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Changes in the redox state of cells affect proteins, lipids, and nucleic acids in different ways. (hindawi.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)
active site - A region in proteins and nucleic acids (that participate in chemical reactions), where reacting molecules (substrates) bind and make specific contacts necessary for chemical catalysis. (rcsb.org)

Bioinformatic algorithms allowing predicting of biomolecular folding for proteins, peptides, and RNAs, even though sometimes successful, have all their limitations. (biosyn.com)
RNA molecules in solution may adopt secondary structures that are only partially determined by thermodynamics since RNA molecules can undergo conformational changes during interaction with other RNAs, RNA binding proteins or RNA binding peptides. (biosyn.com)
The reason why Peter Lansbury and others used the term 'natively unfolded' for a-synuclein and other proteins, especially peptides, is that they do not exist, to a significant degree, in the same kind of stable structure that larger native proteins like myoglobin do. (alzforum.org)
There are 20 different alpha amino acids commonly found in nature that can covalently link with each other to form short peptides or longer proteins. (rcsb.org)
Apelin peptides are cognate ligands for the apelin receptor, a G-protein-coupled receptor (GPCR). (phoenixpeptide.com)

In a rat model of myocardial infarction, intracoronary S100A1 adenoviral gene transfer restored sarcoplasmic reticular calcium transients and load, normalized intracellular sodium concentrations, reversed the pathologic expression of the fetal gene program, restored energy supply, normalized contractile function, preserved inotropic reserve, and reduced cardiac hypertrophy 1 week post-myocardial infarction. (wikipedia.org)

Our chemical-shift based secondary structure analysis reveals the human DBNDD1 as an intrinsically disordered protein. (springer.com)
2021 ), https://pfam.xfam.org/ ] predicts human DBNDD1 mainly as an intrinsically disordered protein (IDP) and also the recently released AlphaFold database (Jumper et al. (springer.com)
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)
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)

Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. (embl.de)

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)

Here, we used a microscopy-based method, Fluorescence Correlation Spectroscopy (FCS), to analyze different antenna proteins at the particle level. (bvsalud.org)

We also collaborate with other groups for Mossbauer, electron-nuclear double resonance (ENDOR), X-ray absorption and X-ray crystallography studies of proteins prepared in our laboratory. (uga.edu)
Cryo-EM, on the other hand, requires less protein and has evolved to achieve resolutions comparable to X-ray crystallography ( García-Nafría, J., & Tate, C. G. 2021 ). (drgpcr.com)
Crystallography and NMR spectroscopy indicate that these internal ions can be located between the G-quartet planes as well as in the thymine loops, but the precise ion coordination has been firmly established in only a few cases. (lu.se)
NMR spectroscopy or X-ray crystallography, but important width measurements at a single resonance frequency (or questions remain concerning the energetics, stability, and magnetic field strength), making it difficult to separate dynamics of this structurally diverse nucleic acid class. (lu.se)

This protein may function in stimulation of Ca2+-induced Ca2+ release, inhibition of microtubule assembly, and inhibition of protein kinase C-mediated phosphorylation. (wikipedia.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)
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)

Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. (embl.de)
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)
Their amino acid sequences suggest that they are mainly cytosolic or nuclear proteins partly associating with membranes (Talbot et al. (springer.com)
alignment - A comparison of two or more gene or protein sequences in order to determine their degree of similarity in amino acid or bases, respectively. (rcsb.org)
amino acid - A building block of proteins is an alpha amino acid which contains a basic amino group, an acidic carboxyl group, and a hydrogen or organic side chain attached to the central carbon atom. (rcsb.org)

Here, we present the backbone and side chain nuclear magnetic resonance assignments for the human DBNDD1 protein. (springer.com)
Triple resonance NMR experiments recorded using 2H, 13C, 15N -labelled C60S yielded assignments for the majority of the backbone resonances. (ndltd.org)
To investigate the reaction catalysed by IdmH, 88% of the backbone NMR resonances were assigned, and using chemical shift perturbation of [ 15 N]-labelled IdmH it was demonstrated that indanomycin binds in the active-site pocket. (iucr.org)

