Intermediates protein structure secondary. Medical search. Frequent questions

This is consistent with a 'global collapse' model of folding rather than a framework model in which folding is initiated from fully preformed local secondary structural elements. (au.dk)
The major transition state for the folding of barnase, for example, has some fully formed secondary and tertiary structural elements in the major transition state, and barnase appears to form by a framework process. (au.dk)
Large polypeptides that form a-helix or ß-sheet structures are currently beyond the reach of rotational spectroscopists, but the recent ion-drift experiments [13-15] on acetyl-(alanine)7-lysine suggest that the first direct observations of the structural motifs found in protein and peptide secondary structure using high resolution spectroscopy may not be far off. (kent.edu)
The models of the active mitoribosome explain how mRNA binds through a dedicated protein platform on the small subunit, tRNA is translocated with the help of the protein mL108, bridging it with L1 stalk on the large subunit, and nascent polypeptide paths through a newly shaped exit tunnel involving a series of structural rearrangements. (nature.com)
In contrast, the absence of Sgs1 or Pif1 helicases did not inhibit replication through structural barriers, though Pif1 did facilitate replication of a telomeric protein barrier. (uthscsa.edu)
Our analyses reveal fundamental differences in the replication of DNA structural versus protein barriers, with Srs2 helicase activity exclusively required for fork progression through hairpin structures. (uthscsa.edu)
They provide structural evidence that this protein is a novel N-succinyl-L-ornithine transcarbamylase. (nih.gov)
The structural analysis shows that the mutated site is exposed and has a coil secondary structure on the domain region. (tu-muenchen.de)
The project should involve both studies of protein function by the applicant researchers and structural studies by the PSI:Biology network. (nih.gov)
Example-appear in each structural domain of the signalling protein calmodulin and in the muscle protein troponin-C . (vigyansarovar.com)
As a continuation of this work, we analyzed here the effects of this substitution on the structural properties of proteins capable of adopting multiple conformations (folded, and different partially folded states, e.g. a molten globule-like intermediate) at mild denaturing conditions. (usf.edu)
Why do hydrogen bonds between atoms of the polypeptide backbone, form both helix and pleated structures, instead of only one structural type? (stackexchange.com)
Also cleaves Nef and Vif, probably concomitantly with viral structural proteins on maturation of virus particles (By similarity). (proteopedia.org)
They aimed to address the shortcomings of the revolutionary AlphaFold2, which, despite predicting protein structures with remarkable accuracy and dramatically advancing structural biology, lacked accessible code and training data. (cbirt.net)
The secondary structural analysis further validates the stability owing to higher α-helices. (springeropen.com)
Some functions are performed by disordered protein structural parts. (alzforum.org)
The work provides the first structural and dynamics characterization of human RBMS1 protein, that controls the expression of c-myc proto-oncogene inside the human cell by its interaction with 7 base pair consensus sequence within the 21 bp promoter/ autonomous origin of replication region 2 kb upstream of c-myc proto-oncogene. (neelsb.com)
Our analysis suggests that the bending action of HU on DNA is mediated by a mechanical clamping mechanism, in which metastable structural intermediates sampled during the hinge motions of the β-arms in the free state are presculpted to bind DNA. (ox.ac.uk)
Using SWAXS and Raman spectroscopy, we investigated reversibility of the unfolding for each hydration regime for various structural levels including overall molecular shape, secondary structure, hydrophobic and hydrogen bonding interactions. (lu.se)

Some primary carbon metabolism-related enzymes were up-regulated by JA to provide sufficient metabolism intermediates and energy for tuber development. (biomedcentral.com)
Helix-turn-helix motif are involved in many processes that includes DNA repair, RNA metabolism, and protein-protein interaction . (vigyansarovar.com)
Sieradzki K, Tomasz A. Alterations of oscillated between 0.5 and 1.0 g/ in autolysis ( 2 , 3 ) and in the cell wall cell wall structure and metabolism ac- mL. (cdc.gov)
The proteins, termed apolipoproteins, play an important role in lipoprotein metabolism. (medscape.com)

