Protein nuclear magnetic resonance biomolecular. Medical search. Frequent questions

Nuclear magnetic resonance spectroscopy of proteins (usually abbreviated protein NMR) is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins, and also nucleic acids, and their complexes. (wikipedia.org)
MOLMOL is a molecular graphics program designed for display and analysis of biological macromolecules, particularly protein or DNA structures determined by nuclear magnetic resonance spectroscopy. (biomedcentral.com)
Systematic analysis of the chloroplast and its photosynthetic machinery has begun, using a combination of two-dimensional gels, mass spectroscopy, protein sequencing and genome databases. (biomedcentral.com)
Experimental methods of multi-dimensional NMR spectroscopy, dynamics and theoretical description of spin system evolution, multiple resonance NMR technique for structural studies of proteins and nucleic acids by NMR spectroscopy, contemporary methods of structural biology, studies of complex biomolecular systems. (muni.cz)
We show that one of the apo conformations and one of the holo conformations are identical, whereas the two remaining conformations are only detectable by nuclear magnetic resonance spectroscopy in either the apo or holo form. (rcsb.org)
In our group we study protein molecules using nuclear magnetic resonance (NMR) spectroscopy. (au.dk)
At iNANO we use NMR spectroscopy to determine the structures of proteins in their physiological, watery milieu, since 3D structures provide important insights into protein function. (au.dk)
ROA spectroscopy is able to probe the chiral peptide backbone of proteins, and as such the ROA spectrum of a protein contains a wealth of structural information from within the whole molecule, across the whole vibrational spectrum. (gla.ac.uk)
This means that ROA spectroscopy can provide invaluable structural information for proteins that are precluded from analysis by other techniques, and also cast new light on the structures of proteins that have not been well defined. (gla.ac.uk)
The group uses biomolecular NMR spectroscopy coupled to biochemical, biophysical and computational methods to study the structure/function activity of proteins (or protein domains) involved in human diseases (e.g. cancer, genetic diseases). (hsr.it)
Universal saturation transfer analysis (uSTA) builds on existing nuclear magnetic resonance spectroscopy to provide an automated workflow for quantitating protein-ligand interactions. (mdc-berlin.de)
We use NMR spectroscopy for such characterizations of the positively or negatively charged groups of proteins and nucleic acids. (utmb.edu)
Nuclear magnetic resonance spectroscopy, Radiolabeling, Biomolecules-Analysis, Isotope Labeling-methods, Nuclear Magnetic Resonance, Biomolecular Here we describe a protocol for the labeling of proteins that facilitates their study using a technique that is sensitive to millisecond conformational exchange restrict to techniques of labeling with isotopes (stable or radioactive): do not use for radioisotope tracer studies of "labeled" cells, microorganisms or chemicals Pris: 1862 kr. (firebaseapp.com)
Nuclear magnetic resonance (NMR) spectroscopy is the only method that provides high resolution structures in solution. (bacatec.de)
The scientific program stated early on Monday morning with a lecture series with the focus on the basic aspects of biomolecular NMR-spectroscopy and the structure determination of proteins, nucleic acids, and their complexes. (bacatec.de)

Abietane-Type Diterpenoids Inhibit Protein Tyrosine Phosphatases by Stabilizing an Inactive Enzyme Conformation. (colorado.edu)
A (19)F, (13)C- rotational-echo double-resonance NMR strategy was used to determine the structure of an inhibitor in the digitalis receptor site, and it showed that the ouabain derivatives adopt a conformation in which the sugar extends out of the plane of the steroid ring system. (ox.ac.uk)
Comparison of simulations (total of 13 ns) of the free protein and of the bound protein conformation (in isolation or DNA-bound) reveals intrinsic flexibility in certain parts of the molecule. (uzh.ch)

Knowledge of the sequence of the Human Genome and thus, in principle, of basically the sequences of all proteins in humans, widens the demand for specialists able to determine structures of the individual constituent parts of biomolecular complexes of as well as the complexes in their entirety. (bacatec.de)