This conformational change exposes a large hydrophobic pocket between helix 3, 4, and the hinge region of S100A1 that is involved in virtually all calcium-dependent target protein interactions. (wikipedia.org)
As the assembly was carried out in the absence of ATP, this suggests that formation of the holoenzyme from the individual subcomplexes is solely driven by protein-protein interactions at the interface. (upstate.edu)
Unlike reversible disassembly, which requires ATP hydrolysis on V 1 to break protein-protein interactions, Oxr1p mediated disassembly of V-ATPase is ATP independent and therefore a novel mode of activity regulation. (upstate.edu)
The characterization of RNA and RNA interactions is closely related to transcription, for example, gene expression levels are investigated within a biological context. (biosyn.com)
Over the last decades, a variety of RNA methods have been developed for the study of RNA-DNA, RNA-RNA, and RNA-protein interactions including RNA complexes with ligand molecules. (biosyn.com)
The mapping of RNA-protein or RNA-RNA interactions by protein pull-down or affinity pull-down methods allow studying RNA structures, as well as RNA-protein, and RNA-RNA interactions. (biosyn.com)
Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin-spin interactions. (muni.cz)
Allostery - This is a type of effect seen in proteins where the binding of a molecule, ion etc. to one location can have an impact of the structure and interactions at another location. (rcsb.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)

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)
Many chromatin-associated proteins contain two sequence motifs rich in phenylalanine/tyrosine residues of unknown function. (diamond.ac.uk)

Protein dynamics plays an important role in protein function. (rcsb.org)
This includes gene, protein and metabolic networks, cellular architecture and intracellular dynamics, cell communication and motility, cell division and differentiation, tissue formation and organogenesis, tissue and organ functions, changes in population characteristics as a consequence of interaction of organisms with their physical environment, with individuals of their own species, and with organisms of other species. (nih.gov)
The combination of these diverse methods contributes to a holistic understanding of the intricate dynamics and functions of these signaling proteins. (drgpcr.com)
Articles, abstracts, and book chapters citing Globals Software (Globals Unlimited, Globals for Spectroscopy, and Globals for Images aka SimFCS) by authors not affiliated with the Laboratory for Fluorescence Dynamics (LFD). (uci.edu)

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)

The E. coli O123 O-antigenic polysaccharide and its repeating unit were characterized, and the chemical structure for E. coli O123 was entirely consistent with the O antigen gene cluster sequences of E. coli O123 and the Salmonella O58 isolates. (microbiologyresearch.org)
Fig. 1: Photochemistry of light-oxygen-voltage receptors and sequences of proteins under study. (nature.com)
2009 ). The designated dysbindin paralogs show very limited sequence homology which raised the question whether DBNDD1 and DBNDD2 are dysbindin-like proteins or proteins that share a less conserved domain with DTNBP1 in the context of otherwise unrelated sequences (Ghiani and Dell'Angelica 2011 ). (springer.com)
We performed a Basic Local Alignment Search Tool (BLAST) analysis to identify regions of local similarity between the human DBNDD1 and protein sequences from other species (Fig. 1 ). (springer.com)
2019 ) was used, https://www.ebi.ac.uk/Tools/msa/clustalo/ ] of human DBNDD1 and similar protein sequences found by a BLAST search in other selected species. (springer.com)

The problem with simply applying the same techniques to proteins in sf9 cells was the significantly lower concentration of target proteins and short lifetime of cells, making it difficult to collect high quality multi-dimensional NMR spectra for nuclear Overhauser effect spectroscopy (NOESY) which would give precise information about how different atoms are spaced inside individual molecules. (analytica-world.com)

