InteractionsCrystallographyTertiaryCatalyticInactive ConformationStructuralGlobular proteinsMoleculesEnzymeReceptorsStabilityChemistryKineticMacromolecular structures at high resolutionInsightsSecondary structureToxicityMolecular mechanismsMacromoleculesHistoneRibosomeCellularTransmembranePolypeptideGeneKinasesInhibitorsResiduesTarget proteinsPoorly understoodMass spectrometrySolubilityPhysiologicalSignal transductionPhysiologically relevantSolventDynamicsDenaturantChaperonesBiological functionsPathwayPathogenesisFluorescentLigandHeterogeneityHelicesSubstrateBiologicallyPrion proteinNeurofibrillary TanglesAdoptAdoptsContrastTyrosineTransitionCrystal structuresModulateAmyloidMutationsSequenceAtomsMembranesFundamentalTemperatureTransportersMoleculeRegulation
Interactions20
- Epigenetics acts through two mechanisms: (1) modifications to chromosomal proteins that alter the 3D conformation of the genome and/or protein-DNA interactions and (2) chemical modification of the DNA strand itself ( Kondo, 2009 ). (frontiersin.org)
- The study of MscL, a highly convenient model system, will give us basic understanding and the first example of what type of intramolecular interactions, sequence motifs, and conformations make membrane proteins sensitive to a physiologically relevant mechanical stimulation. (usda.gov)
- 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)
- Olsen and his team use these protein structures to model interactions with other molecules, including potential new drugs. (medicalxpress.com)
- Previous theories proposed that B-casein had a random or 'spaghetti'-like shape and as a result, interactions with other milk proteins were also nonspecific. (usda.gov)
- However, the task of predicting protein-protein interactions between a new virus and human cells is extremely challenging due to scarce data on virus-human interactions and fast mutation rates of most viruses. (biomedcentral.com)
- Additionally, we employ an additional objective which aims to maximize the probability of observing human protein-protein interactions. (biomedcentral.com)
- Virus infection involves several types of protein-protein interactions (PPIs) between the virus and its host. (biomedcentral.com)
- In this work, we cast the problem of predicting virus-human protein interactions as a binary classification problem and focus specifically on emerging viruses that has limited experimentally verified interaction data. (biomedcentral.com)
- Binding of a small molecule to the sensor (e.g. glucose or neurotransmitters), interactions of a sensor with another protein (e.g. cellular signal transduction networks), or changes in the physical environment of the sensor such as a strong electrical field (e.g. detection of electrochemical pulses along a neuron) are typical chemical events. (nature.com)
- X-ray structures revealed that in protein conjugates, the carbonyl can be twisted by specific interactions with two or three amino acid side-chains. (nature.com)
- Scientists at the Pacific Northwest National Laboratory in Richland, Wash., have used an established technique to observe real-time interactions between single protein molecules for the first time. (the-scientist.com)
- Proposed by Peter Wolynes at the University of California, San Diego, 2 this theory states that weak interactions between relatively unstructured proteins initiate protein-protein binding. (the-scientist.com)
- rium properties, completely determined by the interactions within crystal structures of 38 nonhomologous proteins, we find that it the system. (lu.se)
- TM84 traps the enzyme-tRNA complex in a novel 'aminoacylation-like' conformation, forming novel interactions with the KMSKS loop and the tRNA 3'-end. (ox.ac.uk)
- Ribosome interactions anchor the Sec61/TRAP complex in a conformation that renders. (lu.se)
- Ribosome interactions anchor the Sec61/TRAP complex in a conformation that renders the ER membrane locally thinner by significantly curving its lumenal leaflet. (lu.se)
- We propose that TRAP stabilizes the ribosome exit tunnel to assist nascent polypeptide insertion through Sec61 and provides a ratcheting mechanism into the ER lumen mediated by direct polypeptide interactions. (lu.se)
- A large difference in internal structure between different DNA conformations for surfactant systems point to the role of hydrophobic interactions. (lu.se)
Crystallography7
- In such structural studies, Beese uses X-ray crystallography, a technique that involves shining X-rays through a crystallized protein and deducing the molecule?s structure from the resulting pattern of diffracted spots. (scienceblog.com)
- To solve protein structures, Olsen's lab uses a powerful technique called X-ray crystallography. (medicalxpress.com)
- At present it offers more information about protein-protein interaction dynamics than can be obtained with conventional structural biology techniques such as nuclear magnetic resonance (NMR) and X-ray crystallography. (the-scientist.com)
- Room-temperature X-ray crystallography provides unique insights into protein conformational heterogeneity, but obtaining sufficiently large protein crystals is a common hurdle. (iucr.org)
