• 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)
  • The extraordinary stability against proteolytic degradation in presence of proteases and ability to generate stable helical secondary structures, such as, 14- 12- and alternate 10/12-helices, with as few as 4-6 amino acids are the two main reasons behind the booming entry of β-peptides into peptidomimetics. (uni-goettingen.de)
  • Direct experimental determination of helical macro-dipole moment of peptides being extremely challenging, the possible effects of helical macro-dipole moment has only been theoretically proposed. (uni-goettingen.de)
  • The most promising Ags were submitted to a more in-depth biophysical investigation of their structure and conformation stability, and for their capacity to interact with neutralising antibodies (Abs) and peptides. (europa.eu)
  • Protein aggregation can be described as the fibrilization or formation of insoluble structures from completely or partially unfolded peptides [2] . (wikibooks.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)
  • Protein complexes perform a diversity of functions in natural biological systems. (mdpi.com)
  • While computational protein design has enabled the development of symmetric protein complexes with spherical shapes and hollow interiors, the individual subunits often comprise large proteins. (mdpi.com)
  • All-atom simulations of 4E10, PGZL1, 10E8 and LN01 docked onto HIV-like membranes consistently form phospholipid complexes at key complementarity-determining region loop sites, solidifying that stable and specific lipid interactions anchor bnAbs to membrane surfaces. (elifesciences.org)
  • 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)
  • Molecular dynamics simulation studies were performed on two best protein-ligand complexes to check their stability. (ijpsr.com)
  • 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)
  • first generated a list of encounter complexes using a method known as Brownian docking (BD), an established method to predict protein-protein complexes [6]. (biologists.com)
  • Based on the high contact area between CYP1A1 and CPR, the authors concluded that CYP1A1 and CPR formed strongly-bound and stable transient complexes in the membrane. (biologists.com)
  • Each definition is valid and will often overlap, i.e. a compact structural domain that is found amongst diverse proteins is likely to fold independently within its structural environment. (wikipedia.org)
  • Structural heterogeneity can be probed by various experimental techniques. (biorxiv.org)
  • Other projects in the lab focus on the mechanism of protein misfolding, the structural and energetic mechanism of signaling, computational identification of folding modules, and the role of ligand binding. (berkeley.edu)
  • But just as it had originally been the case in other fields of synthetic chemistry, such as molecular or solid state chemistry, the outcome of such a deposition with respect to the structure of the individual molecule or the structural arrangement of many molecules is very hard to predict without prior experimental input. (degruyter.com)
  • Some functions are performed by disordered protein structural parts. (alzforum.org)
  • Structural comparison to mesophilic acylphosphatases reveals significant differences in the conformation of the L5 loop connecting strands 4 and 5. (rcsb.org)
  • The plasma membranes are composed of various different constituents, but among all, membrane proteins are unanimously accepted as one of the major structural and functional pillars of the plasma membranes by the scientific community. (uni-goettingen.de)
  • NMR spectroscopy as a powerful technique is often used to investigate on structural and conformational studies on proteins and drug compounds. (sharif.edu)
  • 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)
  • One cryoEM and over 50 high-resolution X-ray crystallographic structures are available for antagonist- or agonist-bound A 2A AR and for its ternary complex with an agonist and an engineered G protein, making this receptor an excellent model system for investigating GPCR structural dynamics. (nature.com)
  • The N2A segment of titin functions as a pivotal hub for signal transduction and interacts with various proteins involved in structural support, chaperone activities, and transcriptional regulation. (gdch.app)
  • Protein Phosphatase 2A (PP2A) is a widely expressed family of protein phosphatases made of a core dimer, composed of a catalytic (C) subunit and a structural (A) subunit, in association with a third variable regulatory (B) subunit. (ac.be)
  • 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)
  • 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)
  • 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)
  • 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)
  • Reversible protein aggregation typically results from weaker protein interactions. (wikibooks.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)