Thus, while the adenine site preferences of the spliceosome and of phage GA may be due to protein factors, the preferred adenine is predisposed in the free RNA to conformational rearrangement involved in formation of the active complexes. (rcsb.org)
1-7] Molecular moments of inertia, derived from spectra fitting, are used to determine conformational structures, and atomic coordinates can be determined to within a picometer or less. (kent.edu)
Many neurodegenerative diseases, also termed as protein conformational diseases [ 1 ], are characterised by accumulations of misfolded proteins that often share morphological and biochemical features and can colocalise with several other proteins, including various chaperone proteins. (biomedcentral.com)
Chaperone proteins have therefore been implicated as potent modulators of protein conformational disorders, suppressing toxicity of misfolding proteins and modifying early events in the aggregation process in a cooperative and sequential manner reminiscent of their functions in de novo protein folding [ 5 ],[ 6 ]. (biomedcentral.com)
A conformational ensemble derived using NMR methyl chemical shifts reveals a mechanical clamping transition that gates the binding of the HU protein to DNA. (ox.ac.uk)

Some dipeptides are known to have physiological or cell-signalling effects although most are simply short-lived intermediates on their way to specific amino acid degradation pathways following further proteolysis. (hmdb.ca)
It is anticipated that this integrated approach will lead to an in depth understanding of the folding pathways of these diverse protein systems. (elsevierpure.com)
The accumulation of misfolded proteins may adversely affect neuronal connectivity and plasticity and trigger cell death signalling pathways [ 2 ]. (biomedcentral.com)

Together with previous findings, these results indicate that non-native interactions within the alpha-domain intermediate are directly responsible for the unusual optical properties observed during refolding, and that this intermediate accumulates as a consequence of its intrinsic stability in a folding process where the formation of stable structure in the beta-domain constitutes the rate-limiting step for the majority of molecules. (ox.ac.uk)
This RP-box affected the efficiency of filament assembly as well as protein-protein interactions in the filament, as shown by sedimentation assays and electron microscopy. (ox.ac.uk)
We also cannot exclude the possibility that the structures of both proteins and polymers determine the balance between attractive and repulsive forces that drive protein-polymer interactions. (usf.edu)
There might be cases where some interactions might be unfavorable in some configuration, but there might be other interactions nearby which stabilize the entire structure. (stackexchange.com)
Particular protein structures arise because of a potentially very complex interplay of interactions within a chain, with other chains (from other subunits in a multimeric protein or from chaperones or other biomolecules) and with the solvent which includes water, lipids, ions, small molecules. (stackexchange.com)
It functions as a molecular chaperone, aiding the refolding of non-native proteins, and plays a critical role in stabilisation of the cytoskeleton through interactions with several cytoskeletal components, such as actin, intermediate filaments and microtubules [ 7 ]. (biomedcentral.com)
Understanding specificity of protein-DNA interactions is a long-standing question that has been attempted to understand many times by scientists all over the world. (neelsb.com)
The work has implications for understanding general mechanism of protein-DNA interactions that involves sliding, hopping and diffusion during stochastic target search process in a dense nucleus. (neelsb.com)
rium properties, completely determined by the interactions within crystal structures of 38 nonhomologous proteins, we find that it the system. (lu.se)

His research sped a shift in many biologists' attention from organismic biology, the study of creatures great and small, to molecular biology, which focuses on the individual biochemical reactions that underpin all living processes and on the molecules - usually proteins - responsible for catalyzing those reactions. (stanford.edu)
The oxygen atom in water has four nonbonding electrons, and the oxygen atom in formaldehyde carries two pairs of unshared electrons, represented by four dots on the oxygen atoms of the two molecules in the Lewis structure. (nationalacademies.org)
FIGURE 2.1 Lewis structures for formaldehyde (left) and water (right) show the presence of four electrons (each represented by a dot) on the oxygen atoms of the two molecules.These electrons are not involved in the formation of any bond. (nationalacademies.org)
Viroids are non-encapsidated, single-stranded (ss), 250-400 nucleotide (nt)-long circular RNA molecules that do not encode proteins (1, 2). (degruyter.com)
In the intermediate range of water contents between 37 wt% and 60 wt%, the system is phase separated and the thermal denaturation involves two processes: melting of protein crystals and unfolding of protein molecules. (lu.se)
On aver- comprising some 1015 protein molecules. (lu.se)
A cardiomelic developmental field has also been postulated to relate the genetic heterogeneity of HOS (and other similar syndromes) to a cascade of molecules, including the brachyury, sonic hedgehog, bone morphogenetic protein, retinoic acid receptor, and transforming growth factor beta families. (medscape.com)