- Overall, our results illustrate the promise of serial methods for room-temperature crystallography, as well as future avant-garde crystallography experiments, for PTP1B and other proteins. (iucr.org)
- X-ray crystallography offers detailed insights into protein structure. (iucr.org)
- larger amplitude are sampled and do not converge even in nano- about protein flexibility has come from x-ray crystallography, in the second-length simulations (8, 9). (lu.se)
Tertiary1
- Temperature and denaturant effects on the tertiary conformation of B-casein were significantly different. (usda.gov)
Catalytic3
- discovery that FTase remains in the same basic shape, or conformation, throughout its catalytic process. (scienceblog.com)
- 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)
- Comparison with the structures of four different RT and non-nucleoside inhibitor complexes reveals that only minor domain rearrangements occur, but there is a significant repositioning of a three-stranded beta-sheet in the p66 subunit (containing the catalytic aspartic acid residues 110, 185 and 186) with respect to the rest of the polymerase site. (ox.ac.uk)
Inactive Conformation1
- This suggests that NNIs inhibit RT by locking the polymerase active site in an inactive conformation, reminiscent of the conformation observed in the inactive p51 subunit. (ox.ac.uk)
Structural9
- Due to the lack of structural information of T1r receptors, their functional mechanisms have so far been conjectured from the crystallographic observation on the other class C GPCR members. (nature.com)
- Hydrogen-deuterium exchange studies in conjunction with mass spectrometry indicate that the T182A mutation disrupts the core of the protein, thereby increasing overall structural dynamics. (ncbs.res.in)
- 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)
- Structural and biochemical analysis of a bacterial homolog, ASTBnm, in complex with its native substrate (not bile acids, but a vitamin A precursor, pantoate) show a new binding site that is consistent with classical proposals for elevator-type transport mechanisms. (elifesciences.org)
- 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)
- Consequently, different classes of fluorophores whose response mechanisms directly probe delicate local structural changes could be more generalizable tools to build fluorescent biosensors. (nature.com)
- This review critically focuses on opportunities to employ protein-graphene oxide structures either as nanocomposites or as biocomplexes and highlights the effects of carbonaceous nanostructures on protein conformation and structural stability for applications in tissue engineering and regenerative medicine. (mdpi.com)
- However, the mechanism of formation and the structural and functional properties of aggregates formed from these three peptides are different in such a way that they do not cross-seed each other despite sharing a common amino acid composition. (ibecbarcelona.eu)
- 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)
Globular proteins2
- Contrary to globular proteins, B-casein appears to adopt more compact conformation at elevated temperature, which provides further evidence to support our previous hypothesis of cold denaturation. (usda.gov)
- The results confirm that, as for globular proteins, highly specific polypeptide sequential traits govern the assembly pathway, final fine structure, and cytotoxic properties of amyloid conformations. (ibecbarcelona.eu)
Molecules6
- They plan to continue studying a7 in various cell types and how it interacts with other molecules and proteins. (phys.org)
- Structure of atoms, molecules and chemical bonds. (pathfinderacademy.in)
- While mechanobiological processes employ diverse mechanisms, at their heart are force-induced perturbations in the structure and dynamics of molecules capable of triggering subsequent events. (wustl.edu)
- This review focuses on the bacterial mechanosensitive channels of large (MscL) and small (MscS) conductance and their eukaryotic homologs, with an emphasis on the outstanding issues surrounding the function and mechanism of this fascinating class of molecules. (wustl.edu)
- On aver- comprising some 1015 protein molecules. (lu.se)
- Determining the structure of a target with its ligand is key in guiding the development of new drug molecules. (technologynetworks.com)
Enzyme12
- Glycine decarboxylase, or P-protein, is a pyridoxal 5'-phosphate (PLP)-dependent enzyme in one-carbon metabolism of all organisms, in the glycine and serine catabolism of vertebrates, and in the photorespiratory pathway of oxygenic phototrophs. (nih.gov)
- Together, the structures of these configurations produce the equivalent of a stop-motion animation of the enzyme?s reaction path. (scienceblog.com)
- Thus, pharmaceutical companies including Schering-Plough, Bristol Myers-Squibb and a subsidiary of Johnson & Johnson are now testing drugs that jam FTase to block the function of mutant Ras proteins and other substrates of the enzyme that are important in uncontrolled growth. (scienceblog.com)
- However, those initial structure determinations still did not explain the details of how the enzyme works, said Beese. (scienceblog.com)