These include electron paramagnetic resonance (EPR), resonance Raman, FTIR, and UV/visible/near-IR absorption and natural and magnetically induced circular dichroism (CD and MCD). (uga.edu)

Oxr1p belongs to the group of TLDc domain containing proteins that are highly conserved in higher eukaryotes. (upstate.edu)
As an outcome human DBNDD1 revealed a high sequence identity to dysbindin domain-containing proteins from other Hominidae (e.g. (springer.com)

a protein required for the differentiation of the set of six touch receptor neurons in this nematode. (embl.de)
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)
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)

Sensitivity-enhanced two-dimensional heteronuclear shift correlation NMR spectroscopy. (microbiologyresearch.org)
Two proteins putatively involved in the persistence of Mycobacterium tuberculosis infection have been investigated by heteronuclear nuclear magnetic resonance (NMR) spectroscopy and other methods. (ndltd.org)
Multidimensional heteronuclear NMR spectroscopy was applied to recombinant wild-type (Wt) and Cys60→Ser (C60S) TPx, both of which are clearly folded but display slightly different spectral characteristics. (ndltd.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)
that allow interaction with trimeric G proteins, which regulate second messengers like cAMP or Ca2+. (drgpcr.com)

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)

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)
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)

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)

In this review, we assess the potential role of putative gut microbiota products in the etiopathogeny of Parkinson's disease, with a special emphasis on functional bacterial amyloid proteins, bacterial biosurfactants, endotoxins and short-chain fatty acids. (techscience.com)
The formation of functional complexes involving GPCRs and β-arrestins hinges on their specific conformational states, influenced by their intricate three-dimensional structures. (drgpcr.com)

The degree of conformational order in the prefibrillar aggregates is not yet known, I don't think. (alzforum.org)
Hsp70, Hsp90, and their co-chaperones are crucial members of the proteostasis network that are able to recognize misfolded proteins, aberrant condensates and protein aggregates, triaging proteins for refolding or degradation. (encyclopedia.pub)

Perturbation of this nature was also observed in magnetically aligned bicelles by 31P solid-state NMR spectroscopy and spin relaxation experiments. (phoenixpeptide.com)

Highly divergent hypotheses have been put forward regarding the makeup of the prions, including that they consist of nucleic acid only or protein only, are lacking both protein and nucleic acid, or are a polysaccharide. (medscape.com)

HMGB1 is an abundant protein, 10 6 molecules per cell [ 7 ], which has been postulated as a redox sensor [ 8 ]. (hindawi.com)
RNA molecules are functionally diverse and involved in many cellular processes such as catalysis, ligand binding, and protein recognition. (biosyn.com)

When we're taught biochemistry, we see proteins in their physiologically active forms. (alzforum.org)

They combined "in-cell" nuclear magnetic resonance (NMR) spectroscopy, a bioreactor system and cutting-edge computational algorithms to determine protein structures in crowded intracellular environments for the first time. (analytica-world.com)
Thus, they combined a sparse sampling -based rapid NMR measurement scheme with state-of-the-art computational methods employing statistical techniques like Bayesian inference , methods tailored to elucidate protein structures efficiently based on a limited amount of structural information from in-cell NMR spectra with inherently low-sensitivity. (analytica-world.com)
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)

More detailed information of completely dehydrated alkali ions (usually K+ or Na+) about the internal ions can be obtained by measuring the coordinated to the buried carbonyl oxygens of the nucleotide spin relaxation rate(s) over a wide range of resonance bases. (lu.se)

These amyloid plaques are immunoreactive with antibodies to the prion protein and do not immunoreact with antibodies to other amyloidogenic proteins, such as the amyloid-beta (which is deposited in Alzheimer disease). (medscape.com)

This has made it difficult to see what each protein inside the cells does in its natural environment, despite the obvious biomedical benefits of knowing e.g. how a particular protein reacts when cells are subjected to chemical stimuli, like pharmaceutical drugs. (analytica-world.com)
For biomedical applications, we are combining rational design and combinatorial methods to create designer protein therapeutics and diagnostic agents. (stanford.edu)