  • In molecular biology, a protein domain is a region of a protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. (wikipedia.org)
  • Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions. (wikipedia.org)
  • Our work provides an experimental perspective into the communication of stability effects through the NQO1 dimer, valuable to understand at the molecular level the effects of disease-associated variants, post-translation modifications and ligand binding cooperativity in NQO1. (preprints.org)
  • Identifying the molecular states relevant to protein functioning is necessary for our understanding of biological processes. (biorxiv.org)
  • Many complex molecular systems absorb light in the UV spectral range, including those of paramount biological importance, like DNA bases or proteins. (cea.fr)
  • Further, computational simulation analysis was used to show the interaction patterns of ZnPc-1 and ZnPc-2 with penicillin binding protein 2a (PBP2a) of S. aureus and FimH lectin protein (PDB:4XO8) of E. coli to elucidate the dark molecular antibacterial mechanism of the compounds. (bvsalud.org)
  • See also David Thirumalai's Emerging Ideas on the Molecular Basis of Protein and Peptide Aggregation ' (.pdf). (alzforum.org)
  • Understanding the molecular forces and other physico-chemical processes behind the folding conformation and transmembrane dynamics of these protein domains are an integral part in the process of developing updated synthetic transmembrane protein domains. (uni-goettingen.de)
  • As no experimental structure is available, we provide a model of the TMPRSS2 equilibrium structure and its fluctuations by relaxing an initial homology structure with extensive 330 microseconds of all-atom molecular dynamics (MD) and Markov modeling. (rsc.org)
  • A combination of molecular simulation with hydrogendeuterium-exchange mass spectrometry and electron paramagnetic resonance spectroscopy reveal an asymmetry across the membrane: ATP-induced conformational changes in the cytosolic cavity promote unfolded pre-protein structure, while the exterior cavity favours its formation. (elifesciences.org)
  • Given the tight relation between protein structure and function, we present a set of methods to analyze protein topology, implemented in the VLDP program, relying on Laguerre space partitions built from series of molecular dynamics snapshots. (nature.com)
  • We characterized 5 atypical BSE-H isolates by analyzing their molecular and neuropathologic properties during transmission in transgenic mice expressing homologous bovine prion protein. (cdc.gov)
  • 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)
  • His research sped a shift in many biologists' attention from organismic biology, the study of creatures great and small, to molecular biology, which focuses on the individual biochemical reactions that underpin all living processes and on the molecules - usually proteins - responsible for catalyzing those reactions. (stanford.edu)
  • His discoveries laid the groundwork for our understanding of how a newborn protein accurately folds up into its adult shape within milliseconds - an insight that's informed molecular biology ever since. (stanford.edu)
  • However, it still appeared to leave the door open to various interpretations of what was the molecular detail of the conformation that caused the non-ideality. (gr.jp)
  • Significance Statement Proteins perform their biological functions by changing their shapes and interacting with each other. (biorxiv.org)
  • Understanding the sequence determinants of the energy landscape is therefore fundamental to the biological process that proteins carry out as well as protein folding itself. (berkeley.edu)
  • Typical applications of design include novel therapeutic strategies, control principles for existing biological systems, or sensors for the presence of small molecules [3], but designed sequences can also provide an objective experimental assessment of functional hypotheses, where designs are synthesized and their effect on the cellular context can be tested in vitro and, in turn, in vivo. (dagstuhl.de)
  • The detection and evaluation of concentration of influenza virus proteins in biological samples is critical in a broad range of medical and biological investigations regarding the concern over potential outbreaks of virulent influenza strains in animals and humans. (omicsonline.org)
  • Existing chemical and optogenetic methods for post-translationally controlling intracellular protein function have provided valuable insight into natural biological processes and facilitated the engineering of synthetic cellular functions but are mainly limited to single-input/single-output, digital control schemes. (tjbrunette.org)
  • TSPO is a ubiquitous mitochondrial protein and is involved in numerous biological functions. (uni-regensburg.de)
  • Pauling believed that protein shapes-independently of amino acid sequences-determined antibody specificity and biological specificity in general. (ucpress.edu)