- Now, however the new series of FTase structures published in Nature have revealed some startling new details of the enzyme?s action, said Beese. (scienceblog.com)
- For one thing, the scientists realized that the enzyme doesn?t release its product - the Ras protein attached to the farnesyl molecule - until another substrate molecule arrives to bind to FTase. (scienceblog.com)
- At the heart of any fluorescent signal transduction mechanism is the phenomenon of conformational coupling which Jacques Monod referred to as the "secret of life", because it constitutes the molecular basis of most biological processes such as enzyme control, ligand transport across membrane, motor proteins, or cellular signal transduction 3 . (nature.com)
- Nouvelles avancées dans la structure et la régulation de la Protéine Phosphatase 2A : les raisons pour lesquelles PP2A ne doit plus être considérée comme une enzyme passive et non spécifique. (ac.be)
- Les nouvelles avancées sur le sujet, particulièrement sur la structure et la régulation basée sur des modifications post-traductionnelles de PP2A, soulignent bien l'importance de la composition de l'holoenzyme PP2A dans les multiples rôles de cette enzyme majeure. (ac.be)
- 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)
- 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)
- 3 This article will review the recent advances in the structure and regulation of this fascinating enzyme. (ac.be)
Receptors5
- T1rs are class C G-protein coupled receptors (GPCRs), and the extracellular ligand binding domains (LBDs) of T1r1/T1r3 and T1r2/T1r3 heterodimers are responsible for binding of chemical substances eliciting umami or sweet taste. (nature.com)
- UT Southwestern researchers have identified the structure of a key member of a family of proteins called nicotinic acetylcholine receptors in three different shapes. (phys.org)
- Nicotinic acetylcholine receptors are members of a broader super-family of proteins called Cys-loop receptors that function as ion channels on cell surfaces and are found in the membranes of many cell types. (phys.org)
- The team says that these newly identified structures for a7 could eventually be used as a template for pharmaceutical companies to develop new medicines that target this and related nicotinic acetylcholine receptors . (phys.org)
- Cell signaling: Hormones and their receptors, cell surface receptor, signaling through G-protein coupled receptors, signal transduction pathways, second messengers, regulation of signaling pathways, bacterial and plant two-component signaling systems, bacterial chemotaxis and quorum sensing. (pathfinderacademy.in)
Stability3
- These advances establish a third mechanism of chromatin reconfiguration, raising fundamental questions about the stability of nucleosomes in nonreplicative phases of the cell cycle and the cellular machinery responsible for incorporating histone variants into nucleosomes (Mizuguchi, 2004). (sdbonline.org)
- Stability of protein and nucleic acid structures. (pathfinderacademy.in)
- Here, we have characterized the aggregation kinetics, seeding ability, morphology, conformation, stability, and toxicity of amyloid fibrils formed by a 20-residue domain of the islet amyloid polypeptide (IAPP), as well as of a backward and scrambled version of this peptide. (ibecbarcelona.eu)
Chemistry1
- Fluorescent protein biosensors have unlocked major advances in cell biology, neurobiology, clinical chemistry, environmental monitoring, and agricultural technologies 1 . (nature.com)
Kinetic3
- The methodology will include site-directed mutagenesis, covalent protein modifications, patch- clamp measurements, thermodynamic and kinetic analysis of dose-response curves and rates of transitions, videomicroscopy, and molecular modeling. (usda.gov)
- Kinetic data obtained from ensemble FRET measurements suggest that the conformation of refolding intermediate is altered by the GroEL cavity, which leads to a folding pathway that is different from the spontaneous refolding pathway. (uni-muenchen.de)
- Here we show using crystal structure, thermodynamic and kinetic analyses, that this natural antibiotic employs a unique and previously undescribed mechanism to inhibit LeuRS. (ox.ac.uk)
Macromolecular structures at high resolution2
- The two first methods allow obtaining large macromolecular structures at high resolution. (biorxiv.org)
- X-ray diffraction (XRD) and nuclear magnetic resonance (NMR) were the two most widely used techniques for the determination of macromolecular structures at high resolution, but both have limitations relating to particle size, the hydrophobic nature of macromolecules, and the amount of sample available. (technologynetworks.com)
Insights1
- In summary, this study revealed significant novel aspects of the GroEL folding mechanism and provided insights into the basis of rate acceleration of the substrate protein by the chaperonin. (uni-muenchen.de)
Secondary structure4
- The study of hydrogen bond evolution during the course of simulation revealed that the root mean square deviation, radius of gyration and secondary structure formation, all depend significantly on the number hydrogen bonds formed. (mdpi.com)
