• The main purpose of these models is to gain insights regarding the function of the flexible protein, extending the structure-function paradigm from folded proteins to intrinsically disordered proteins. (wikipedia.org)
  • Constructing ensembles for intrinsically disordered proteins" (PDF). (wikipedia.org)
  • However, previous work by this team of researchers from the University of Notre Dame and The University of Chicago has shown that, contrary to popular belief, intrinsically disordered proteins, which sample a variety of conformational forms the way the autotransporter proteins do, can remain quite extended in water even if they have high ratios of hydrophobic to charged amino acids. (anl.gov)
  • It is the apoAI protein on preb-HDL that displays a unique conformation with the exposed binding sites specifically for free cholesterol. (pnnl.gov)
  • 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)
  • How does an amino acid sequence that is unfolded when it leaves the ribosome manage to fold properly into a highly ordered, lightning-fast enzyme or sturdy structural protein? (anl.gov)
  • X: any amino acid except Pro) present in newly synthesized protein in yeast and mammalian cells. (elifesciences.org)
  • However, when the adaptive process goes continuously during the many generation, the population of cells can use a special genetic mechanisms for the adaptation to 2 H 2 O. For example, mutations of geens can be resulted in amino acid replacements in molecules of proteins, which in turn could cause a formation of a new isoenzymes, and in the special cases - even the anomal working enzymes of a newer structure type. (o8ode.ru)
  • 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)
  • The ionizable amino acid side chains of proteins are usually located at the surface. (lu.se)
  • At the ribosome, the processed mRNA is translated to produce proteins from amino acid units. (cdc.gov)
  • The possibility to define custom motifs and search for their occurrence in other proteins permits the identification of recurrent arrangements of residues that could have structural implications. (biomedcentral.com)
  • Protein-ligand interactions were observed with key residues of the macromolecular target. (bvsalud.org)
  • The extreme thermostability of PhAcP can be attributed to an extensive ion-pair network consisting of 13 charge residues on the beta sheet of the protein. (rcsb.org)
  • We have completed a systematical analysis of how temperature, pH, presence of charged residues, but most importantly backbone conformation and dynamics affect isomerization rates as determined by NMR in the case of designed Asn/Asp polypeptide-models. (elte.hu)
  • We concluded that spontaneous deamidation prompted backbone isomerization of Asn/Asp residues resulting in - most cases - the insertion of an extra methylene group into the backbone poses a threat to the structural integrity of proteins. (elte.hu)
  • E protein construct comprising the full-length E sequence or residues 1 to 75 (EFL) was produced, purified from E. coli inclusion bodies, and reconstituted into phosphatidylethanolamine (PE) membranes under voltage-clamp conditions. (medicalwritersnewshubb.com)
  • In addition, the effects of post-translational modifications (PTM) on the E protein function were explored by palmitoylating all the cysteine residues (Cys40, Cys43, Cys44) in every subunit in the EFL pentamers of SARS-CoV-2 E protein channels. (medicalwritersnewshubb.com)
  • The team investigated if the transmembrane (TM) site formed EFL functional substructures, for which ETM was produced comprising viral E protein residues 8 to 38, by solid-phase peptide synthesis and assessed ETM functionality in-vitro . (medicalwritersnewshubb.com)
  • The voltage experiments showed that the E protein was most likely a voltage-gated pore regulated by electrowetting and a hydrophobic gating motif (comprising Phe20, 23, and 26 residues) located in the pore's center. (medicalwritersnewshubb.com)
  • Because the superposition is about 300 residues long (and the protein chains are longer), it is hard to see details of this superposition in the complexity. (proteopedia.org)
  • Even though the degree of conformational freedom is extremely high, flexible/disordered protein generally differ from fully random coil structures. (wikipedia.org)
  • The determination of a structural ensemble for an IDP from NMR/SAXS experimental parameters involves generation of structures that agree with the parameters and their respective weights in the ensemble. (wikipedia.org)
  • Our studies reveal a stable prefusion conformation of the spike immunogen with slight differences in the S1 subunit compared with published spike ectodomain structures. (nih.gov)