Using heteronuclear NMR spectroscopy, we have determined the structure of this hairpin to an overall precision of 2.0 A. Both adenine bases stack into the helix, and while all available NOE and coupling constant data are consistent with both possible A.U base pairs, the base pair involving the 5'-proximal adenine appears to be the major conformation. (rcsb.org)
Here we aim to characterize pre-selected oligomers of polydisperse protein assemblies regarding their secondary, tertiary, and quaternary structure using a combination of MS, IM-MS and gas-phase spectroscopy techniques. (fu-berlin.de)
Rotational spectroscopy provides the highest resolution structures of amino acids and peptides - the building blocks of life. (kent.edu)
The isotope synthesis projects provide practical experience in peptide synthesis, purification, and analysis of intermediates using NMR, IR, and MS. Other students have tackled the rotational spectroscopy of these species. (kent.edu)
In particular, ultrafast XFEL spectroscopy is used to evaluate the methionine-S-Fe bond in cytochrome c, and its entatic control by the protein in determining function (electron transfer vs. apoptosis). (stanford.edu)
The structures of the intermediates will be studied by visible and UV resonance Raman scattering, by tryptophan fluorescence, by infrared spectroscopy and by spin labeled EPR spectroscopy. (elsevierpure.com)

Supersecondary structures can also be considered as an intermediate between secondary and tertiary structures. (vigyansarovar.com)
Recent improvements in the accuracy of structure-based methods for the prediction of nuclear magnetic resonance chemical shifts have inspired numerous approaches for determining the secondary and tertiary structures of proteins. (ox.ac.uk)

These proteins undergo a spontaneous transition from a soluble, often partially folded form into an insoluble, beta-sheet rich amyloid fibril. (fu-berlin.de)
Neither the natively unfolded nor the partially folded intermediate conformations are affected by the familial Parkinson's disease point mutations. (nih.gov)
We attribute this effect to the increased propensity of their partially folded intermediates to aggregate, rather than to any changes in the monomeric natively unfolded species. (nih.gov)
To this end, we have selected several proteins (α-lactalbumin, apomyoglobin, carbonic anhydrase, staphylococcal nuclease, and cytochrome c) and examined them at different conditions where they exist in different partially folded conformations (pH, temperature, salt concentrations, presence of cofactors). (usf.edu)
We were especially interested in the relative sensitivity of partially folded (e.g. molten globule) conformations of these proteins to the presence of polymers as these conformations are often the most sensitive to the environment. (usf.edu)

Phoratoxin expresses different features that are typical for membrane active proteins, it is compact, contains many basic amino acid residues and it contains one weakly polar flat face. (wikipedia.org)
The structure of the rate-determining transition state has been mapped out at the resolution of individual side chains by using the protein engineering method on 74 mutants that have been constructed at 37 of the 64 residues. (au.dk)
It suggests that such mutation might not effect the protein function although the both residues do not share very close phisicochemical properties. (tu-muenchen.de)
The protein-DNA interaction is stabilized by nonspecific contacts between the DNA backbone and residues in α 2 and the turn between α 2 and α 3. (vigyansarovar.com)
We used far-UV CD to test the changes in the protein secondary structure, near-UV CD to monitor changes in the tertiary structure, and quenching of intrinsic protein fluorescence by acrylamide to evaluate changes in the solvent accessibility of aromatic residues. (usf.edu)
The fACCD were found 16.18-82.47 kDa proteins having 149-750 amino acid residues. (springeropen.com)
We extended the boundary by 5 residues which lead to expression of highly stable RBMS1 protein. (neelsb.com)