- During the previous funding period, we have been able to determine the overall structure of MscL, its topology, secondary structure and multimerism, and to evaluate energetic and spatial parameters that characterize conformational transitions in native MscL. (usda.gov)
- We have shown in this work that urea and guanidine hydrochloride (GdmCl) disrupt secondary structure of B-casein through different molecular mechanisms. (usda.gov)
- 2016). Here, we show that ATP enhances this process by modulating secondary structure formation within the translocating protein. (elifesciences.org)
Toxicity1
Molecular mechanisms3
- Biosensor development depends on a deep understanding of molecular mechanisms that transduce the chemical reactions (events) into a fluorescent signal, which can be challenging to establish. (nature.com)
- In the present study, a bioinformatics approach was used to investigate the molecular mechanisms and prognosis of ACC. (cancerindex.org)
- [ 2 ] All dementia share common molecular mechanisms responsible for disease etiology and progression, such as hypoxia and oxidative stress, neuroinflammation, mitochondrial bioenergetics, neurodegeneration, and blood-brain barrier permeability. (medscape.com)
Macromolecules3
- Radiation can disrupt the structure of the DNA (and other macromolecules), thereby disrupting normal cell and organ functions. (cdc.gov)
- 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)
Histone3
- Change in the 3D structure of DNA is enacted via post-translational modifications of the histone proteins at the center of the simplest DNA structure, the nucleosome. (frontiersin.org)
- Histone modifications can lead to either tightly packed and inactive conformations or open and accessible DNA (termed heterochromatin and euchromatin respectively). (frontiersin.org)
- 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)
Ribosome2
Cellular11
- There is a drastic mismatch between the 'functional' phenomenology collected at the organismal and cellular levels and the molecular description of mechanosensory mechanisms. (usda.gov)
- Specialized cell structures called ribosomes are the cellular organelles that actually synthesize the proteins (RNA transcription). (cdc.gov)
- This unfolding is a local phenomena and can also be observed when the substrate is transferred from DnaK/J system (bacterial Hsp70) to GroEL, indicating the possibility of the existence of this conformational heterogeneity in vivo as the protein follows the cellular chaperone pathway. (uni-muenchen.de)
- FTase works as a cellular seamstress, connecting a fatty farnesyl molecule to newly built protein enzymes when they emerge from the cell?s production machinery. (scienceblog.com)
- However, experimental approaches to unravel PPIs are limited by several factors, including the cost and time required, the generation, cultivation and purification of appropriate virus strains, the availability of recombinantly expressed proteins, generation of knock in or overexpression cell lines, availability of antibodies and cellular model systems. (biomedcentral.com)
- It is expected that the enhancement of gene expression efficiency with a shrunken DNA conformation would also be a rather general mechanism in living cellular environments. (nature.com)
- Gene expression in living cells is strictly self-regulated to ensure that the correct amounts of proteins are made at the most appropriate timing and location for maintaining cellular homeostasis. (nature.com)
- To elucidate the complex mechanism of gene regulation in living cellular systems, it is necessary to closely investigate each phase of gene expression and also to shed light on the cooperative effects between transcription and translation. (nature.com)
- Although intracellular signal transduction is often portrayed as a protein kinase 'domino effect', the counterbalancing function of phosphatases, and thus the control of phosphatase activity, is equally relevant to proper regulation of cellular function. (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)
- These proteins have been implicated in a number of cellular processes and linked to a variety of tumors. (diamond.ac.uk)
Transmembrane5
- The class C GPCR structure is characterized by the presence of a large extracellular domain upstream of the hepta-helical transmembrane region, which is commonly found among GPCRs. (nature.com)
- The receptor activation mechanism of the class A GPCR members, consisting solely of the transmembrane region, has been considered to occur via agonist binding, which changes the conformational dynamics of the protein by lowering the transition energy between the different states, and results in the transition towards the active-state conformation 9 . (nature.com)
- The analysis of mutations now allows us to narrow the search for functionally important regions to the short N-terminal helix, two transmembrane domains of the protein, and the loop between them. (usda.gov)