  • Subsequently, a variety of further patterns and regularities ( e.g. , [ 2 - 4 ]) in protein structures have been found, that have proven useful in the context of protein structure determination and quality assessment of determined structures. (biomedcentral.com)
  • In particular, the facilities for defining and searching for structural motifs now available in Swiss-PdbViewer include an interactive visual interface for defining structural motifs, and a machinery that is able to quickly search very large collections of structures for such motifs. (biomedcentral.com)
  • Actual algorithms work on both protein sequences and structures, some of them accounting also for conformational fluctuations around the native state and the protein microenvironment. (uab.cat)
  • 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)
  • Current hypotheses on protein folding suggest that folding is initiated by formation of secondary structures followed by association of the hydrophobic regions of the emerging structure to orient them toward the interior of the protein in a process termed hydrophobic collapse. (anl.gov)
  • Fernández-Busnadiego, an expert in cryo-electron microscopy, mentions two main factors: 'First of all, cryo-electron microscopy has only been optimized in recent years to look at protein structures with almost molecular resolution. (mpg.de)
  • We proposed that a cell theoretically could in principle synthezise a big number of forms of [ 2 H]labeled macromolecules with somewhat different structures and conformations, so that a cell could easily select a preferable one from al these species in a course of adaptation to 2 H 2 O, that is the best suitable namely for that conditions. (o8ode.ru)
  • The larger Rep proteins, Rep78 and Rep68, assemble into stable, hexameric oligomers on specific secondary structures on the 3' and 5' termini of the single stranded viral DNA. (utoledo.edu)
  • Our studies are aimed at understanding how these proteins assemble on DNA structures and the specificity of their interaction with DNA. (utoledo.edu)
  • Proteins from thermophilic organisms must retain their native structures under extreme conditions, where their homologues from mesophilic organisms denature. (berkeley.edu)
  • I agree with you that we also want to examine the earlier, less stable structures. (alzforum.org)
  • Input structures can be either a combined protein databank (PDB) structure file, or a directory of such files, and produces graphs. (github.com)
  • For the first time crystal structures of wild-type bovine pancreatic ribonuclease A and its markedly less stable variant modified at position Ile106 were determined at different pressures. (udg.edu)
  • But we are still far away from an unbiased structure prediction of thermodynamically and/or kinetically stable structures of molecules on surfaces. (degruyter.com)
  • It adds missing hydrogen atoms to protein structures (PDB-format) and detects reasonable protonation states, tautomers, and hydrogen coordinates of both protein and ligand molecules. (proteins.plus)
  • Specialized cell structures called ribosomes are the cellular organelles that actually synthesize the proteins (RNA transcription). (cdc.gov)
  • 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)
  • Structural analysis of GFP-nanobody complexes revealed that the two nanobodies induce subtle opposing changes in the chromophore environment, leading to altered absorption properties. (cipsm.de)
  • 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)
  • The similarity of the general architecture between the PTC-E(M) and the previously determined PTC-A(M) strongly suggests that the progenitor M complexes of all botulinum serotypes may have similar molecular arrangement, although the neurotoxins apparently can take very different conformation when they are released from the M complex. (nature.com)
  • BoNTs are secreted as progenitor complexes (PTC) with a non-toxic-non-hemagglutinin protein (NTNH) and a few neurotoxin associated proteins (NAPs) with or without hemagglutinin activity (HA). (nature.com)
  • Depending on the number of proteins forming the complex, three kinds of complexes, viz . (nature.com)
  • Molecular dynamics simulation studies were performed on two best protein-ligand complexes to check their stability. (ijpsr.com)
  • Protoss is a fully automated hydrogen prediction tool for protein-ligand complexes. (proteins.plus)
  • Rarey, M., Fast automated placement of polar hydrogen atoms in protein-ligand complexes. (proteins.plus)
  • Rarey, M., Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes. (proteins.plus)