We developed an innovative methodology to directly measure local electrostatic potentials for every residue of proteins and nucleic acids. (utmb.edu)
Applications to intrinsically disordered proteins and conformationally flexible nucleic acids are particularly useful because structure-based analysis of electrostatics is not straightforward for such molecules. (utmb.edu)
Due to their mobility broadening their probability distributions, the vast majority of counterions around proteins, nucleic acids, and their complexes are unresolved even in high-resolution crystal structures. (utmb.edu)
Complexes of biological macromolecules, such as proteins and nucleic acids, are involved in important biological events such as transcription, protein synthesis, and protein degradation. (bacatec.de)
Besides aspects on the determination of structures of proteins and nucleic acids the focus was also on the presentation of methodological advances as well as the determination of dynamics of biological macromolecules. (bacatec.de)

The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. (biomedcentral.com)
In practice, this eliminates virtually all 13C present in proteins and other macromolecules. (westminster.ac.uk)

citation needed] Protein NMR utilizes multidimensional nuclear magnetic resonance experiments to obtain information about the protein. (wikipedia.org)
The development of the analysis of ROA spectra has largely been based upon the correlation of ROA spectra of proteins of known structure with structural information from alternative sources, chiefly X-ray crystallography and multidimensional nuclear magnetic resonance (NMR). (gla.ac.uk)

Journal of Biomolecular NMR , 45 (3), 311-318. (johnshopkins.edu)

Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance (BMRZ), J.W. Goethe University of Frankfurt, Marie-Curie-Strasse, D-60439 Frankfurt/Main, Germany. (rcsb.org)
Magnetic Resonance in Chemistry , 41 (10), 853-865. (au.dk)
Our research field is biophysical chemistry of proteins, DNA, and their interactions. (utmb.edu)
Research in the Lorieau group integrates Biophysics, Physical Chemistry, Structural Biology and Biochemistry in elucidating the interplay between biomolecular structure, dynamics, chemistry and function. (lorieau.com)

ssNMR data may be used to annotate and refine existing structures in regions of the protein not fully resolved by crystallography (including ligand-binding sites and mobile solvent accessible loop regions). (nih.gov)
The most important parameter archived in the BMRB is assigned chemical shifts, which can be used directly to determine protein secondary structure and to assist in the determination of their solution structures, to identify interactions of small molecules with target proteins for drug discovery, and to characterize protein-protein interactions. (biomedcentral.com)
With a basis for the correlation between the ROA spectrum and the known crystal structure (or NMR structure) being well established, it is possible to interpret the ROA spectra of proteins that do not have (for whatever reason) well defined structures. (gla.ac.uk)
Biomolecular electrostatics has been a subject of computational investigations based on 3D structures. (utmb.edu)
We use solution and solid-state NMR to characterize the structures and dynamics of membrane proteins, and the curvature and fusion of membranes. (lorieau.com)
We use NMR to characterize the structures and mechanism of viral fusion proteins and the role of membrane curvature. (lorieau.com)
He has made important contributions in our lab by solving solution NMR structures of membrane proteins, collecting high-resolution NMR structural data and refining structures with RDCs. (lorieau.com)
Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175. (rostlab.org)
Obtaining highly resolved three dimensional structures of disease-related biomolecular assemblies is therefore of highest interest for pharmaceutical industry. (bacatec.de)
The resolution and time saving provided in this experiment was crucial for solving the structures of these two proteins. (johnshopkins.edu)

Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin-spin interactions. (muni.cz)
Inter-oligomer interactions of the human prion protein are modulated by the polymorphism at codon 129. (ox.ac.uk)
This result provides evidence for conformational differences between the beta(O) allelic forms, showing that the core region of the protein including position 129 is actively involved in inter-oligomer interactions, consistent with NMR observations. (ox.ac.uk)
The simulation identifies protein-DNA interactions that are poorly resolved or only surmised from the NMR ensemble. (uzh.ch)
Single water molecules and water clusters dynamically optimize the complementarity of polar interactions at the "wet" protein-DNA interface. (uzh.ch)
Chill, J.H. The disordered cellular multi-tasker WIP and its protein-protein interactions: a structural view. (chill-lab.com)
Simple and efficient machine learning frameworks for identifying protein-protein interaction relevant articles and experimental methods used to study the interactions. (leibniz-fli.de)
A high-throughput solid-phase microplate protein-binding assay to investigate interactions between myofilament proteins. (leibniz-fli.de)
Towards a rigorous network of protein-protein interactions of the model sulfate reducer desulfovibrio vulgaris hildenborough. (leibniz-fli.de)
Design of novel ligands of CDP-methylerythritol kinase by mimicking direct protein-protein and solvent-mediated interactions. (leibniz-fli.de)
Quantitative studies of biomolecular interactions, dynamics and structure at the molecular level establish the necessary foundation for analyzing higher levels of biological complexity. (lu.se)
Carbohydrate-protein interactions are frequently characterized by dissociation constants in the μM to mM range. (uni-luebeck.de)
Therefore, NMR experiments that take advantage of fast exchange are well suited to study carbohydrate-protein interactions. (uni-luebeck.de)
Two types of NMR experiments have been extremely valuable to analyze carbohydrate-protein interactions at atomic resolution. (uni-luebeck.de)
Protein-protein interactions involving intrinsically disordered proteins are important for cellular function and common in all organisms. (elifesciences.org)
Experiments together with molecular modeling using NMR chemical shifts suggest that new interactions involving intrinsically disordered proteins may evolve via a low-affinity complex which is optimized by modulating direct interactions as well as dynamics, while tolerating several potentially disruptive mutations. (elifesciences.org)
At multiple time points during evolution, new or modified proteins - and consequently new potential interactions between proteins - have emerged. (elifesciences.org)
The findings shed light on fundamental principles of how new protein-protein interactions emerge and evolve on a molecular level. (elifesciences.org)
A next step for the future will be to investigate how other protein-protein interactions have evolved and to identify general underlying patterns. (elifesciences.org)
A deeper knowledge of how this molecular evolution happened will broaden our understanding of present day protein-protein interactions and might aid the design of drugs that can mimick proteins. (elifesciences.org)

However, precise analyses of glycan ligands binding with heavily modified pathogen proteins can be confounded by overlapping sugar signals and/or compounded with known experimental constraints. (mdc-berlin.de)

A comprehensive analysis has identified and localized all yeast nucleoporins in nuclear pore complexes. (biomedcentral.com)
Bacterial protein complexes investigation using blue native PAGE. (leibniz-fli.de)
NMR structure analysis: For small molecules, Accessible proteins and ligand-protein complexes. (science.eus)
In the course of practice-oriented case studies, which were presented in the second half of the week, more detailed knowledge on structure determination of biomolecular complexes was taught. (bacatec.de)
This is normally associated with fast dissociation rates of the corresponding complexes, in turn leading to fast exchange on the nuclear magnetic resonance (NMR) chemical shift time scale and on the NMR relaxation time scale. (uni-luebeck.de)
We demonstrate the power of a combined transfer NOE/STD NMR approach for the analysis of carbohydrate-protein complexes using selected examples. (uni-luebeck.de)

We are working on three areas of research: 1) Biomolecular Electrostatics , 2) Protein-DNA Dynamics , and 3) HMGB1 Biochemistry . (utmb.edu)
With a combination of solution- and solid-state Nuclear Magnetic Resonance spectroscopies, computational tools and other biophysical methods, our research focuses on membrane protein structure and dynamics, membrane protein biochemistry, the development of theory and techniques to enhance the precision and resolution of structural and dynamic information by NMR, and the investigation of molecular dynamics as it relates to enzymatic catalysis and kinetics. (lorieau.com)

Protein dynamics plays an important role in protein function. (rcsb.org)
In our group we investigate the structure and dynamics of proteins, and how these impact their function in the biological environment. (chill-lab.com)

