Experimental protein conformation. Medical search. Frequent questions

The pathogenic form of Clinical manifestations of CWD include weight loss this protein appears to be devoid of nucleic acids and sup- over weeks or months, behavioral changes, excessive sali- ports its own amplification in the host. (cdc.gov)
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)
The AlphaFold method is not designed to predict structures for complexes of protein with other proteins, nucleic acids or small molecule ligands. (febs.org)

Intrinsically disordered regions (IDRs) lacking a fixed three-dimensional protein structure are widespread and play a central role in cell regulation. (iucr.org)
We have recently improved all-atom simulation models to work with both folded and intrinsically disordered proteins," wrote Zheng. (asu.edu)
I will present my recent progress on the formation of membrane-less organelles through liquid-liquid phase separation of intrinsically disordered proteins, and my future plans for this work. (asu.edu)
Zheng is currently working on modeling intrinsically disordered proteins, including force field development, experimental data interpretation and liquid droplet formation. (asu.edu)
Before entering the intrinsically disordered protein field, he focused on understanding protein folding mechanisms by developing advanced sampling and reaction coordinate methods. (asu.edu)
The most extreme examples of this kind of behavior are provided by intrinsically disordered proteins (IDPs) that adopt a plethora of diverse conformations in their free state but, at least some of them, might become fully or partially well ordered upon partner molecule binding [ 8 , 9 ]. (biomedcentral.com)
eLife , 2016) implied that the N-terminus of the magnesium transporter A (MgtA) protein (from hereon called Keif) is intrinsically disordered, but the advantage of this disordered feature to the function of the protein is still unknown. (lu.se)

An intramolecular click reaction results in the formation of a photoswitchable bridge, which can be used for controlling conformational domains in peptides and proteins. (beilstein-journals.org)
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 influence of three sodium salts, covering a wide range of the Hofmeister series, on the conformation of three proline-based peptide models in aqueous solution is examined using a combination of nuclear magnetic resonance spectroscopy and molecular dynamics simulations. (uni-koeln.de)
Describe protein folds in terms of secondary structural elements and the restrictions on peptide structure imposed by the planarity of the peptide bond. (manchester.ac.uk)
On comparing i,i+4 and i,i+7 spacings of PSCaa and cysteine in a model peptide without a preferred conformation, it was seen that the thiol-ene click reaction takes place efficiently in both cases. (beilstein-journals.org)
In contrast to common bivalent thiol reactive azobenzene switches [1-5] , the PSCaa described here ( Scheme 1 ) is an α-amino acid containing, besides an azobenzene unit, a vinyl function that can react specifically with a cysteine within a putative conformational domain of a peptide or a protein by light-induced thiol-ene click reaction [6-9] . (beilstein-journals.org)
From such experiments, important constraints on the protein or peptide conformation can be derived. (huji.ac.il)
Some of you may be annoyed by the fact I call Abeta a protein, and yes, indeed, it is a peptide, but let's just simplify it, calling it a protein for now. (lu.se)
Thus, in this study, the structure of the Keif peptide part have been investigated by using both atomisic molecular dynamics (MD) and coarse-grained Monte Carlo (MC) simulations, as well as different experimental techniques such as circular dichroism (CD, ongoing) and small-angle X-ray scattering (SAXS). (lu.se)

In vivo, large RNAs rely on proteins to fold to their native conformation. (nih.gov)
Shortly after SARS-CoV emerged at the turn of the 21st century, the spike (S) protein (particularly in its native conformation) was identified as the immunodominant antigen of the virus3. (who.int)

The backbone conformation has been experimentally recognized as responsible for the early-stage structural forms of a polypeptide. (medscimonit.com)
MATERIAL/METHODS: The polypeptide chains of all the proteins in the Protein Data Bank were transformed into their early-stage structural forms. (medscimonit.com)
Basic knowledge of protein structure: polypeptide conformation. (lu.se)
[13] [14] Because proteins share a common structural feature known as the polypeptide backbone, all proteins have the potential to misfold under some circumstances. (wikipedia.org)