  • We show that NQO1apo has a minimally stable folded core holding the protein dimer and with FAD and dicoumarol ligand binding sites populating binding non-competent conformations. (preprints.org)
  • Ligand 1, ZINC03851216 depicted a stable hydrogen bond with Asn 99 residue on the protein and the complex stabilized after 10ns during the 50ns simulation time. (ijpsr.com)
  • In response to ligand binding, different A 2A AR amino acids either alter their sole stable conformations or vary relative probabilities of coexisting stable conformations 16 , 17 . (nature.com)
  • 2.There is a known phenomenon, called "induced fit", whereby a target protein undergoes conformational changes upon ligand binding. (cecam.org)
  • also investigated the effects of CPR binding on the opening of ligand tunnels between the buried CYP active site and the protein surface. (biologists.com)
  • While the authors could not draw causal inferences between CPR binding and changes in the conformations of the ligand tunnels, their RAMD simulations showed that the binding of CPR to CYP1A1 alters the distribution of egress pathways. (biologists.com)
  • NQO1 displays a remarkable functional chemistry, capable of binding different functional ligands that modulate its activity, stability and interaction with proteins and nucleic acids. (preprints.org)
  • We have found that although protein stability can be altered by single amino acid substitution, evolution for optimal function requires more subtle and delocalized mechanisms.Recent results implicate structure in the unfolded state as playing an important and novel role for the thermostability of these proteins. (berkeley.edu)
  • To address the first problem, we need scientists who develop methods for estimating changes in protein stability of binding upon mutations. (cecam.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)
  • We start by docking the peptide onto a curated scaffold library generated from chopped up repeat protein junctions that range from 80-121aa. (tjbrunette.org)
  • Once the signal peptide and GPI signal have both been cleaved, the initial 253 amino acid protein is just 208 amino acids. (cureffi.org)
  • However, Pauling never ceased advocating his valence bond theory, which continued to be used, for example, to explain the planarity of the peptide bond in proteins. (ucpress.edu)
  • There are specific problems of protein-protein docking, protein-peptide docking and protein-drug docking with corresponding areas of applications. (cecam.org)
  • Amyloid-β (Aβ) is a peptide fragment consisting of 39 - 43 amino acid residues, which is produced by successive proteolytic cleavages of the amyloid precursor protein (APP) 1 . (biorxiv.org)
  • In this initial study, we combine single-molecule Förster resonance energy transfer (FRET) spectroscopy, fluorescence lifetime imaging (FLIM), and image analysis using deep learning (codes are available at https://github.com/hoisunglab/FNet ) to interrogate several steps during the aggregation process of the 42-residue Aβ peptide (Aβ42), including dimerization, formation of stable oligomers, and fibril elongation. (biorxiv.org)
  • A peptide can bind to itself or to other proteins in the cell in an unnatural way. (wikibooks.org)
  • Ancillary protein-lipid contacts reveal surprising contributions from antibody framework regions. (elifesciences.org)
  • The modeling platform developed here uncovers insights into lipid participation in antibodies' recognition of membrane proteins and highlights antibody features to prioritize in vaccine design. (elifesciences.org)
  • 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)
  • Protein aggregation is implicated as the cause of pathology in various diseases such as Alzheimer's and Parkinson's disease. (biorxiv.org)
  • Aggregation to form fibrils is also highly heterogeneous in terms of the number of strands in a fibril and the elongation speed and conformation of fibrils. (biorxiv.org)
  • This heterogeneity in all stages of aggregation explains diverse and sometimes irreproducible results of experimental studies of amyloid-β. (biorxiv.org)
  • Although fibrils are known to be toxic, a number of experimental studies also suggest that a subset of soluble oligomers, transiently appearing during the aggregation process, are more responsible for disease pathology than the fibril itself 2 - 6 . (biorxiv.org)
  • Despite tremendous effort to understand aggregation of Aβ to form oligomers and fibrils, experimental results vary widely and there is no consensus on the model for these processes 7 . (biorxiv.org)
  • Due to the lack of quantitative experimental results, there is no comprehensive aggregation model that includes heterogeneity of aggregation pathways. (biorxiv.org)
  • Protein Aggregation has become a topic of growing interest in recent years, especially in pharmaceutical research. (wikibooks.org)
  • Protein aggregation is often encountered during late research stages or manufacturing of biopharma. (wikibooks.org)
  • Protein aggregation occurs when inter-chain contacts with other parts of that protein or other proteins. (wikibooks.org)