However, a group of proteins called 'intrinsically disordered proteins' are flexible in their shape and lack a stable three-dimensional structure. (elifesciences.org)
analyzed the amino acid sequences of two specific intrinsically disordered proteins from different organisms to reconstruct the versions of the proteins that were likely found in their common ancestors 450-600 million years ago. (elifesciences.org)

Ligand binding to an extracellular orthosteric pocket propagates conformational change to the receptor cytosolic region to promote binding and activation of downstream signalling effectors such as G proteins and β-arrestins. (nih.gov)
The N-terminal domain of the Tn916 integrase protein (INT-DBD) is responsible for DNA binding in the process of strand cleavage and joining reactions required for transposition of the Tn916 conjugative transposon. (uzh.ch)
Based on analysis of the binding enthalpy and binding heat capacity, we have reasoned that dehydration of the protein-DNA interface is incomplete. (uzh.ch)
Free energy to estimate the binding affinity for identified compounds and target proteins. (bvsalud.org)
Spatial clustering of protein binding sites for template based protein docking. (leibniz-fli.de)
The NMR structure of Ros87 shows that the putative prokaryotic Cys2His 2 zinc-finger sequence is indeed part of a significantly larger zinc-binding globular domain that possesses a novel protein fold very different from the classical fold reported for the eukaryotic classical zinc-finger. (cnr.it)
Mapping of the amino acids necessary for the DNA binding onto Ros87 structure reveals the protein surface involved in the DNA recognition mechanism of this new zinc-binding protein domain. (cnr.it)
Metal-dependent folding and stability of nuclear hormone receptor DNA-binding domains. (ox.ac.uk)
The nuclear/hormone receptors are an extensive family of ligand-activated transcription factors that recognise DNA targets through a highly conserved, structurally autonomous DNA-binding domain. (ox.ac.uk)
Mass spectrometry reveals that the protein charge distribution changes with the uptake of zinc and that metal binding is co-operative. (ox.ac.uk)
A crucial residue that stabilises the equilibrium structure of the DBD fold itself is a cysteine residue situated in the hydrophobic core of all known nuclear hormone receptors (but not involved in metal binding): it appears to be conserved absolutely for its unique combination of size and hydrophobicity. (ox.ac.uk)
In general, it is possible to analyze ligand binding by observing either protein signals or ligand resonances. (uni-luebeck.de)
Whereas transferred nuclear Overhauser effect (NOE) experiments deliver bioactive conformations of carbohydrates binding to proteins, saturation transfer difference (STD) NMR spectra provide binding epitopes and valuable information about the binding thermodynamics and kinetics. (uni-luebeck.de)

Molecular docking results verified the interaction between active ingredients and key targets, among which rustication and quercetin had high docking affinity with key target proteins MAPK1 and CCND1. (bvsalud.org)
AutoDock Vina molecular docking module to estimate the validation from the compounds and target proteins. (bvsalud.org)
Results and conclusion: The results demonstrated that QDDHG has 18 active compounds and 13 target proteins of QDDHG exerted a crucial role in treatment of DKD. (bvsalud.org)
NMR spectral assignment: For accessible target proteins. (science.eus)

PROTEIN BIOTECHNOLOGY , from design of engineered proteins to the structure of membrane protein targets for ligand discovery and biomolecular medicine. (iit.it)
Our particular capacities thereby include: biomolecular NMR with highest sensitivity and resolution (at 800 MHz), 19F NMR, automated metabolic studies and ligand screening, customised NMR method development. (science.eus)

However, the techniques are now being applied to large, polytopic membrane proteins including receptors, ion channels, and porins. (nih.gov)
G-protein-coupled receptors (GPCRs) modulate many physiological processes by transducing a variety of extracellular cues into intracellular responses. (nih.gov)

Computational techniques are valuable tools for the discovery of protein-protein interaction inhibitors: The 14-3-3σ case. (leibniz-fli.de)
The ancestral proteins were then 'resurrected' by recreating them in test tubes and their characteristics and properties analyzed with experimental and computational biophysical methods. (elifesciences.org)

volume = {285}, number = {32}, pages = {24307--24312}, abstract = {Inhibitory serpins are metastable proteins that undergo a substantial conformational rearrangement to covalently trap target peptidases. (cnrs.fr)