GPCR signaling is a complex process modulated by protein conformational states. (drgpcr.com)

Therapeutic tiny or short modified antisense oligonucleotides (Tiny ASOs) can block gene expression or modulate splice-switching! (biosyn.com)

Consideration of related TPx crystal structures indicates that the missing cross peaks correspond to a region of the protein that must display conformational plasticity necessary for the mechanism of action suggesting that the spectrum is affected by conformational exchange processes. (ndltd.org)
The team's pioneering NMR work had already succeeded in elucidating high-resolution protein structures inside bacteria (non-eukaryotes). (analytica-world.com)
Despite their contributions, these methods often lack cellular auxiliary structures and proteins. (drgpcr.com)

In particular, they identified a significantly different conformation in a localized region of one of the proteins compared to its reference structure in dilute solution. (analytica-world.com)
The infectious agent in the prion disease is composed mainly or entirely of an abnormal conformation of a host-encoded glycoprotein called the prion protein. (medscape.com)
The replication of prions involves the recruitment of the normally expressed prion protein, which has mainly an alpha-helical structure, into a disease-specific conformation that is rich in beta-sheet. (medscape.com)

To tackle this challenge, a team from Tokyo Metropolitan University led by Assistant Professor Teppei Ikeya and Professor Yutaka Ito applied nuclear magnetic resonance (NMR) spectroscopy measurements to specific proteins expressed inside sf9 cultured insect cells, a strain of cells originally derived from a type of moth larva widely used for protein production. (analytica-world.com)
Such magnetic relaxation dispersion (MRD1) structural polymorphism of quadruplexes ( 2, 5, 6 ), but little measurements have been used to study ion binding (via 23Na is known about the energetics and kinetics of ion binding. (lu.se)

S100 proteins are localized in the cytoplasm and/or nucleus of a wide range of cells, and involved in the regulation of a number of cellular processes such as cell cycle progression and differentiation. (wikipedia.org)
This review describes recent advances in the role of human HMGB proteins and other proteins interacting with them, in cancerous processes related to oxidative stress, with special reference to ovarian and prostate cancer. (hindawi.com)
Fe-S clusters are present in more than 300 different types of enzymes or proteins and play crucial roles in fundamental life processes such as respiration, photosynthesis and nitrogen fixation. (uga.edu)
Yet, these proteins play important roles in many processes that require the protein to interact with a number of other proteins. (elifesciences.org)
at the same time developing protein and peptide-based tools that will allow us to manipulate cellular processes on a molecular level. (stanford.edu)

Since RNA-binding proteins (RBPs) are key players in the post-transcriptional regulation of gene expression precise knowledge of their binding sites is critical for determining their molecular function and for understanding their roles in cell development and disease. (biosyn.com)

For example, alkaline vacuole/lysosome are deficient in autophagy, Golgi pH regulates its ability to glycosylate proteins and failure to maintain endosomal pH perturbs with its ability to recycle receptors to the Plasma membrane or, the trans-Golgi. (upstate.edu)
The bulk of protein secretion and membrane protein insertion is conducted by the ubiquitous Sec translocon. (elifesciences.org)

Three S. enterica isolates had O antigen gene clusters with homology to the Escherichia coli O123 O antigen region. (microbiologyresearch.org)

The dysbindin domain-containing protein 1 (DBNDD1) is a conserved protein among higher eukaryotes whose structure and function are poorly investigated so far. (springer.com)
The dysbindin (dystrobrevin-binding protein) protein family is a group of evolutionarily related proteins of moderate size (Mw 13-45 kDa) in higher Eukaryotes. (springer.com)

NMR spectra of recombinant sigJ recovered from inclusion bodies and in the soluble fraction differed, though both forms yielded dispersed resonances consistent with the protein containing a globular component. (ndltd.org)