  • This work identifies Drosophila S2 cells as a clinically-relevant platform suited for the production of 'difficult-to-make' proteins from Plasmodium parasites, and identifies a PfRH5 sequence variant that can be used for clinical production of a non-glycosylated, soluble full-length protein vaccine immunogen. (nature.com)
  • Today, recognition and classification of sequence motifs and protein folds is a mature field, thanks to the availability of numerous comprehensive and easy to use software packages and web-based services. (biomedcentral.com)
  • The smaller replication proteins, Rep40 and Rep52, require ATP to bind DNA, show no sequence specificity in DNA binding and lack the N-terminal nuclease domains. (utoledo.edu)
  • The long-term goal of our research is to understand the structural and dynamic information encoded in the linear sequence of amino acids. (berkeley.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)
  • 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)
  • For many functional RNA families [11], decades of research have produced a deep understanding of the sequence and structural basis underlying their biological function(s). (dagstuhl.de)
  • Owing to the discrete nature of RNA sequence and popular structural representations (e.g. secondary structure), RNA design has inspired the contribution of a large number of diverse algorithms [9, 20, 14, 4] for the inverse folding problem, i.e. the design of an RNA sequence which preferentially and effectively folds into a predefined (secondary) structure. (dagstuhl.de)
  • Crystallographic models of proteins with about 50% sequence identity differ by about 1 Å RMSD [3] [4] . (proteopedia.org)
  • The morph shows the 334-residue sequence of the query (FtsZ) changing from the query conformation to the conformation of the superposed target (tubulin). (proteopedia.org)
  • Unlike conventional antibodies, the small, stable nanobodies are functional in living cells. (cipsm.de)
  • 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)
  • 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)
  • Our understanding on this functional chemistry is limited by the difficulty of obtaining structural and dynamic information on many of these states. (preprints.org)
  • Moreover, targeting protein functional motions bears a great potential to control and modulate proteins' activities and interactions in physio-pathological contexts. (biorxiv.org)
  • The low metastability of preb-HDL has made a structural/functional characterization of this particle difficult. (pnnl.gov)
  • Here we demonstrate that PSRP1 is not a bona fide ribosomal protein, but rather a functional homologue of the Escherichia coli cold-shock protein pY. (cipsm.de)
  • The TM domain, individually, did not form physiologically functional substructures of the viral E protein. (medicalwritersnewshubb.com)
  • What we have found is that in order to achieve their high temperature sensitivity, the ion channel needs to undergo extreme structural changes in their functional state, and these extreme changes compromise protein stability," Qin explains. (buffalo.edu)
  • This new approach has been shown to preserve mobility and enzymatic activity of transmembrane proteins in the resulting nSLB. (lu.se)
  • Here we report the selection of camelid-derived single-domain antibodies (nanobodies) that modulate the conformation and spectral properties of the green fluorescent protein (GFP). (cipsm.de)
  • A molecular dynamics simulation of the novel bioactive compounds with the targeted protein was performed. (bvsalud.org)
  • 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)
  • Protein conformation is critically linked to function and often controlled by interactions with regulatory factors. (cipsm.de)
  • These techniques provide valuable insights on proteins' functioning and interactions with their environment. (biorxiv.org)
  • Ca2 + -Glutamic residue interactions altered E protein conformation and favored ion channel opening and the flow of ions into and through the channels. (medicalwritersnewshubb.com)
  • 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)
  • Furthermore, alternative conformations or overlapping entries that might be annotated in the original protein structure are removed, as they could disturb the analysis of molecular interactions. (proteins.plus)
  • long range interactions within the protein molecule. (flashcardmachine.com)
  • Calculation procedures first generate a pool of random conformers (initial pool) so that they sufficiently sample the conformation space. (wikipedia.org)
  • Low energy difference between the envelope (Cs symmetry) and twisted (C2 symmetry) conformations of the THF molecule leads to the interconversion between the two conformers. (researchgate.net)
  • Results indicate three stable conformers: twisted trans (global energy minimum), twisted gauche- and twisted gauche+. (researchgate.net)