This demonstration and Baldwin's follow-on findings simplified the analysis of proteins, accelerating the pace of discovery in medicinal chemistry and drug development. (stanford.edu)

The most relevant example of polydisperse systems are probably amyloid forming proteins occurring in neurodegenerative disorders such as Alzheimer's and Parkinson's disease. (fu-berlin.de)
We have previously shown that increasing the hydrophobicity of PEG by adding a methyl group to every other monomer unit allowed the resulting polymer to alter protein folding and inhibit protein aggregation to amyloid fibrils. (usf.edu)
C-reactive protein,mannose-binding lectin, and serum amyloid P component activate complement and act as opsonins. (msdmanuals.com)
Serum amyloid A and alpha-1 acid glycoprotein are transport proteins, and fibrinogen is a coagulation factor. (msdmanuals.com)

The equilibrium and kinetics of folding of the single-domain protein chymotrypsin inhibitor 2 conform to the simple two-state model. (au.dk)
The impact of the structure of the early intermediates on the overall folding kinetics will be examined. (elsevierpure.com)

These findings provide new information on the putative role of succinylated intermediates in arginine biosynthesis and on the evolution of transcarbamylases. (nih.gov)
And, a large number of protein biosynthesis, degradation and assembly-related were up-regulated by JA to promote tuber protein biosynthesis and maintain strict protein quality control during tuber development. (biomedcentral.com)
The biosynthesis can be divided into enzymes responsible for the biosynthesis of the core structure (XcnAFHIJKL), including the hydroxymalonyl-ACP (XcnBCDE), in proteins involved in an interesting drug activation mechanism (XcnAG) and for a resistance conferring inactivation pathway (XcnMN). (uni-frankfurt.de)

Fig. 4: Cryo-EM structure of Rubisco-M35 complexes. (nature.com)
DNA sequences that form secondary structures or bind protein complexes are known barriers to replication and potential inducers of genome instability. (uthscsa.edu)
These aggregates may consist of oligomeric complexes of non-native secondary structures and demonstrate poor solubility in aqueous or detergent solvents [ 3 ]. (biomedcentral.com)
Plasma lipoproteins are macromolecular complexes of lipids and proteins that are classified by density and electrophoretic mobility. (medscape.com)

To address this issue, we investigated the influence of the primary and secondary coordination sphere on CuII-catalyzed S-nitrosylation by developing a series of azurin variants with varying catalytic capabilities. (stanford.edu)
A desaturase (XcnN) and a saccharopine dehydrogenase-like enzyme (XcnM) are essential for this unusual transformation via two new identified intermediates and the catalytic reaction is regulated by the response regulator OmpR. (uni-frankfurt.de)

During the splicing of introns out of pre-mRNA, the 2'-OH of the bulged adenine participates in the transesterification reaction at the 5'-exon and forms the branch-point residue of the lariat intermediate. (rcsb.org)
mRNA localisation requires primary sequences and secondary structures often localised in their 3'UTR (3). (europa.eu)
RNA binding proteins recognize these sequences and assemble with their mRNA target into mRNPs. (europa.eu)
Mutations affecting zipcodes, RBPs or motor-proteins required for neuronal mRNA localization were shown to lead to severe neurodegenerative diseases as ALS, FXTAS and FXS (7), underlining the need to understand the mechanisms that drive neuronal mRNA transport. (europa.eu)
Inhibiting the localisation of this mRNA leads to a significant reduction of CamKIIa protein at postsynaptic densities and a strong reduction of cognitive abilities in animal models (12). (europa.eu)
Also in this specific case, it is not understood how RBPs, potential adaptors and motor proteins, which are essential for the transport of CaMKIIa-mRNA are mechanistically contributing to its correct localisation. (europa.eu)
We report models of the translating fungal mitoribosome with mRNA, tRNA and nascent polypeptide, as well as an assembly intermediate. (nature.com)
Binding of mRNA requires extended mitoribosomal proteins of the small subunit, and movement of tRNA is realized through additional proteins of the large subunit. (nature.com)
The transcription of COX-1 yields a 2.7-kilobase (kb) messenger ribonucleic acid (mRNA) that encodes a 576-residue, 65-kd protein. (medscape.com)
Conversely, the transcription of COX-2 yields a 4.5-kb mRNA that encodes a 70-kd protein with roughly 70-75% homology to the COX-1 protein. (medscape.com)