The latter represents a conformationally modified form of a normal cellular PrP C , which is a normal host protein found on the surface of many cells, in particular neurons. (medscape.com)

Additionally, our data provide a proof of concept that the FCS method is well suited to measure proteins sizes (oligomerization state) and fluorescence intensities (photon counts) of antenna proteins per single particle (monomers and oligomers). (bvsalud.org)
Lipid-specific oligomerization of the Marburg virus matrix protein VP40 is regulated by two distinct interfaces for virion assembly. (uci.edu)

See also David Thirumalai's Emerging Ideas on the Molecular Basis of Protein and Peptide Aggregation ' (.pdf). (alzforum.org)
Interestingly, these variable regions determine the differential effects of Hsp70 isoforms on the aggregation or degradation of the Alzheimer's-disease-related protein tau [ 16 ] . (encyclopedia.pub)

See allosteric protein. (rcsb.org)

The most accurate high-resolution solution structure of human apo-S100A1 protein (PDB accession code: 2L0P) has been determined by means of NMR spectroscopy in 2011. (wikipedia.org)
This would fundamentally change our conventional thinking about protein structure-function relationship, no? (alzforum.org)
I do not think there is a contradiction to the conventional thinking of protein structure-function relation. (alzforum.org)
Researchers from Tokyo Metropolitan University have successfully determined the high-resolution three-dimensional structure of proteins inside living eukaryotic cells. (analytica-world.com)
Unique statistical analysis with the help of Bayesian inference is applied to calculate the accurate 3D structure of the proteins with unprecedented precision. (analytica-world.com)
With this new data, the team were able to elucidate the 3D structure of three model proteins with unprecedentedly high resolution, with a precision of 0.5 Angstroms (0.05 nanometers) for the position of the protein's main chain atoms. (analytica-world.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)
2016). Here, we show that ATP enhances this process by modulating secondary structure formation within the translocating protein. (elifesciences.org)
This ability to exploit structure within a pre-protein is an unexplored area of protein transport, which may apply to other protein transporters, such as those of the endoplasmic reticulum and mitochondria. (elifesciences.org)
C: The genomic structure of the human preproapelin gene as found in the human PAC 454M7 clone (GenBank accession no. (phoenixpeptide.com)

It also modulates gene transcription and recombination [ 7 ]. (hindawi.com)

The cryo-EM analysis also revealed a population of free V 1 bound to Oxidation Resistance 1 (Oxr1p), a poorly characterized protein that has been implicated in protecting cells from oxidative stress. (upstate.edu)
shown in red), a poorly characterized protein implicated in oxidative stress response. (upstate.edu)

S100 genes include at least 19 members which are located as a cluster on chromosome 1q21. (wikipedia.org)
Human dysbindin domain-containing protein 1 (DBNDD1) is encoded by the gene DBNDD1 at chromosome locus 16q24.3. (springer.com)

The technique promises insight into the intracellular behavior of disease-causing proteins and novel drug screening applications, allowing in-situ visualization of how proteins respond to biochemical stimuli. (analytica-world.com)

Spectral density mapping at multiple magnetic fields suitable for C-13 NMR relaxation studies. (muni.cz)

Anatomy18

Organisms5

Diseases12

Chemicals and Drugs84

Analytical, Diagnostic and Therapeutic Techniques and Equipment66

Psychiatry and Psychology4

Phenomena and Processes61

Disciplines and Occupations7

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture4

Information Science13

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Nucleic acids3

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Intrinsically disordered6

Undergo conformational changes1

Mass spectrometry1

Fluorescence Correlation1

Crystallography4

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Amino-acid5

Backbone3

Interactions12

Residues2

Dynamics4

Lipids1

Sequences5

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Electron1

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Membranes2

Millisecond2

Biophysical Chemistry1

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Modulate1

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Higher eukaryotes2

Consistent1

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Allosteric1

Structure10

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