  • Due to specific influence on the system equilibrium high pressure can act as a filter that enables to identify and investigate higher energy protein conformers. (udg.edu)
  • In this paper, we describe an extension of DeepView/Swiss-PdbViewer through which structural motifs may be defined and searched for in large protein structure databases, and we show that common structural motifs involved in stabilizing protein folds are present in evolutionarily and structurally unrelated proteins, also in deeply buried locations which are not obviously related to protein function. (biomedcentral.com)
  • We have obtained evidence for a surprising conclusion: RNase H folds in an apparently hierarchical fashion in which the most stable individual element folds first. (berkeley.edu)
  • We demonstrate that restricted mobility (such as being part of a secondary structural element) may safeguard against Asn to Asp spontaneous isomerization, but this protective factor is most effective in the case of off-pathway folds which can slow the reaction by several magnitudes compared to their on-pathway counterparts. (elte.hu)
  • The applicability of Hα detected spectral approach was probed for proteins to characterize them under physiological conditions. (elte.hu)
  • This proposal concentrates on NMR structural studies of apoAI/preb-HDL particles, and plan to collect 3D/4D-NMR experiments at high-field, such as 750/800 MHz, for an NMR spectral assignment and structural calculation of apoAI/preb-HDL. (pnnl.gov)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • TRIM7 targets ΦQ-containing proteins for proteasomal degradation in a mechanism reminiscent of the N-end rule and which allows it to potently inhibit viral replication. (mdpi.com)
  • Going forward, the team will test the extent of collapse in an even wider range of sequences, to more fully understand the importance of maintaining a highly expanded conformation prior to folding. (anl.gov)
  • In the case of proteins, structure superposition is often performed without reference to the sequences of the proteins. (proteopedia.org)
  • These methods dramatically increase the likelihood of producing proteins that cannot fold or assemble appropriately. (cipsm.de)
  • 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)
  • The morph makes it easy to see that the core fold is stable, while the larger changes occur in surface loops. (proteopedia.org)
  • It utilizes a new per-residue backbone metric -- the Ramachandran number -- to provide easily readable "pictures" (multi-angle pictures or MAPS) of protein conformations, ensembles, and trajectories. (github.com)
  • Palmitoylation of ≥1 cysteine residue promoted the formation of open and stable E protein pores. (medicalwritersnewshubb.com)
  • The structure of disordered proteins may be approximated by running constrained molecular dynamics (MD) simulations where the conformational sampling is being influenced by experimentally derived constraints. (wikipedia.org)
  • Herein, we have used hydrogen/deuterium exchange monitored by mass-spectrometry (HDXMS) to investigate the structural dynamics of NQO1 in three ligation states: without ligands (NQO1apo), with FAD (NQO1holo) and with FAD and the inhibitor dicoumarol (NQO1dic). (preprints.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)
  • We focus on the dynamics of the pseudorotation process, in particular, the lifetime of the THF conformations and their mutual rearrangements. (researchgate.net)
  • 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)
  • 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)
  • We model a protein as a network of atoms connected by springs and deform it along the least-energy directions. (biorxiv.org)
  • However it has proved challenging to identify a heterologous expression platform that can produce a soluble protein-based vaccine in a manner compliant with current Good Manufacturing Practice (cGMP). (nature.com)
  • This toolbox allows to delineate conformation-specific routines to assist in the identification of aggregation-prone regions and to guide the optimization of more soluble and stable biotherapeutics. (uab.cat)
  • This is thought to make globular proteins stable and soluble in the watery environment of the cell. (anl.gov)
  • The protein-protein interaction networks between MDM2 gene and its co-expressed genes were constructed by Gene-MANIA tool. (bvsalud.org)
  • Together with its interaction partner HAP40, shown in purple, huntingtin is more stable. (mpg.de)
  • The research of my laboratory is focused on nucleic acid enzymology, nucleic acid protein interaction and more recently on the development of modified human albumin for the treatment of shock. (utoledo.edu)