3) Protein interactions and enzyme characterization. (manchester.ac.uk)
The acquired knowledge will lead to a better understanding of protein-surface interactions and will set directions for biosensor optimizations. (tue.nl)
Stability, dynamics and interactions of proteins: packing and electrostatics. (lu.se)
Over the past several years, we have engineered a range of proteins with new functions, including protein-protein interactions that are specific enough to control complex biological processes in mammalian cells (Kapp*, Liu* et al. (ucsf.edu)
Computed values for the 12 E9 DNase alanine mutants showed reasonable agreement with experimental DeltaDeltaG data, particularly for interactions not mediated by interfacial water molecules. (ox.ac.uk)
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)
Functional interactions perturb this state by shifting the equilibrium towards 'active conformations' that are present but are low-populated in the apo state. (biomedcentral.com)
Future work in this study might also include investigation of the surface and membrane interactions, as well as analysis of the protein dynamics. (lu.se)

Proteins are dynamic entities that undergo many structural transitions and fluctuations, which are essential to their biological functions. (europa.eu)
Hybrid methods that combine computational biophysics with experimental structural biology have proved successful in describing protein conformation, namely their 3D shape. (europa.eu)
This is now becoming possible through the use of hybrid methods, which combine computational biophysics with experimental structural biology and overcome the limitations of either approach alone. (europa.eu)
Analyze and manipulate structural data (including the use of the Protein Data Bank in Europe). (manchester.ac.uk)
Since the 1970s, the structural biology community has archived experimental protein structures in the Protein Data Bank ( PDB ), a freely available global resource that now contains over 180,000 structures. (febs.org)
Predicting and designing the structures of proteins with biologically useful accuracy has been a key challenge in computational structural biology and molecular engineering. (ucsf.edu)
[15] However, only a relatively small number of proteins are linked to proteopathic disorders, possibly due to structural idiosyncrasies of the vulnerable proteins. (wikipedia.org)
Protein structural biology. (embl.org)
Since the early 1970s, the structural biology community has archived its experimental structures in the PDB, a freely available global resource that now contains over 180,000 structures. (embl.org)
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)
In conjunction with the recognition of the functional role of internal dynamics of proteins at various timescales, there is an emerging use of dynamic structural ensembles instead of individual conformers. (biomedcentral.com)
We constructed the web application CoNSEnsX (Consistency of NMR-derived Structural Ensembles with eXperimental data) allowing fast, simple and convenient assessment of the correspondence of the ensemble as a whole with diverse independent NMR parameters available. (biomedcentral.com)

[10] Furthermore, evidence has emerged that small, non-fibrillar protein aggregates known as oligomers are toxic to the cells of an affected organ, and that amyloidogenic proteins in their fibrillar form may be relatively benign. (wikipedia.org)

You will learn how proteins are produced, how they fold into their secondary and tertiary structures and how they interact with each other. (manchester.ac.uk)
We are also predicting protein structures by simulating folding pathways, taking advantage of our experimental results and an approach that dynamically integrates local and global information. (openwetware.org)
The course aims to provide a deeper understanding of some of the most important experimental methods used to determine the three-dimensional structures of proteins, as a basis for understanding their biological functions. (lu.se)
The AlphaFold system builds on this huge body of experimental information and generates its predictions by analysing the relationship between these known protein structures and huge amounts of protein-sequence data. (febs.org)
Many proteins function as complexes, hence the predicted structures available in the database may not necessarily provide insights into the function of the protein. (febs.org)
It was subsequently realised that proteins (or domains) with similar amino-acid sequences have similar overall 3D structures, and that the degree of this similarity (measured by the root-mean-square distance, or RMSD, between corresponding atoms in the two models) is correlated with the degree of sequence similarity. (embl.org)
In November 2020, more than 60 years after the first protein structures were determined experimentally, AlphaFold was recognised as the best-performing method for predicting 3D protein structure by the assessors of the 14th round of the biennial CASP experiment. (embl.org)
Thus, the AlphaFold predictions were consistently very similar to the experimentally determined structures of the proteins included in this round of CASP. (embl.org)
When DeepMind decided to predict the structures of a huge number of proteins and started to think about how to disseminate the 3D models freely and openly, an obvious partner to collaborate with was the European Bioinformatics Institute, EMBL-EBI, the European home of many biological data resources used by the AlphaFold team, including PDBe and UniProt. (embl.org)
Crystal structures often deviate from the natural system: Proteins, especially membrane-bound ones, do not necessarily crystallize in their biologically active structures and the measures needed to obtain suitable GPCR crystals tend to increase the diversity between the natural environment and the crystal. (gauss-centre.eu)
Protein NMR is the method of choice for determining protein structures at the atomic level in solution. (biomedcentral.com)
It should be kept in mind that all representations of protein structures are actually models of the 'real' ones and thus can have different types of errors. (biomedcentral.com)
The general aim of the course is to enable students to acquire an advanced understanding of proteins with an emphasis on their three-dimensional structures, the connection of structures to biological function and how these structures are produced. (lu.se)
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)