- Following these data, in collaboration with Dr. H. R. Guy (NIH), we built molecular models for the E. coli MscL in the closed, closed-expanded and open conformations and found that the channel can not be gated solely with gate that is placed within the transmembrane domain as was previously proposed (Spencer et al. (usda.gov)
- For the PIV5 fusion protein, the fusion peptide (FP) and the transmembrane domain (TMD) show striking membrane-dependent conformations. (lu.se)
Polypeptide4
- Profiles showing the AMSD variation along the polypeptide chain are states, such as alternative side-chain conformations. (lu.se)
- The specific functional structure of natural proteins is determined by the way in which amino acids are sequentially connected in the polypeptide. (ibecbarcelona.eu)
- The conserved Sec61 protein-conducting channel facilitates polypeptide translocation and coordinates cotranslational polypeptide-processing events. (lu.se)
- In cells, the majority of Sec61 is stably associated with a heterotetrameric membrane protein complex, the translocon-associated protein complex (TRAP), yet the mechanism by which TRAP assists in polypeptide translocation remains unknown. (lu.se)
Gene11
- The protein encoded by this gene belongs to the family of Na+/K+ and H+/K+ ATPases beta chain proteins, and to the subfamily of Na+/K+ -ATPases. (wikipedia.org)
- ATP1B3+protein,+human at the U.S. National Library of Medicine Medical Subject Headings (MeSH) Human ATP1B3 genome location and ATP1B3 gene details page in the UCSC Genome Browser. (wikipedia.org)
- The novel innovation and significance resides within its potential to provide (1) an expanded understanding of the mechanism through which a maternal high fat diet reprograms primate gene expression and (2) a simple intervention (essential nutrient supplementation with neither diet nor behavioral modification) with tremendous potential impact given the current obesity epidemic and the lack of efficacious therapeutics. (nih.gov)
- High density arrays of extraordinarily sensitive integrated microring resonators will allow many gene and protein signatures to be simultaneously quantitated from a single patient sample. (nih.gov)
- GENE-PRODUCT P185 research-areas: Biochemistry & Molecular Biology web-of-science-categories: Biochemistry & Molecular Biology number-of-cited-references: 169 times-cited: 41 usage-count-last-180-days: 0 usage-count-since-2013: 9 journal-iso: Adv.Protein Chem. (icr.ac.uk)
- AFM observation of the DNA conformation indicates that longer DNA takes shrunken conformation with a higher segment density in the reaction mixture for gene expression, in contrast to the stiff conformation of shorter DNA. (nature.com)
- We propose an underlying mechanism for the favorable effect of longer DNA on gene expression in terms of the enhancement of access of RNA polymerase to the shrunken conformation. (nature.com)
- Due to the complexity of gene regulation, unveiling the complete mechanism of gene regulation has been a long-standing quest. (nature.com)
- The expression level from luc 25.7k is 1000-times higher than that with luc 1.7k, indicating that the protein yield per target gene is increased by 1000-times of magnitude for a longer template, luc 25.7k (Fig. 1 d). (nature.com)
- What does this gene/protein do? (cancerindex.org)
- 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)
Kinases2
- 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)
- The human genome encodes two active Vaccinia-related protein kinases (VRK), VRK1 and VRK2. (diamond.ac.uk)
Inhibitors4
- A research team at the Medical University of South Carolina (MUSC) has discovered a new mechanism for a class of anti-cancer drugs known as E1 inhibitors. (medicalxpress.com)
- In the article, Olsen and his team report that they have discovered a new site on a protein, SUMO E1, which is a target for E1 inhibitors. (medicalxpress.com)
- Their next step is to use the information from the 3-D structure to design more specific and efficient inhibitors with strong antitumor properties. (medicalxpress.com)
- Mechanism of inhibition of HIV-1 reverse transcriptase by non-nucleoside inhibitors. (ox.ac.uk)
Residues6
- Variants produced by substitution of Cys(972) and Cys(353) by Ser using site-directed mutagenesis have distinctly lower specific activities, supporting the crucial role of these highly conserved redox-sensitive amino acid residues for P-protein activity. (nih.gov)
- The pairs of residues on S1 and S2 predicted to be proximal in either closed or open conformations were mutated to Cys, and the effects of coupling were tested with patch-clamp and biochemically using Western blots. (usda.gov)
- 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)
- We also determined the crystal structures of several mutants of BmK M1, a representative scorpion alpha-like toxin that contains an identical non-proline cis peptide bond as that observed in BmK M7, in which residues within or neighboring the cis peptide bond were altered. (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)
- Thiol-reactive Prodan derivatives (top left) can be site-specifically coupled to proteins via cysteine residues. (nature.com)
Target proteins2