  • Following this, the differentially expressed genes (DEGs) were included in Gene Ontology enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, protein‑protein interaction network and survival analyses. (cancerindex.org)
  • 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)
  • They are single-chain molecules present on host cellular membranes and belong to the complement control protein family. (medscape.com)
  • The antibodies induced by one protein variant were shown to be qualitatively similar to responses induced by other vaccine platforms. (nature.com)
  • MorphoSys , a biotechnology company focused on fully human antibodies, and Heptares Therapeutics , a developer of new medicines targeting G protein-coupled receptors (GPCRs), have signed an agreement to discover novel antibody therapeutics targeting GPCRs-membrane proteins involved in a broad range of biological processes and diseases. (centerwatch.com)
  • We believe that by combining Heptares' unique StaR platform for generating stable GPCRs as antigens with our antibody discovery technology, we will be able to unlock the immense potential of therapeutic antibodies against GPCRs. (centerwatch.com)
  • Heptares' StaRs offer a breakthrough solution to the main challenge associated with making antibodies against GPCRs, namely producing purified and properly folded protein for use as an antigen against which antibodies are raised. (centerwatch.com)
  • Ylanthia's genetic composition translates into unprecedented structural diversity of the antibodies and offers optimized developability features. (centerwatch.com)
  • We show that the geometric descriptors of the initial nucleophilic attack of the isomerization can be used to classify local conformation and contribute to the design of stable protein drugs, antibodies or the assessment of the severity of mutations. (elte.hu)
  • Now Rubén Fernández-Busnadiego from the Department of Molecular Structural Biology at the MPI of Biochemistry and Stefan Kochanek, head of the Department of Gene Therapy at the University Hospital Ulm, have succeeded in decoding the molecular, three-dimensional structure of the huntingtin protein. (mpg.de)
  • When we're taught biochemistry, we see proteins in their physiologically active forms. (alzforum.org)
  • The Plasmodium falciparum reticulocyte-binding protein homolog 5 (PfRH5) has recently emerged as a leading candidate antigen against the blood-stage human malaria parasite. (nature.com)
  • In the present study, the 3D conformation of Plasmodium falciparum SPECT ( Pf SPECT) protein was predicted using homology modelling and refined by 50 nanoseconds of MD simulation. (ijpsr.com)
  • Our use of different hydrogen exchange methods to study three different types of intermediates of E. coli ribonuclease H (the acid molten globule, the higher energy conformations of the native state and a kinetic folding intermediate) has been particularly powerful. (berkeley.edu)
  • Despite its deleterious impact on fitness, protein aggregation is a generic property of polypeptide chains, indissociable from protein structure and function. (uab.cat)
  • Protein aggregation is behind the onset of neurodegenerative disorders and one of the serious obstacles in the production of protein-based therapeutics. (uab.cat)
  • The development of computational tools opened a new avenue to rationalize this phenomenon, enabling prediction of the aggregation propensity of individual proteins as well as proteome-wide analysis. (uab.cat)
  • These studies spotted aggregation as a major force driving protein evolution. (uab.cat)
  • Here we review how the advent of predictive tools has change the way we think and address protein aggregation. (uab.cat)
  • PFG-NMR is used to better understand protein unfolding and to quantitatively characterize the degree of denaturation and aggregation. (elte.hu)
  • See also David Thirumalai's Emerging Ideas on the Molecular Basis of Protein and Peptide Aggregation ' (.pdf). (alzforum.org)
  • The co-chaperone Hep1 is required to prevent the aggregation of mitochondrial Hsp70 proteins. (cipsm.de)
  • The techniques of ensemble calculation are relatively new on the field of structural biology, and are still facing certain limitations that need to be addressed before it will become comparable to classical structural description methods such as biological macromolecular crystallography. (wikipedia.org)
  • This structural heterogeneity is not occasional and is frequently linked with specific biological function. (biorxiv.org)
  • 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 authors believe their work will provide important information toward understanding basic questions of protein folding and tests long-held theories about how this remarkable biological process works. (anl.gov)