It's computationally generated to mimic bioactive conformation (which can be found in a protein-ligand co-complex). (nih.gov)
Includes protein crystallization, data collection at MAX IV, data processing, structure determination and modelling, as well as a simple exercise in ligand docking. (lu.se)
Ligand binding to G protein-coupled receptors (GPCRs) is thought to induce changes in receptor conformation that translate into activation of downstream effectors. (pasteur.fr)
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)
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)

By contrast, only 11% of human proteins have had their structure determined experimentally. (febs.org)
This means that for every known sequence in the UniProt data resource there will be either an experimentally determined structure (in the Protein Data Bank, PDB), or a predicted structure in AlphaFold DB, or the structure can be readily modeled using traditional structure-prediction techniques based on models for similar sequences in PDB or AlphaFold DB. (embl.org)

For example, solution NMR is limited to protein size, whereas SAS can be used for small molecules as well as for large multi-molecular assemblies. (wikipedia.org)
To provide core knowledge of the form, function and role of protein molecules in biological processes and further enable an understanding of biological phenomena at the molecular level. (manchester.ac.uk)
The over-all goal of my research program is to understand how complex biological molecules adopt their functional, 3-dimensional conformations: The Protein and RNA Folding Problem. (openwetware.org)
AlphaFold models do not include any non-protein components such as cofactors, metals, ligands including drug-like molecules, ions, carbohydrates and other post-translational modifications. (febs.org)
Large scale screening of therapeutic molecules and antibodies are underway aiming to target the spike protein and consequently prevent infection. (biorxiv.org)
For example, proteins that are normally unfolded or relatively unstable as monomers (that is, as single, unbound protein molecules) are more likely to misfold into an abnormal conformation. (wikipedia.org)

Select appropriate experimental techniques for protein purification and characterization (conformation and stability), and describe the relative precision of various approaches and the assumptions implied by each method. (manchester.ac.uk)

There is considerable use of graphs and underlying theory in the description of properties of proteins and how these are studied. (manchester.ac.uk)
The course covers both the principles that determine the properties of proteins and the experimental methods that are used to study these properties in modern molecular protein science. (lu.se)

As a result, AlphaFold is able to produce near experimental-quality structure predictions for a wide range of proteins. (febs.org)

In addition to continuing the experimental protein and RNA folding studies, new research areas in the Sosnick lab involve the rational design of proteins and RNAs to control their structure and function, and the expansion of the computational component. (openwetware.org)
I. Develop computational methods for modeling & design of proteins, in the program Rosetta ( www.rosettacommons.org ). (ucsf.edu)

In the interaction with proteins, lead binds with virtually every available functional group, including sulfhydryl, amine, phosphate, and carboxyl groups, with sulfhydryl having the highest affinity. (cdc.gov)

Experimental results are compared with molecular dynamics simulations. (tue.nl)
Analysis of virulence related gene expression and computational simulations of pivotal proteins involved in pathogenesis demonstrate that myricetin downregulates the saeR global regulator and interacts with sortase A and α-hemolysin. (nature.com)
Understanding this motion has been a long-standing goal of experimental techniques, such as nuclear magnetic resonance (NMR), and, in the last decades, molecular simulations. (lu.se)
Simulations offer excellent temporal and spatial resolution, but suffer from the use of an approximate energy model (force field) and from the practically obtainable simulation lengths often being insufficient for sampling all relevant conformations. (lu.se)
Molecular simulations can potentially fill this gap, but have not been applicable to disordered proteins due to shortcomings of the energy function used. (asu.edu)
However, it was quickly discovered through both simulations and experiments that Keif in fact adopts extended conformations instead. (lu.se)

