.gov)
  • In fact, several neurodegenerative diseases have a common feature: the accumulation of aggregate proteins of amyloid structure present in the brain. (zientzia.eus)
  • 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)
  • There are 189281 VWA domains in 166516 proteins in SMART's nrdb database. (embl.de)
  • Phyletic distributions of eukaryotic signalling domains were studied using recently developed sensitive methods for protein sequence analysis, with an emphasis on the detection and accurate enumeration of homologues in bacteria and archaea. (embl.de)
  • Previously undetected bacterial homologues were identified for# plant pathogenesis-related proteins, Pad1, von Willebrand factor type A, src homology 3 and YWTD repeat-containing domains. (embl.de)
  • 1) We have investigated the structure of the membrane-interacting domains of the fusion proteins of the parainfluenza virus 5 (PIV5) and human immunodeficiency virus (HIV). (lu.se)
  • Inteins are self-splicing protein elements found in viruses and all three domains of life. (lu.se)
  • In contrast to authentic α-peptides, however, the α/β-peptides are poorly recognized by protease enzymes. (wisc.edu)
  • It plays an important role in the structural conformation of almost all proteins and enzymes found in the body. (online-family-doctor.com)
  • During sporulation, bacterial cells synthesize insecticidal inclusion bodies consisting of proteins (Cry proteins) active against larvae of invertebrates species (1). (scielo.br)
  • In addition, the aggregation of one type of protein can influence the aggregation of other protein species, allowing what is known as coaggregation. (zientzia.eus)
  • Lower left shows a co-crystal structure of the α/β-peptide (multicolor) bound to a protein partner (gray) (PDB 3O43). (wisc.edu)
  • Figure 2 shows the crystal structure of a 38-residue α/β-peptide (yellow, orange and blue) bound to an engineered partner protein (gray) that represents a critical portion of the HIV protein gp41. (wisc.edu)
  • Prearranged positive allosteric modulators (PAMs) inspired by photopharmacology are synthesized and applied to the glucagon-like peptide-1 receptor (GLP-1R), a class B G protein-coupled receptor. (wiley.com)
  • 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)
  • As opposed to single strand (ss) DNA binding proteins such as SSB and RPA, which protect and occlude ssDNA from recombination, RAD52/Redβ SSAPs promote recombination and share several biochemical similarities. (nature.com)
  • Accurate in silico predictions of ligand-protein binding affinities continues to be a primary objective of structure-based pharmaceutical design because of its putative value for drug discovery. (nature.com)
  • Intrinsically disordered regions (IDRs) lacking a fixed three-dimensional protein structure are widespread and play a central role in cell regulation. (iucr.org)
  • Our method guaranties preservation of the protein structure during the transition and allows to access conformations that are unreachable with classical normal mode analysis. (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)
  • Nevertheless, experimental protein structure determination remains a time consuming and costly process. (biorxiv.org)
  • Here you can show the Ramachandran plot for any protein structure. (proteopedia.org)
  • Cysteines are one of the most rarely used amino acids, but when conserved in proteins they often play critical roles in structure, function, or regulation. (hindawi.com)
  • 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)
  • And that is that many proteins need the help of the txaperones to get their native structure. (zientzia.eus)
  • In fact, proteins that already have an adequate three-dimensional structure (native structure) can also undergo deolations and form reactive intermediaries. (zientzia.eus)
  • On the one hand, the freshly synthesized protein folding process to obtain a native and active structure. (zientzia.eus)
  • 2) For the HIV fusion protein gp41, we have determined the oligomeric structure of the membrane-proximal external region (MPER) and the TMD. (lu.se)
  • We find that this domain is trimerized in the lipid membrane with a helix-turn-helix conformation, suggesting that this domain stabilizes the trimer structure of gp41 and promotes membrane curvature during the fusion process. (lu.se)
  • The Protein Data Bank (PDB) is a valuable resource for three-dimensional structural information on glycoproteins and protein-carbohydrate complexes. (iucr.org)
  • In proteins where cysteine is not within the active site, activity can be modulated by changing conformation or by influencing its regulatory role, for example, iron sulfur complexes (ISCs) in aconitase possess cysteines required for its activity [ 7 ]. (hindawi.com)
  • And it also establishes that prion strains can be accounted for solely by the ability of the protein to misfold into more than one conformation. (bbc.co.uk)
  • Meanwhile, the Florida team isolated three different strains of yeast prion - each of which originated from the same protein molecule. (bbc.co.uk)
  • Lipid-specific oligomerization of the Marburg virus matrix protein VP40 is regulated by two distinct interfaces for virion assembly. (uci.edu)
  • Redox proteomics has taken advantage of the thiol specificity of ICAT reagents not only to identify targets of ROS but also to quantify oxidative thiol modifications in individual proteins. (hindawi.com)
  • A His -or Strep-tag II can be added to either terminus, greatly simplifying protein purification and detection after expression. (qiagen.com)
  • Detection of the most likely ligand binding mode, the presence of multiple stable binding conformations, insufficient equilibration, and determining an adequate sampling time (especially when significant protein side chain and backbone residue flexibility is possible) are the most critical aspects of FEP, and have been recently reviewed in detail 8 . (nature.com)
  • Comparison of simulations (total of 13 ns) of the free protein and of the bound protein conformation (in isolation or DNA-bound) reveals intrinsic flexibility in certain parts of the molecule. (uzh.ch)
  • Here, we show that Rab25 associates with FIP2 and can recruit this effector protein to endosomal membranes. (anl.gov)
  • The β-sheet conformation causes negative Gaussian curvature and membrane dehydration, which are required for membrane merger, while the α-helical conformation resides in low-curvature lamellar membranes and forms three-helix bundles. (lu.se)
  • Based on analysis of the binding enthalpy and binding heat capacity, we have reasoned that dehydration of the protein-DNA interface is incomplete. (uzh.ch)
  • To gain a better understanding of how certain dementia-specific pathologic proteins interact with sleep-regulating brain centers and influence cognition, two different transgenic mouse models were studied. (uantwerpen.be)
  • Controlling the biodistribution of protein- and nanoparticle-based therapeutic formulations remains challenging. (uw.edu)
  • As evaluated by co-immunoprecipitation experiments, the dsDNA recombination function relates to the Redα-Redβ protein-protein interaction, which requires not only contacts in the C-terminal domain but also a region near the N-terminus. (nature.com)
  • In addition, several proteins that are not previously linked with blood-biomaterial interaction are presented and discussed. (ibecbarcelona.eu)
  • Free energy perturbation (FEP) calculations are attractive for predicting ligand-protein binding affinities via molecular simulations as well as for reducing the duration of the lead optimization phase of pharmaceutical development, which is as an individual stage the most expensive part of drug discovery 1 , 2 . (nature.com)
  • Broadly used in modern drug design, molecular docking methods explore the ligand conformations adopted within the binding sites of macromolecular targets. (mdpi.com)
  • 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)
  • Here, we describe further development of an in vivo library selection platform based on self-assembling protein nanoparticles encapsulating their own mRNA genomes (synthetic nucleocapsids or synNCs). (uw.edu)