  • Hydrostatic pressure in range 0.1-1.5 GPa is used to modify biological system behaviour mostly in biophysical studies of proteins in solution. (udg.edu)
  • The biological need - the strong temperature sensitivity of the receptors - apparently requires a larger energy than what reversible structural changes in the protein can afford," he says. (buffalo.edu)
  • Nanobody-induced changes were detected by ratio imaging and used to monitor protein expression and subcellular localization as well as translocation events such as the tamoxifen-induced nuclear localization of estrogen receptor. (cipsm.de)
  • Preexisting antivector immunity can severely compromise the ability of Salmonella enterica serovar Typhimurium live vaccines to induce protective CD8 T-cell frequencies after type III secretion system-mediated heterologous protein translocation in orally immunized mice. (cipsm.de)
  • Aminoacyl tRNA synthetases are a class of enzymes that ensure the fidelity of protein synthesis by attaching amino acids to their cognate tRNAs. (utoledo.edu)
  • Cells depend on their DNA for coding information to make various classes of proteins that include enzymes, certain hormones, transport proteins, and structural proteins that support life. (cdc.gov)
  • In computational chemistry, conformational ensembles, also known as structural ensembles, are experimentally constrained computational models describing the structure of intrinsically unstructured proteins. (wikipedia.org)
  • 1 Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. (nih.gov)
  • Our laboratory uses a combination of biophysical, structural and computational techniques to understand these features. (berkeley.edu)
  • Structural comparison to mesophilic acylphosphatases reveals significant differences in the conformation of the L5 loop connecting strands 4 and 5. (rcsb.org)
  • The structural differences between two optimally superposed models are usually measured as the Root Mean Square Deviation ( RMSD ) between the superposed alpha-carbon positions (excluding deviations from the non-superposed positions). (proteopedia.org)
  • Activated receptors directly or indirectly regulate cellular biochemical processes (eg, ion conductance, protein phosphorylation, DNA transcription, enzymatic activity). (msdmanuals.com)
  • Such proteins are flexible in nature, lacking a stable tertiary structure, and therefore cannot be described with a single structural representation. (wikipedia.org)
  • Ensembles are models consisting of a set of conformations that together attempt to describe the structure of a flexible protein. (wikipedia.org)
  • The three-dimensional structure of proteins has been an extensively studied topic for several decades. (biomedcentral.com)
  • 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)
  • With the help of cryo-electron microscopy, the recently awarded Nobel Prize winning method, researchers have now decoded the three-dimensional, molecular structure of the healthy human huntingtin protein. (mpg.de)
  • An improved understanding of the structure and the function of the huntingtin protein could contribute to the development of new treatment methods in the future. (mpg.de)
  • The second reason is that the huntingtin protein is very flexible in its structure. (mpg.de)
  • Now that we know the exact structure of huntingtin, we can further study which areas of huntingtin are particularly important and how other proteins cooperate with huntingtin functionally. (mpg.de)
  • This would fundamentally change our conventional thinking about protein structure-function relationship, no? (alzforum.org)
  • 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)
  • I do not think there is a contradiction to the conventional thinking of protein structure-function relation. (alzforum.org)
  • Intrinsically disordered regions (IDRs) lacking a fixed three-dimensional protein structure are widespread and play a central role in cell regulation. (iucr.org)
  • DoGSiteScorer is a grid-based method that uses a Difference of Gaussian filter to detect potential binding pockets 1 - solely based on the 3D structure of the protein - and splits them into subpockets. (proteins.plus)
  • most prevalent and stable form of helical structure in naturally occurring proteins. (flashcardmachine.com)
  • StaRs enable antibody discovery by stabilizing the GPCR protein outside the cellular membrane in the correct conformation. (centerwatch.com)
  • 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)
  • Protein folding is one of the fascinating unanswered questions in biology. (anl.gov)
  • Autotransporter proteins then remain in an unfolded state in the periplasm until they pass through the outer bacterial membrane, folding properly along the way. (anl.gov)