Their unique hourglass-shaped architecture is highly conserved among different bacterial membrane proteins and other biological channels. (ibecbarcelona.eu)
G-protein coupled receptors (GPCRs) are membrane proteins that transmit the effects of extracellular ligands to effect changes in the intracellular G-protein signaling system. (gauss-centre.eu)

Protein secondary and three- dimensional structure. (lu.se)
2016). Here, we show that ATP enhances this process by modulating secondary structure formation within the translocating protein. (elifesciences.org)

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)

Myricetin affects both surface proteins and secreted proteins which indicate that its action is unrelated to inhibition of the agr quorum sensing system. (nature.com)
These findings provide insight into the molecular basis for human antibody recognition of paramyxovirus surface proteins and the mechanisms of SOSV neutralization. (cdc.gov)

Majority of both experimental 11 - 14 and computational 15 - 17 efforts for inhibitor design are focused on the receptor binding domain (RBD) despite the fact that this region is highly mutation prone. (biorxiv.org)
The Abeta plaques are a pathological hallmark of Alzheimer's disease, Abeta is the first biomarker that is altered, heritable forms of Alzheimer's rely on mutations in the Abeta protein* or enzymes involved in its production, and a mutation that reduces Abeta production protects against AD. (lu.se)

, 2020. Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody. (invivogen.com)

In 21st International Symposium on Experimental Algorithms (SEA 2023). (dagstuhl.de)

abstract = "The performance of protein biosensors is strongly determined by the conformation of proteins immobilized on the sensor surface. (tue.nl)
abstract = "We report on an anomalous X-ray reflectivity study to locate a labelled residue of a membrane protein with respect to the lipid bilayer. (huji.ac.il)

Could you provide insights into the experimental approaches used to explore the functional effects of IL18RAP isoforms and their specific contributions to IL18 signaling? (creativebiomart.net)
Mass spectrometry, mutagenesis, and functional assays investigate the impact of post-translational modifications on IL18RAP's conformation and function. (creativebiomart.net)
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)
We isolated six mAbs recognizing the functional attachment protein hemagglutinin-neuraminidase (HN) and 18 mAbs against the fusion (F) protein. (cdc.gov)

1 , 2 Largely expressed on the surface of SARS-CoV-2, the spike (S) protein plays a crucial role in binding to the host angiotensin-converting enzyme 2 (ACE2) through the receptor-binding domain (RBD) and facilitating viral entry, 3 , 4 which is therefore considered as one of the most preferred targets against SARS-CoV-2. (biorxiv.org)
Our predictions generate hypotheses on protein conformations controlling biological processes - such as protein recognition, signal transduction, and enzyme active site gating - and are laying the foundation for our work reengineering and "reshaping" protein interfaces and active sites for new functions. (ucsf.edu)

The aggregation of the protein Amyloid-beta (Abeta) into plaques outside the nerve cells has been recognized in patients with Alzheimer's disease since 1905. (lu.se)

Beyond aiding in the prediction of structure from sequence, the relevance of folding studies is underscored by the involvement of misfolded conformers in a variety of human diseases and the role of "natively-unfolded" proteins in regulation, recognition, and binding. (openwetware.org)
Experimental and computational analyses of the energetic basis for dual recognition of immunity proteins by colicin endonucleases. (ox.ac.uk)
Im proteins are broadly cross-reactive yet specific inhibitors binding cognate and non-cognate DNases with K(d) values that vary between 10(-4) and 10(-14) M, characteristics that are explained by a 'dual-recognition' mechanism. (ox.ac.uk)
In this work, we addressed for the first time the energetics of Im protein recognition by colicin DNases through a combination of E9 DNase alanine scanning and double-mutant cycles (DMCs) coupled with kinetic and calorimetric analyses of cognate Im9 and non-cognate Im2 binding, as well as computational analysis of alanine scanning and DMC data. (ox.ac.uk)

We analyzed substitutions in the arginine cage DRY motif and in the conserved asparagine N(3.35)119, which are pivotal molecular switches for receptor conformation and activation. (pasteur.fr)