- The result is a 3-D model that allows them to visualize the interaction of potential drug compounds with target proteins (see accompanying video). (medicalxpress.com)
- Whereas most fluorescent labels require genetic modification of target proteins, I-SO attaches covalently to the protein of interest and changes its fluorescence during a binding event. (the-scientist.com)
Poorly understood3
- The mechanisms of cryoprecipitation are poorly understood, but several factors have been investigated. (medscape.com)
- Furthermore, the underlying molecular mechanism of carcinogenesis is poorly understood, and prognostic prediction of ACC has low accuracy. (cancerindex.org)
- How proteins mediate this curvature generation is a fundamental question that is still poorly understood. (lu.se)
Mass spectrometry1
- 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)
Solubility1
- The solubility of cryoglobulins has been found to be partially related to the structure of component immunoglobulin heavy and light chains. (medscape.com)
Physiological2
- We hypothesize that B-casein exists as a largely but not entirely disordered conformation under physiological conditions (25oC and neutral pH). (usda.gov)
- 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)
Signal transduction1
- In the accompanying article 2 , we have uncovered a subtle, but powerful, fluorescent signal transduction mechanism (Figure 1) that we anticipate will enable development of new fluorescent biosensors. (nature.com)
Physiologically relevant1
- Here, we report cryo-EM structures of multiple physiologically relevant states of lipid bilayer-embedded human MRP4, including complexes between MRP4 and two widely used chemotherapeutic agents and a complex between MRP4 and its native substrate. (rcsb.org)
Solvent1
- Evidence that the folding pathway inside the cage differs from that of spontaneous folding was obtained by observing the effect of external perturbations (e.g. mutations in substrate protein and use of different solvent conditions) on the rate of spontaneous and GroEL assisted folding reactions. (uni-muenchen.de)
Dynamics3
- This study demonstrated that it is necessary to gain insight into protein dynamics under external electric field stress, in order to develop the novel food processing techniques that can be potentially used to reduce or eradicate food allergens. (mdpi.com)
- We have brilliant colleagues who are in the forefront of their respective research and focused on an understanding of protein structure and dynamics, and how we might understand how life actually works by probing these things at an intimate level of detail. (nih.gov)
- Protein conformation fluctuation dynamics is a stochastic process," says lead investigator H. Peter Lu, a staff scientist at PNNL. (the-scientist.com)
Denaturant1
- One of the two populations is as compact as the native state, whereas the other is as extended as the unfolded protein in denaturant. (uni-muenchen.de)
Chaperones1
- Molecular chaperones assist the folding of newly synthesized and denatured proteins in acquiring their native state in the crowded intracellular environment. (uni-muenchen.de)
Biological functions3
- Significance Statement Proteins perform their biological functions by changing their shapes and interacting with each other. (biorxiv.org)
- The unique biological functions of milk proteins arise directly from their three-dimensional shape, which in turn determines the properties of products made from them. (usda.gov)
- proteins could carry out their biological functions. (lu.se)
Pathway3
- The observation that fully folded T182A moPrP has a MG-like structure, and that it misfolds to oligomers much faster than does wt moPrP, suggests that a MG-like intermediate, whose structure resembles that of fully folded T182A moPrP, might be populated early on the pathway of misfolding of wt moPrP to oligomers. (ncbs.res.in)
- These results describe a novel pathway for regulating transcription using variant histones to modulate chromatin structure (Santisteban, 2000). (sdbonline.org)
- Protein translocation across the endoplasmic reticulum (ER) membrane is an essential step during protein entry into the secretory pathway. (lu.se)
Pathogenesis2
- Understanding the interaction patterns between a particular virus and human proteins plays a crucial role in unveiling the underlying mechanism of viral infection and pathogenesis. (biomedcentral.com)
- Methylene diphenyl diisocyanate (MDI) is among the leading chemical causes of occupational asthma world-wide, however, the mechanisms of disease pathogenesis remain unclear. (cdc.gov)
Fluorescent4
- Fluorescent labeling of proteins by fluorophore Prodan is a useful tool to measure protein conformational changes via color switching, however, structure-based rules that predict where to emplace fluorophores that elicit robust fluorescent responses are challenging to establish. (nature.com)
- A conformationally sensitive fluorescent color-switching mechanism. (nature.com)
- Accordingly, fluorescent biosensors are created by coupling distinct protein conformations to changes in the electronic structure of a fluorophore, or pairs of fluorophores that have been engineered into the protein. (nature.com)