What about the molecule that translates the RNA sequences into proteins? (riken.jp)

A typical study might involve how two proteins interact with each other, possibly with a view to developing small molecules that can be used to probe the normal biology of the interaction ("chemical biology") or to provide possible leads for pharmaceutical use (drug development). (wikipedia.org)
However, in large molecules such as proteins the number of resonances can typically be several thousand and a one-dimensional spectrum inevitably has incidental overlaps. (wikipedia.org)
You try to find molecules that fit the mold perfectly and inhibit the action of this protein. (ebc.com.br)
The signals observed in in vivo carbon-13 nuclear magnetic resonance (13C NMR) spectra are from 'mobile' molecules, i.e. those with relatively unrestricted motion. (westminster.ac.uk)
The ease with which the ROA spectra of biological molecules can be successfully measured lends itself perfectly to the ever-growing demand for biomolecular structural information, especially in the context of proteomics and the Human Genome Project. (gla.ac.uk)

This review describes the spectroscopic experiments and data analysis methods (including assignment) used to generate high-resolution structural data for membrane proteins. (nih.gov)
Many functionally important motions occur on the microsecond and low millisecond time scale and can be characterized by nuclear magnetic resonance relaxation experiments. (rcsb.org)
Through experiments in mice and cell culture models, she aims to understand which proteins are required for signal transmission between cells, how they get to the right location, and how they work together. (dal.ca)

The source of the protein can be either natural or produced in a production system using recombinant DNA techniques through genetic engineering. (wikipedia.org)

Spectral density mapping at multiple magnetic fields suitable for C-13 NMR relaxation studies. (muni.cz)
Our principal experimental tool is nuclear magnetic resonance (NMR), in particular nuclear spin relaxation measurements. (lu.se)

The Brazilian team, formed by some 30 scientists, utilizes nuclear magnetic resonance tools in one of the most modern pieces of equipment installed in Latin America, the supercomputer Santos Dumont, at the National Scientific Computing Laboratory (LNCC), linked to the Ministry of Science, Technology, and Innovation. (ebc.com.br)

The smallest proteins today are about one hundred amino acids in length. (riken.jp)
RNA polymerase today is huge, but its catalytic core is composed of a small protein domain called double-psi beta-barrel (DPBB), which is about 80 amino acids in length. (riken.jp)
However, efficient labeling of proteins with selected amino acids necessitates auxotrophic hosts, which are often not available. (firebaseapp.com)
The specific order of amino acids in a protein determines its shape and structure, which in turn controls what the protein can do. (elifesciences.org)

Depending on the environment of atoms within the protein, the nuclei of individual atoms will absorb different frequencies of radio signals. (wikipedia.org)

As the database of ROA spectra of polypeptides and proteins has grown, it has been possible to tighten up the assignment of ROA spectral bands and band patterns to aspects of known structural content. (gla.ac.uk)
This project presents an up-to-date collection of newly obtained ROA spectra of a large number of proteins across a range of structural class types. (gla.ac.uk)
It is hoped that the result of this work will provide a basis for the future analysis of protein ROA spectra that is both mathematically rigorous and convenient. (gla.ac.uk)
Because most receptor proteins to which carbohydrates bind are rather large with molecular weights significantly exceeding 30 kDa, the analysis of the corresponding protein spectra is not trivial, and only very few studies have been addressing this issue so far. (uni-luebeck.de)

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. (colorado.edu)

These tools also facilitate examination of theoretical models on biomolecular electrostatics. (utmb.edu)

Protein information is encoded in a DNA sequence, which is then transcribed into RNA, and RNA is further translated into a protein. (riken.jp)
Protein flexibility and rigidity predicted from sequence. (rostlab.org)
The system uses both global and local information (i.e., features from the entire protein such as secondary structure composition, protein length, and fraction of surface residues, and features from a local window of sequence-consecutive residues). (rostlab.org)
The most important local feature was the evolutionary exchange profile reflecting sequence conservation in a family of related proteins. (rostlab.org)