The interconversion between protein conformations, occurring at multiple timescales, is fundamental for the biological function of proteins. (lu.se)

ed glycoprotein, the prion protein. (cdc.gov)
mutations of the prion protein gene (3). (cdc.gov)

The 90 KDa heat shock protein (Hsp90) is a highly conserved molecular chaperone crucially involved in maintaining cellular homoeostasis in organisms from most kingdoms of life with the exception of archea 1 . (nature.com)

The protein must then fold during or after the translocation process. (elifesciences.org)

Hsp90's diverse array of clientele implicate the chaperone in several associated biological functions and place it at the intersection of various fundamental cellular pathways, where it acts as a central hub in maintaining numerous protein interaction networks 1 . (nature.com)
By building new functions through a combination of computational design and experimental engineering, I also hope to learn how molecular design principles shape systems-level properties of biological functions. (ucsf.edu)

We, therefore, need continuous descriptions of protein conformational space in the form of energy landscapes in order to properly understand their mechanisms of action. (europa.eu)
Here we present the available experimental evidence to distinguish between those mechanisms and discuss the possible interpretations. (nih.gov)
These mechanisms include the ability of lead to inhibit or mimic the action of calcium and to interact with proteins. (cdc.gov)

Different conformations of active receptors were detected (for wild-type CXCR4, D133N, and N119S), suggesting that different receptor conformations are able to trigger G(alpha)(i) activity. (pasteur.fr)
Infection of human cells by the novel coronavirus (SARS-Cov-2) involves the attachment of the receptor binding domain (RBD) of the spike protein to the peripheral membrane ACE2 receptors. (biorxiv.org)

Nevertheless, even the conformational heterogeneity of globular proteins due to their internal dynamics requires the use of such representations. (biomedcentral.com)

In this proposal, we present a new hybrid methodology that leverages recent innovations in cryo-electron microscopy image analysis to examine continuous dynamics and free energy landscapes of large, multi-domain proteins, which are not achievable with existing methods. (europa.eu)
We also aim at an understanding of the forces that underpin the three-dimensional structure of proteins, as well as a basic understanding of the methods used in structure-based drug design. (lu.se)
demonstrate basic knowledge of how nuclear magnetic resonance (NMR), neutron diffraction and small-angle X-ray and neutron scattering can be used to produce specific information in addition to X-ray crystallography · assimilate and critically evaluate the scientific literature dealing with protein structure and function, particularly in terms of the experimental methods. (lu.se)
Training in the relevant theoretical and experimental methods described for the study of protein structure and dynamics. (lu.se)
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)
What experimental methods are commonly employed to study the expression patterns and regulation of IL18RAP across different cell types and conditions? (creativebiomart.net)
What experimental methods are used to elucidate the effects of post-translational modifications, such as glycosylation, on IL18RAP's structure and function? (creativebiomart.net)
For example, the two most commonly used experimental methods, Förster resonance energy transfer (FRET) and small-angle X-ray scattering (SAXS), have yielded qualitatively different results for the effect of chemical denaturants on unfolded proteins. (asu.edu)
Basic exercises using other experimental methods A number of exercises are carried out as demonstrations. (lu.se)

The anti-HN mAbs all target the globular head of the HN protein and can be organized into 4 competition-binding groups that exhibit epitope diversity. (cdc.gov)

A tabular approach to the sequence-to-structure relation in proteins (tetrapeptide representation) for de novo protein design. (medscimonit.com)
The sequence-to-structure and structure-to-sequence relation is critical for predicting protein structure. (medscimonit.com)
Finally, the signal sequence is cleaved and the pre-protein is either folded or trafficked onwards. (elifesciences.org)
Sameer Velankar and Gerard Kleywegt, from the Protein Data Bank in Europe, and Alex Bateman, Head of Protein Sequence Resources, all at EMBL's European Bioinformatics Institute (EMBL-EBI), explore the research avenues opened up by the AlphaFold database and explain the method's limitations. (febs.org)
The protein folding problem was first introduced in 1968 and referred to the challenge to predict the 3D structure of a protein based solely on its sequence of amino acids. (febs.org)
This protein-sequence information has also been generated by scientists all over the world, mainly through genome sequencing, and is made available through public resources, such as UniProt and MGnify hosted at EMBL-EBI. (febs.org)
90% sequence identity to the protein of interest. (febs.org)
This development represents a step-change for molecular biology - for the first time in history, for almost every protein of known sequence, a high-quality 3D model will be readily available. (embl.org)