  • There are several diseases linked to protein aggregation. (wikibooks.org)
  • The reversibility of this type of aggregation can change when environmental factors such as protein concentration, salt concentration, or pH are varied [5] . (wikibooks.org)
  • In order for us to understand protein aggregation, we need to understand more about protein folding in general. (wikibooks.org)
  • Binding of FAD significantly decreases protein dynamics and stabilizes the FAD and dicoumarol binding sites as well as the monomer:monomer interface. (preprints.org)
  • For instance, many proteins share the same native structure yet their cellular dynamics and function, in other words their energy landscapes, are different. (berkeley.edu)
  • The complex pharmacology of G-protein-coupled receptors (GPCRs) is defined by their multi-state conformational dynamics. (nature.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)
  • While many studies have been focused on the membrane structure, the dynamics of such systems are crucial for the function of the membrane including membrane bound proteins. (lu.se)
  • Transport of proteins across membranes is a fundamental process, achieved in every cell by the 'Sec' translocon. (elifesciences.org)
  • The encapsulation and compartmentalisation of cells has necessitated the evolution of machineries that conduct proteins across membranes, including for protein secretion and organellar import. (elifesciences.org)
  • They are single-chain molecules present on host cellular membranes and belong to the complement control protein family. (medscape.com)
  • Mounting evidence suggests that the genetic disorders/mutation and diseases change not only the protein expression patterns but also membranes themselves. (lu.se)
  • Native membrane derived polymer-supported lipid bilayers (nSLBs) are poised to bridge the gap between live cell experiments and traditional model membrane architectures that by offering a combination of accessibility by surface sensitive analytical instrumentation and a composition which more closely resembles cellular membranes by displaying a diversity of endogenous membrane proteins, lipids, and carbohydrates. (lu.se)
  • The primary structure (string of amino acids) of a protein ultimately encodes its uniquely folded three-dimensional (3D) conformation. (wikipedia.org)
  • Aβ interacts with many proteins either specifically or non-specifically as a monomer and various oligomeric forms 8 . (biorxiv.org)
  • The obtained results from computational studies showed that ZnPc-2 binds firmly through bonds with the 1MWT protein from S. aureus. (bvsalud.org)
  • From combining experimental and computational results, we can conclude that this strategy can be applied to different types of bacterial infections. (bvsalud.org)
  • Here, we report the computational design of protein pores formed by two concentric rings of ɑ-helices that are stable and mono-disperse in both water-soluble and membrane protein forms. (tjbrunette.org)
  • This understanding can be realistically achieved only by a successful combination of experimental and computational techniques. (cecam.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)
  • both corroborate other experimental data [7,8] and computational studies [9-11]. (biologists.com)
  • of relevance here is N-linked glycosylation , where the glycan is covalently bound to a nitrogen (N) atom in an asparagine (N) amino acid in the protein. (cureffi.org)
  • The ionizable amino acid side chains of proteins are usually located at the surface. (lu.se)
  • So, it has been of great scientific interest to design and develop artificial transmembrane protein domains that are able to address the shortcomings of the natural ones. (uni-goettingen.de)
  • This new approach has been shown to preserve mobility and enzymatic activity of transmembrane proteins in the resulting nSLB. (lu.se)
  • Proteins from thermophilic organisms must retain their native structures under extreme conditions, where their homologues from mesophilic organisms denature. (berkeley.edu)
  • But we are still far away from an unbiased structure prediction of thermodynamically and/or kinetically stable structures of molecules on surfaces. (degruyter.com)
  • I agree with you that we also want to examine the earlier, less stable structures. (alzforum.org)
  • Baldwin devoted his career to studying how proteins, which begin life as linear chains of chemical building blocks, quickly assume their characteristic highly complex, functional structures. (stanford.edu)
  • Baldwin developed tools and designed rigorous experiments to show that instead of simply switching in binary fashion from their initial linear conformations into correctly folded final shapes, as had been postulated, proteins transition into their final shapes through short-lived intermediate structures. (stanford.edu)