  • This highly specialized protein folding process has attracted the attention of a team of researchers who have used this bacterial system as a model to determine what allows these unique proteins to maintain their disordered state in the periplasm. (anl.gov)
  • 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)
  • 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)
  • Our studies on the mechanism of folding include investigating the role of topological complexity using permuted proteins, the nature and function of folding intermediates, and studies on the role of mechanical unfolding using single molecule measurements. (berkeley.edu)
  • The ability to detect structural and dynamic information about folding intermediates in vitro provides an excellent opportunity to gain new insights into the energetic aspects of the energy landscape of protein folding. (elte.hu)
  • Protein Folding and Neurodegeneration: Biophysics to the Rescue? (alzforum.org)
  • This does not change our view of protein folding in the least. (alzforum.org)
  • While X-ray crystallography captures single stable states, cryo-EM allows observing conformational ensembles in solution. (biorxiv.org)
  • Effector proteins interacting with the Fc portion of immunoglobulin M (IgM) include complement and complement receptors. (medscape.com)
  • 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)
  • 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)
  • Heteronuclear relaxation studies combined with MD simulations revealed the source of backbone mobility and the nature of structural rearrangements during these transitions. (elte.hu)
  • BackMAP is a Python module (and stand-alone tool) that helps with the visualization of large amounts of structural (space-time) backbone data in a single graph. (github.com)
  • The heterochromatin-enriched HP1 proteins play a critical role in regulation of transcription. (cipsm.de)
  • These proteins are synthesized in the bacterial cytoplasm and cross one membrane into the bacterial periplasm. (anl.gov)
  • As other coronaviruses, 6-9 SARS-CoV-2 exploits host proteins to initiate cell-entry, in particular TMPRSS2 and ACE2, two membrane-bound proteins expressed in the upper and lower respiratory tract. (rsc.org)
  • Due to the lack of detergent solubilization and reconstitution steps, the nSLBs created using this approach contain essentially all of the native lipids, as well as the membrane-associated proteins and carbohydrates from the donor membrane. (lu.se)
  • 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 rationale behind using polyethylene glycol-modified albumin is that this modified protein has a sufficiently large hydrodynamic radius that precludes its passing through defects in capillaries that occur in shock and is thus retained within blood vessels to maintain the oncotic gradient. (utoledo.edu)
  • 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)
  • 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)
  • Current Opinion in Structural Biology. (wikipedia.org)
  • The volume of information included and the relevance to the field of structural biology are compared. (iucr.org)
  • Structural heterogeneity can be probed by various experimental techniques. (biorxiv.org)
  • This observation has led them to try and understand how proteins with high hydrophobic ratios can maintain these extended conformations. (anl.gov)
  • This finding suggests that spacing of hydrophobic amino acids must be under selective pressure in bacterial proteins to facilitate their virulence functions. (anl.gov)
  • We have taken a proteomic and biophysical approach to understand how a protein fine-tunes its landscape to control this feature. (berkeley.edu)
  • We performed cryo-election microscopy and site-specific glycan analysis of one of the leading subunit vaccine candidates from Novavax, which is based on a full-length spike protein formulated in polysorbate 80 detergent. (nih.gov)
  • This study confirms the structural integrity of the full-length spike protein immunogen and provides a basis for interpreting immune responses to this multivalent nanoparticle immunogen. (nih.gov)
  • In vitro assays confirm that both drugs inhibit the human protein TMPRSS2, a SARS-Cov-2 spike protein activator. (rsc.org)
  • Proteins are the molecular machines of the cell. (mpg.de)
  • Direct and indirect ionization of DNA is ultimately responsible for the DNA alterations that adversely affect the structural and genetic integrity of the system. (cdc.gov)
  • They analyzed structural changes in the variants compared to the wildtype pertactin domain by small-angle x-ray scattering (SAXS) at the Biophysics Collaborative Access Team (Bio-CAT) 18-ID x-ray beamline of the APS. (anl.gov)