A new inhibited conformation of the KD is observed in a DFG-out conformation and with the glycine-rich loop adopting a structure that blocks ATP binding to the active site. (rcsb.org)
To improve protein reactivity and reduce non-specific binding, we are performing a fundamental study on the interaction between proteins and a polymeric biosensor surface. (tue.nl)
Binding of FAD significantly decreases protein dynamics and stabilizes the FAD and dicoumarol binding sites as well as the monomer:monomer interface. (preprints.org)
Early stage computational and experimental studies on potential therapeutics have concentrated on the receptor binding domain, although this region is prone to mutations with the possibility of giving rise to widespread drug resistance. (biorxiv.org)
Here, using atomistic molecular dynamics simulation, we study the correlations between the RBD dynamics with physically distant residues in the spike protein, and provide a deeper understanding of their role in the infection, including the prediction of important mutations and of distant allosteric binding sites for therapeutics. (biorxiv.org)
Significant research effort for drug design against COVID-19 is focused on the receptor binding domain of the spike protein, although this region is prone to mutations causing resistance against therapeutics. (biorxiv.org)
We applied time-independent component analysis (tICA) and protein connectivity network model, on all-atom molecular dynamics trajectories, to identify key non-RBD residues, playing crucial role in the conformational transition facilitating spike-receptor binding and infection of human cell. (biorxiv.org)
The anti-F mAbs can be divided into pre- or postfusion conformation-specific categories and further into 8 competition-binding groups. (cdc.gov)

Here, we describe initial characterization of experimental infection in Syrian hamsters, including kinetics of virus dissemination and replication, and the corresponding clinical parameters, immunological responses, and histopathology. (cdc.gov)

The information content of SAS data is illustrated here in the figure on the right, which shows X-ray scattering patterns from proteins with different folds and molecular masses. (wikipedia.org)

the effects of protein conformation on reaction center function. (sharcnet.ca)
Furthermore, vacuum calculations on a smaller model of the active site have allowed us to estimate the entropy contributions to the barrier height and to obtain further insight into the reaction by comparing the small cluster model with the QM/MM model, which includes the entire protein. (lu.se)

We then applied the model to resolving the decades-old controversy in the field, between the FRET and SAXS experiments on the unfolded proteins. (asu.edu)

Our model, based on time-independent component analysis (tICA) and protein graph connectivity network, was able to identify multiple residues, exhibiting long-distance coupling with the RBD opening dynamics. (biorxiv.org)
E9 DNase Phe86 is the primary specificity hotspot residue in the centre of the interface, which is coordinated by conserved and variable hotspot residues of the cognate Im protein. (ox.ac.uk)
Experimental DMC analysis reveals that only modest coupling energies to Im9 residues are observed, in agreement with calculated DMCs using the program ROSETTA and consistent with the largely hydrophobic nature of E9 DNase-Im9 specificity contacts. (ox.ac.uk)
Our study highlights how colicin DNases are able to utilise both conserved and variable amino acids to distinguish cognate from non-cognate Im proteins, with the energetic contributions of the conserved residues modulated by neighbouring specificity sites. (ox.ac.uk)
The best-predicted 95% of residues in AlphaFold models had a median alpha carbon RMSD of 0.96 Å to the experimental models, compared to 2.83 Å for the next-best method. (embl.org)
The AlphaFold information for a specific protein also includes a predicted model-quality score for individual residues. (embl.org)

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)

Our novel interdisciplinary pipeline will involve the use of efficient coarse-grained representations of proteins from computational biophysics coupled with sophisticated image processing tools including 3D reconstruction, classification, and dimensionality reduction. (europa.eu)