- Many fluorescent biosensors exploit conformation-dependent changes in the fluorescence resonance energy transfer (FRET) between two engineered fluorophores that emit at two different colors (wavelength ranges). (nature.com)
Ligand4
- Rhodopsin consists of a protein (rod opsin) and a chromophore ligand (11- cis -retinal) and initiates phototransduction in a specialized organelle called the rod outer segment (OS). (jneurosci.org)
- In conformational coupling, ligand binding or perturbations of the physical environment are associated with changes in the distribution of protein conformational states. (nature.com)
- The results from our computational analysis demonstrated that the drug-likeness, ADMET, and protein-ligand binding affinity of dasatinib are verified successfully. (bvsalud.org)
- 1 In general, a resolution of 3Å or better is required to determine the binding mode of a fragment-sized ligand structure, and such resolution can be routinely achieved using cryo-EM. (technologynetworks.com)
Heterogeneity1
- With Sp-FRET coupled to PIE (Pulsed Interleaved Excitation), we have been able to explore the heterogeneity of the GroEL bound substrate protein and observed a bimodal conformational distribution. (uni-muenchen.de)
Helices3
- 3) when the S1 bundle breaks apart leading to the fully open conformation, S1 helices may dock to a specific site on the inner surface of the pore. (usda.gov)
- The BASS family is characterised by two helices that cross-over in the centre of the protein in an arrangement that is intricately held together by two sodium ions. (elifesciences.org)
- Comparison of structures in the presence and absence of pantoate demonstrates that pantoate elicits a conformational change in one of the cross-over helices. (elifesciences.org)
Substrate6
- how is it that GroEL is able to accelerate the rate of folding of certain proteins, and how do the conformational properties of the substrate change as it undergoes repeated cycling. (uni-muenchen.de)
- By using ensemble FRET and Sp-FRET (Single Pair-Fluorescence Resonance Energy Transfer), we have probed the conformation of the model substrate DM-MBP (Double Mutant Maltose Binding Protein) during different stages of the functional cycle of GroEL. (uni-muenchen.de)
- Anisotropy measurements, probing the freedom of motion of different regions of the GroEL bound protein, revealed that there is a segmental release of the substrate protein from the GroEL surface upon binding of ATP and GroES. (uni-muenchen.de)
- These transporters, many of which are sodium-coupled, have been shown to use an elevator mechanism of transport, but exactly how substrate binding is coupled to sodium ion binding and transport is not clear. (elifesciences.org)
- Here, we solve the crystal structure at 2.3 Å of a transporter from Neisseria meningitidis (ASBT NM ) in complex with pantoate, a potential substrate of ASBT NM . (elifesciences.org)
- The manuscript represents an important contribution to an ongoing discussion about the substrate binding site and mechanism of the Bile Acid Sodium Symporter (BASS) family of transporters. (elifesciences.org)
Biologically2
- To become biologically active, most proteins need to fold into precise three dimensional structures. (uni-muenchen.de)
- Additionally, as there are no upper size limits for samples, complete, functional molecular machines can be imaged in 3D, including one or several ligands, revealing biologically relevant mechanisms. (technologynetworks.com)
Prion protein3
- The pathogenic mutation T182A converts the prion protein into a molten globule-like conformation whose misfolding to oligomers but not to fibrils is drastically accelerated. (ncbs.res.in)
- Delineation of the effects of pathogenic mutations linked with familial prion diseases, on the structure and misfolding of prion protein (PrP), will be useful in understanding the molecular mechanism of PrP misfolding. (ncbs.res.in)
- Here, it has been shown that the pathogenic mutation T182A causes a drastic reduction in the apparent cooperativity and enthalpy of unfolding of the mouse prion protein (moPrP) under misfolding-prone conditions by converting the protein into a molten globule (MG)-like conformation. (ncbs.res.in)
Neurofibrillary Tangles1
- AD is characterized diagnostically by two histologic findings: (1) extracellular amorphus eosinophilic deposits of amyloid consisting of Aβ peptides (a cleavage product of amyloid precursor protein [APP]), which are referred to as amyloid plaques, and (2) intraneuronal aggregates of abnormally modified microtubule-associated protein tau (neurofibrillary tangles) (see the image below). (medscape.com)
Adopt1
- We demonstrated this effect in glucose-binding proteins that adopt distinct conformations in response to glucose. (nature.com)
Adopts2
- 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 piperidine ring adopts a chair conformation. (who.int)
Contrast2
- In contrast, variants in the active conformation accumulated in the ER and caused RD even in the absence of light. (jneurosci.org)