  • Electronic supplementary information (ESI) available: Protein coordinates and the point charges on all the atoms in the MM region (in PDB format) and the equilibrium geometries of the quantum region for all of the studied structures. (lu.se)
  • Antibodies can target epitopes on integral membrane proteins very near to the lipid bilayer surface, even those partially embedded within the headgroup region. (elifesciences.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 overall objective of EuroNeut-41 was to design a vaccine that raises antibodies able to prevent HIV cell fusion by blocking the virus fusion protein gp41 in its pre-fusogenic conformation. (europa.eu)
  • This hypothesis unites a lot of work in the field of and has also provided insight and experimental tests for current theoretical work on protein folding. (berkeley.edu)
  • After obtaining his degree in 1997, he worked as a Wellcome Trust and BBSRC Research Fellow, designing joint theoretical and experimental approaches to study the dynamic conformation of hyaluronan, both free and in the presence of protein, and expanding his research into other polysaccharides and oligosaccharides. (gr.jp)
  • According to our photocatalytic antibacterial mechanism, photogenerated electrons are transferred from Pcs to TiO2 and then react with O2, thus creating ROS, which causes damage to bacterial membrane, protein and biofilm destruction as well. (bvsalud.org)
  • The bulk of protein secretion and membrane protein insertion is conducted by the ubiquitous Sec translocon. (elifesciences.org)
  • As a test-case, the membrane protein FepA is investigated in its full environment, yielding a more precise description of the protein surface. (nature.com)
  • Our study uses classical algorithms such as space partitions and Dijkstra paths search 9 , applied in an original and novel way by taking into account the full representation of a membrane protein including the solvent and the lipid bilayer (Fig. 1 ). (nature.com)
  • The FepA membrane protein is surrounded by a lipid bilayer separating the extracellular medium and the periplasm. (nature.com)
  • Wetlaufer defined domains as stable units of protein structure that could fold autonomously. (wikipedia.org)
  • One study has suggested that a single ancestral enzyme could have diverged into several families, while another suggests that a stable TIM-barrel structure has evolved through convergent evolution. (wikipedia.org)
  • The most important factor governing the folding of a protein into 3D structure is the distribution of polar and non-polar side chains. (wikipedia.org)
  • Some simple combinations of secondary structure elements have been found to frequently occur in protein structure and are referred to as supersecondary structure or motifs. (wikipedia.org)
  • 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)
  • 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)
  • Model building: The automated homology model building was performed using the protein structure-modeling program MODELLER 4.13 Reliability of the predicted homology models was assessed by the ENERGY command of the MODELLER. (org.pk)
  • 2016). Here, we show that ATP enhances this process by modulating secondary structure formation within the translocating protein. (elifesciences.org)
  • This ability to exploit structure within a pre-protein is an unexplored area of protein transport, which may apply to other protein transporters, such as those of the endoplasmic reticulum and mitochondria. (elifesciences.org)
  • His theory was informed by his pioneering work on protein structure, and it was inspired by the intuitive "rule of parsimony" and simplicity. (ucpress.edu)
  • 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)
  • 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)
  • How does a protein know how to fold up, without mistakes and almost instantaneously, into a functional three-dimensional structure? (stanford.edu)
  • This made the CPR structure more compact, adopting a conformation resembling the semi-open one observed in the crystal structure. (biologists.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)
  • Proteins undergo an incredible transformation from one-dimensional sequence information into complex three-dimensional shapes that carry out intricate cellular functions. (berkeley.edu)
  • In addition to the native conformation, a protein sequence populates small fluctuations around the native state, partially unfolded forms and even the globally unfolded conformation. (berkeley.edu)
  • Sequence Analysis: Primary sequence of human gb-crystallin (Accession No. CRGB-HUMAN) was retrieved from the SWISSPROT data bank.9 Sequence homology searches of the Protein databank, PDB10 using the basic BLAST algorithm11 were carried out independently for each primary sequence. (org.pk)
  • Finally, the signal sequence is cleaved and the pre-protein is either folded or trafficked onwards. (elifesciences.org)
  • 2 Protein phosphatase 2A (PP2A) is a very abundant - it accounts for as much as 1% of total cellular proteins - ubiquitous and remarkably conserved enzyme. (ac.be)