Proteins are involved in virtually all biological processes and their structure is key to their function. (manchester.ac.uk)
Analyze data relating to protein function and demonstrate an understanding of associated variables (resolution, Kd, Km & Vmax). (manchester.ac.uk)
The emphasis of the course is on practical applications, for example selecting the best technique to address a particular question on protein structure and function. (manchester.ac.uk)
To elucidate structure-function relationships in GPCR activation, we used bioluminescence resonance energy transfer to directly assess the conformation of mutants of the chemokine receptor CXCR4. (pasteur.fr)
The importance of disorder in protein structure and function is becoming increasingly evident. (asu.edu)
proteinopathic adj ), or proteopathy , protein conformational disorder , or protein misfolding disease , is a class of diseases in which certain proteins become structurally abnormal, and thereby disrupt the function of cells , tissues and organs of the body. (wikipedia.org)
in this misfolded state, the proteins can become toxic in some way (a toxic gain-of-function ) or they can lose their normal function. (wikipedia.org)
In some cases, misfolding of the protein results in a loss of its usual function. (wikipedia.org)

Conversely, broad spectrum therapeutics like drugs and monoclonal antibodies can be generated targeting these key distant regions of the spike protein. (biorxiv.org)
The spike protein of SARS-CoV--a target for vaccine and therapeutic development. (who.int)

Describe the features of proteins which lead to successful folding, post-translational modification and degradation. (manchester.ac.uk)
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)

Micrograph of a section of the cerebral cortex from a person with Alzheimer's disease , immunostained with an antibody to amyloid beta (brown), a protein fragment that accumulates in amyloid plaques and cerebral amyloid angiopathy . (wikipedia.org)

The link between receptor conformation and activity is still insufficiently understood, as current models of GPCR activation fail to take an increasing amount of experimental data into account. (pasteur.fr)
These data provide biophysical evidence for different receptor conformations being active with respect to a single readout. (pasteur.fr)
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)

Less than a year later, more than 350,000 AlphaFold protein structure predictions have been made freely and openly available for anyone to access through the AlphaFold Database (AlphaFold DB), co-developed by DeepMind and EMBL's European Bioinformatics Institute (EMBL-EBI) . (febs.org)
In addition to structure predictions for almost the entire human proteome, AlphaFold DB also includes protein structure predictions for 20 other species of significant biological or medical interest. (febs.org)
Although the availability of predicted 3D models for the known "protein universe" is an exciting prospect with huge impact, there are certain limitations to the AlphaFold method and database that researchers need to be aware of. (febs.org)

AMP-activated protein kinase (AMPK) is a master metabolic regulator for controlling cellular energy homeostasis. (rcsb.org)
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)

Static electric field strengths of 0.001 V/nm and 0.002 V/nm induced conformational changes in the protein but had no significant effect on its surface properties. (mdpi.com)
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)

For example, cystic fibrosis is caused by a defective cystic fibrosis transmembrane conductance regulator (CFTR) protein, [3] and in amyotrophic lateral sclerosis / frontotemporal lobar degeneration (FTLD), certain gene-regulating proteins inappropriately aggregate in the cytoplasm, and thus are unable to perform their normal tasks within the nucleus. (wikipedia.org)

Anatomy2

Organisms7

Diseases1

Chemicals and Drugs52

Analytical, Diagnostic and Therapeutic Techniques and Equipment34

Phenomena and Processes53

Disciplines and Occupations5

Information Science9

Health Care2

Nucleic acids3

Intrinsically disordered7

Peptides2

Peptide7

Native conformation2

Polypeptide4

Interactions8

Structural12

Amyloidogenic Proteins1

Structures14

Ligand5

Experimentally2

Molecules6

Stability1

Properties of proteins2

Range of proteins1

Design of proteins2

Interaction with proteins1

Simulations6

Membrane proteins2

Secondary2

Large proteins1

Surface proteins2

Mutation2

20201

20231

Abstract2

Functional4

Enzyme2

Aggregation1

Recognition4

Pivotal1

Timescales1

Prion protein2

Highly conserved1

Fold1

Biological functions2

Mechanisms3

Receptors2

Heterogeneity1

Methods9

Globular1

Sequence8

Binding8

Kinetics1

Folds1

Reaction2

Experiments1

Residues6

Theoretical and experimental1

Biophysics1

Function8

Spike protein2

Describe2

Antibody1

Receptor3

AlphaFold3

Kinase2

Conformational changes2

Gene1