- By contrast, in our SSX structure the active site is best fitted with a single conformation, but the distal allosteric site is best fitted with alternate conformations. (iucr.org)
Tyrosine2
- 4 While proteins can be phosphorylated on nine amino acids, serine, threonine and tyrosine phosphorylation are by far the most predominant in eukaryotic cells. (ac.be)
- Here, a recently introduced serial sample-support chip system has been used to obtain the first SSX structure of a human phosphatase, specifically protein tyrosine phosphatase 1B (PTP1B) in the unliganded (apo) state. (iucr.org)
Transition1
- 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)
Crystal structures1
- 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)
Modulate1
- Together, the data define a non-enzymatic, thiol-mediated transcarbamoylating mechanism by which GSH may promote immune responses to MDI exposure, and identify specific factors that might further modulate this process. (cdc.gov)
Amyloid2
- The tight sequence/structure relationship governing protein folding does not seem to apply to amyloid fibril formation because many proteins without any sequence relationship have been shown to assemble into very similar β-sheet-enriched structures. (ibecbarcelona.eu)
- Amyloid angiopathy can be identified using stains for amyloidal protein (Congo red, thioflavin-S), or immunohistochemical staining against Aβ (see the image below). (medscape.com)
Mutations2
- 100 identified RP-causing mutations will increase our understanding of rhodopsin structure and function and facilitate development of therapeutic strategies. (jneurosci.org)
- Scope includes mutations and abnormal protein expression. (cancerindex.org)
Sequence3
- Here we show that all of the soluble oligomers tested display a common conformation-dependent structure that is unique to soluble oligomers regardless of sequence. (nih.gov)
- Based on the amino acid sequence and the structure of other ABC transporters, the scientist compiled a model of the structure, but this could not explain the way that OpuA functioned. (rug.nl)
- Finally, the signal sequence is cleaved and the pre-protein is either folded or trafficked onwards. (elifesciences.org)
Atoms2
- We model a protein as a network of atoms connected by springs and deform it along the least-energy directions. (biorxiv.org)
- Hemocyanins typically have high molecular weights and are made of several individual subunit proteins, with each subunit containing two copper atoms and able to bind one oxygen molecule (O 2 ). (newworldencyclopedia.org)
Membranes5
- These proteins harness the sodium ion gradient to transport bile acids across the plasma membranes of enterocytes of the terminal ileum and hepatocytes, respectively. (elifesciences.org)
- Membrane structure and function: Structure of model membrane, lipid bilayer and membrane protein diffusion, osmosis, ion channels, active transport, ion pumps, mechanism of sorting and regulation of intracellular transport, electrical properties of membranes. (pathfinderacademy.in)
- 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)
- 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)
Fundamental2
- This work may thus contribute to advance our fundamental knowledge of the chaperonin system and the basic mechanism of protein folding. (uni-muenchen.de)
- Thus, the accurate description of macromolecular conformational transitions is crucial for understanding fundamental mechanisms of life's machinery. (biorxiv.org)
Temperature3
- At elevated temperature (above 37oC), however, B-casein is likely to assume more compact conformation, leading to self-association and eventually the formation of micelles with other caseins. (usda.gov)
- A large number of single proteins were scanned in an electron microscope at a very low temperature, after which all the images were combined to provide a direct view of the structure. (rug.nl)
- In previous apo room-temperature structures, the active site and allosteric sites adopted alternate conformations, including open and closed conformations of the active-site WPD loop and of a distal allosteric site. (iucr.org)
Transporters4
- These results have implications, not only for ASBT NM but for the BASS family as a whole and indeed other transporters that work through the elevator mechanism. (elifesciences.org)
- The protein belongs to the well-known family of ABC transporters, but it has a unique structure and working mechanism. (rug.nl)
- OpuA belongs to a well-known class of proteins called ABC (ATP-binding cassette) transporters. (rug.nl)
- 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)
Molecule1
- Inheritance of some variant alleles causes a change in conformation of the alpha-1 antitrypsin molecule, leading to polymerization and retention within hepatocytes. (msdmanuals.com)
Regulation2
- In agreement with this, recent findings on the structure and post-translational modifications of PP2A emphasize the importance of PP2A holoenzyme composition in its regulation and pleiotropic activities. (ac.be)
- Intrinsically disordered regions (IDRs) lacking a fixed three-dimensional protein structure are widespread and play a central role in cell regulation. (iucr.org)