  • Domains can either serve as modules for building up large assemblies such as virus particles or muscle fibres, or can provide specific catalytic or binding sites as found in enzymes or regulatory proteins. (wikipedia.org)
  • 1 Reversible protein phosphorylation is an important regulatory mechanism that controls the activities of a myriad of proteins and is thus involved in virtually every major physiological process. (ac.be)
  • Partial or complete deficiencies of the components of the complement system, including its receptors and regulatory proteins, are now described in humans and may be of a genetic or familial origin or acquired. (medscape.com)
  • Recently, 2 atypical, presumably sporadic forms of BSE have been associated with 2 distinct prion strains that are characterized mainly by distinct Western blot profiles of abnormal protease-resistant prion protein (PrP res ), named high-type (BSE-H) and low-type (BSE-L), that also differed from classical BSE. (cdc.gov)
  • These findings demonstrate the capability of an atypical bovine prion to acquire classical BSE-like properties during propagation in a homologous bovine prion protein context and support the view that the epidemic BSE agent could have originated from such a cattle prion. (cdc.gov)
  • Prion diseases are characterized by specific histopathologic lesions and deposits of an abnormal conformational isoform (PrP Sc ) of the host-encoded physiologic prion protein (PrP C ) in the central nervous system. (cdc.gov)
  • PrP Sc but not PrP C is partially resistant to digestion by proteinase K, resulting in an N terminally truncated prion protein termed PrP res that can be detected by Western blot and showing a characteristic banding pattern that reflects the 3 PrP res glycoforms. (cdc.gov)
  • 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)
  • Such buried ionizable groups destabilize the protein and may trigger conformational changes in response to pH variations. (lu.se)
  • Our data shows compelling indication that proposed ligands hold considerable potential for further experimental evaluation. (ijpsr.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)
  • The coat protein can bind helices with bulged adenines at either position, but the 3'-proximal site binds with greater affinity. (rcsb.org)
  • My algorithm to fuse helices and repeat proteins. (tjbrunette.org)
  • Generally proteins have a core of hydrophobic residues surrounded by a shell of hydrophilic residues. (wikipedia.org)
  • It has been generally accepted that the principal driving force in protein folding is the hydrophobic effect4, which results in the burial of the hydrophobic residues in the core of the protein. (org.pk)
  • Because a uniform dielectric ionizable group in a protein relative to the pKa value of the continuum model is a very crude description of the highly same group in a small reference molecule in dilute aqueous heterogeneous protein interior, the dielectric coefficient, eP, solution. (lu.se)
  • α-Synuclein (140 aa) is a natively unfolded protein that is enriched in the presynaptic terminal of the neurons in the brain. (biomedcentral.com)
  • Effector proteins interacting with the Fc portion of immunoglobulin M (IgM) include complement and complement receptors. (medscape.com)
  • Defects in the expression of complement or complement receptors may result in loss of tolerance to self-proteins and the development of immune complex-mediated autoimmune diseases such as systemic lupus erythematosus (SLE). (medscape.com)
  • Among healthy individuals, the number of CR1 receptors on the red blood cells varies widely, yet the phenotypic expression, regulated by 2 codominant alleles, is stable. (medscape.com)
  • 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)
  • 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)
  • 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)
  • The data confirm the central three-helix bundle fold of UN2A and show that this adopts a compact and stable conformation in absence of CARP. (gdch.app)
  • These crystallins should therefore be highly stable. (org.pk)
  • One of the most striking changes in age-related cataract is the post-translational modifications such as racemization, phosphorylation, deamidation, truncation, methylation, and thiolation [ 7 - 9 ], which impose aberrant changes on the conformation and functionality of crystallins. (molvis.org)
  • Glycosylation is the attachment of sugar chains to proteins. (cureffi.org)
  • Proteins with sugar chains attached are called glycoproteins, and the sugar chains are called glycans . (cureffi.org)
  • Most ionizable side chains reside at the protein surface, parent physical significance. (lu.se)
  • We have taken a proteomic and biophysical approach to understand how a protein fine-tunes its landscape to control this feature. (berkeley.edu)
  • From its initial isolation, the properties of HA provided a challenge to classical biophysical methods of analysis, which were primarily developed for proteins and required that the properties approached those of perfect Newtonian solutes. (gr.jp)