I know that they use instruments like nuclear magnetic resonance (NMR) spectrometers to determine the structure of proteins, but I was very excited to be able to hear the story of what happens after the structure is determined as it sounded quite interesting. (riken.jp)

Electrostatics is important for our fundamental understanding of biomolecular functions as well as for drug development. (utmb.edu)
These solution NMR methods allow us to quantitatively investigate biomolecular electrostatics without any use of structure information. (utmb.edu)

Frequently, the interacting pair of proteins may have been identified by studies of human genetics, indicating the interaction can be disrupted by unfavorable mutations, or they may play a key role in the normal biology of a "model" organism like the fruit fly, yeast, the worm C. elegans, or mice. (wikipedia.org)
We further demonstrate that this conformational diversity is an essential prerequisite for the directed movement of the 4'-PP cofactor and its interaction with externally acting proteins such as thioesterases and 4'-PP transferase. (rcsb.org)
Studies on interaction of cucurbit aphid-borne yellow virus proteins using yeast two-hybrid system and bimolecular fluorescence complementation. (leibniz-fli.de)
A cell-based protein-protein interaction method using a permuted luciferase reporter. (leibniz-fli.de)
Classifying protein-protein interaction articles using word and syntactic features. (leibniz-fli.de)
The protein-protein interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. (leibniz-fli.de)

NMR investigations assigned the observable amide resonances to the beta(O) N-terminal segments, showing that it is the core region of PrP (residues 127-228) that is involved in beta(O) formation. (ox.ac.uk)
Modern proteins are made up of about 300 or 400 amino acid residues that are strung together like beads. (riken.jp)
Some of the larger proteins are made up of over 1,000 amino acid residues. (riken.jp)
Labeling occurs by site-specific incorporation of stable isotope labeled tags at cysteine residues or the general labeling of amines and carboxyl groups in protein samples. (firebaseapp.com)

The described case study demonstrates that a simple query of the SPARQL endpoints of the BMRB, UniProt, and Online Mendelian Inheritance in Man (OMIM), can be used in NMR and structure-based analysis of proteins combined with information of single nucleotide polymorphisms (SNPs) and their phenotypes. (biomedcentral.com)
They currently study protein N (nucleocapsid) of dengue fever and Zika. (ebc.com.br)

In silico studies of protein flexibility have attempted to characterize and predict flexible regions based on simple principles. (rostlab.org)

As well as containing detailed information from specific structural elements such as sections of secondary structure and motifs, the ability of ROA to see the molecule as a whole also enables the global fold of the protein to be deduced from the ROA spectrum. (gla.ac.uk)
While the metal-free apo protein and the chemically denatured state have little defined secondary structure, these states were expanded only partially in comparison with the native structure, according to data from small-angle X-ray scattering. (ox.ac.uk)

The integrative understanding of these fundamental biomolecular properties is essential to achieve a comprehensive understanding of biological processes at the nanoscale. (au.dk)

The highly conserved oligomerization domain (OD) of tumor suppressor p53 is essential for its biological functions, and its structure was believed to be the prototype for all three proteins. (ox.ac.uk)
Proteins are the elements that are the driving force of all kinds of biological phenomena, and I am trying to uncover how modern proteins emerged and evolved. (riken.jp)

It's almost a miracle that living organisms have been able to select only useful proteins from 10 130 different variations. (riken.jp)

What makes a yeast nuclear pore? (biomedcentral.com)

The common polymorphism at codon 129 in the human prion protein (PrP) has been shown in many studies to influence not only the pathology of prion disease but also the misfolding propensity of PrP. (ox.ac.uk)
12. C. This gives a Amino-acid selective isotope labeling of proteins offers numerous advantages in mechanistic studies by revealing structural and functional information unattainable from a crystallographic approach. (firebaseapp.com)

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