  • Human NAD(P)H:quinone oxidoreductase 1 (NQO1) is a multi-functional protein whose alteration is associated with cancer, Parkinson´s and Alzheimer´s diseases. (preprints.org)
  • Lipid-specific oligomerization of the Marburg virus matrix protein VP40 is regulated by two distinct interfaces for virion assembly. (uci.edu)
  • Such non-native states on the energy landscape are thought to play a determining function in many cellular processes such as translocation, protein synthesis, degradation, signaling and allostery. (berkeley.edu)
  • Although viewed as a constitutive housekeeping enzyme in the past, PP2A is a highly regulated phosphatase and is emerging as an important regulator of multiple cellular processes involving protein phosphorylation. (ac.be)
  • But advances in the understanding of protein phosphatases make now clear that these enzymes are precisely regulated and are as important as kinases in the regulation of cellular processes involving protein phosphorylation. (ac.be)
  • Homeodomain-interacting protein kinase-2 (HIPK2) is a positive regulator of p53 oncosuppressor function. (aacrjournals.org)
  • Notably, the "unique N2A" (UN2A) subdomain has been shown to interact with the stress-regulated cardiac ankyrin repeat protein (CARP), which contributes to the regulation of sarcomeric stiffness. (gdch.app)
  • The "self"-protein albumin in mouse airway fluid was uniquely modified by GSH-MDI at position 414K, a preferred site of MDI reactivity on human albumin. (cdc.gov)
  • Baldwin propelled leaps in scientists' understanding of how proteins assemble themselves into the three-dimensional shapes that are essential to their function. (stanford.edu)
  • When we're taught biochemistry, we see proteins in their physiologically active forms. (alzforum.org)
  • At the time there were a number of critical, unanswered questions about proteins," said Paul Berg, PhD, emeritus professor of biochemistry and a member of that original group. (stanford.edu)
  • Soft-spoken, of moderate height and slight of build, "Buzz was a giant in the field of protein folding, and a profoundly influential mentor to many," said Peter Kim , PhD, the Virginia and D. K. Ludwig Professor in Biochemistry, who conducted doctorate work under Baldwin's tutelage in the 1980s. (stanford.edu)
  • Only a small fraction of IDRs have been functionally characterized, with heterogeneous experimental evidence that is largely buried in the literature. (iucr.org)
  • A molecule in solution can be viewed as a structurally heterogeneous ensemble, where a finite number of conformational states ( e.g . active-inactive, bound-unbound) may become stable under certain conditions to perform specific tasks. (biorxiv.org)
  • In prokaryotes, SecYEG associates with the motor ATPase SecA to carry out translocation for pre-protein secretion. (elifesciences.org)
  • This paper explores how the protein folding process per se may be exploited to drive protein translocation. (elifesciences.org)
  • The protein must then fold during or after the translocation process. (elifesciences.org)
  • The 414K-MDI conjugation appears to covalently cross- link GSH to albumin via GSH's NH2-terminus, a unique conformation possibly resulting from cyclized mono(GSH)-MDI or asymmetric ( S , N -linked) bis(GSH)-MDI conjugates. (cdc.gov)
  • In the past, most of the attention was focused primarily on protein kinases and on their regulation, mainly because phosphatases were then viewed as simple housekeeping enzymes. (ac.be)
  • This parallel detection of PB1-F2 and NP suggests that applied sensor chip technology may be amenable to an arrow immunosensor for simultaneous detection of all known influenza virus proteins in infected tissues and cells. (omicsonline.org)
  • Simulations estimating protein-membrane interaction strength for PGZL1 variants along an inferred maturation pathway show bilayer affinity is evolved and correlates with neutralization potency. (elifesciences.org)
  • In this study, we report experimental long-range distance distributions by electron paramagnetic resonance (EPR) spectroscopy between the three helixes within the UN2A domain linked to the immunoglobulin domain I81 in the presence and absence of CARP. (gdch.app)
  • In vitro assays confirm that both drugs inhibit the human protein TMPRSS2, a SARS-Cov-2 spike protein activator. (rsc.org)
  • The spike protein of SARS-CoV--a target for vaccine and therapeutic development. (who.int)
  • 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)
  • Long-distance restraints obtained by electron paramagnetic resonance (EPR) spectroscopy revealed that the "unique N2A" (UN2A) domain of the sarcomeric protein titin shows a defined and structured three-helix bundle and preserves this conformation upon binding of the muscle stress response factor CARP (cardiac ankyrin repeat protein). (gdch.app)
  • such charge pairings have been identified as important contributors towards redox protein binding. (biologists.com)