See also David Thirumalai's Emerging Ideas on the Molecular Basis of Protein and Peptide Aggregation ' (.pdf). (alzforum.org)
Many neurodegenerative diseases are characterised by accumulations of misfolded proteins that can colocalise with chaperone proteins (for example, heat shock protein 27 (HSP27)), which might act as modulators of protein aggregation. (biomedcentral.com)

With this technique, we have been able to observe the folding of a lipid binding protein, cytochrome c and sperm whale apo-myoglobin in the submillisecond time domain for the first time. (elsevierpure.com)
We will further test this hypothesis in new studies on the lipid binding protein, cytochrome c and myoglobin systems. (elsevierpure.com)

That dementia is a direct result of neuronal damage and loss associated with accumulations of abnormal protein deposits in the brain. (semcs.net)

A primary example is how copper proteins can promote S-nitrosylation (SNO), which is one of the most important dynamic post-translational modifications, and is crucial in regulating nitric oxide storage and transportation. (stanford.edu)

Interestingly, replication through a protein barrier but not a DNA structure barrier was modulated by nucleotide pool levels, illuminating a different mechanism by which cells can regulate fork progression through protein-mediated stall sites. (uthscsa.edu)
We have employed a multidimensional approach involving electronic absorption, S and Cu K-edge XAS, EPR, and resonance Raman spectroscopies together with QM/MM computational analysis to examine the relationships between structure and molecular mechanism in this reaction. (stanford.edu)
Based on these studies, we proposed a biphasic mechanism, which guarantees that the protein folds into its unique native conformation with high efficiency and fidelity. (elsevierpure.com)

Facilitates rearangement of nucleic acid secondary structure during retrotranscription of genomic RNA. (proteopedia.org)
Virus particles have a nucleic acid genome and may also carry a few viral proteins, which are enclosed in a capsid of viral proteins or an envelope comprised of a small part of the host cell membrane. (fortunejournals.com)

We show that the Srs2 protein facilitates replication of hairpin-forming CGG/CCG repeats and prevents chromosome fragility at the repeat, whereas it does not affect replication of G-quadruplex forming sequences or a protein-bound repeat. (uthscsa.edu)
For decades, deciphering protein structures from sequences has been a pivotal challenge in biology. (cbirt.net)

Since both of these amino acids are also hydrophobic this mutation is thought to have little interference with the folding and stability of the protein. (wikipedia.org)
Buzz was a giant in the field of protein folding, and a profoundly influential mentor to many. (stanford.edu)
Soft-spoken, of moderate height and slight of build, "Buzz was a giant in the field of protein folding, and a profoundly influential mentor to many," said Peter Kim , PhD, the Virginia and D. K. Ludwig Professor in Biochemistry, who conducted doctorate work under Baldwin's tutelage in the 1980s. (stanford.edu)
Structure of the transition state for the folding/unfoldi. (au.dk)
This may be a general feature for the folding of proteins lacking a folding intermediate and is perhaps representative of the early stages of folding for multidomain or multimodule proteins. (au.dk)
Defining the nature of thermal intermediate in 3 state folding proteins: apoflavodoxin, a study case. (irbbarcelona.org)
The origin of the alpha-domain intermediate in the folding of hen lysozyme. (ox.ac.uk)
The underlying assembly pathway is not fully understood to date, but there has been increasing evidence that oligomeric folding intermediates, which occur during the transformation process, are the toxic species in the above-mentioned diseases. (fu-berlin.de)
Cotranslational protein folding inside the ribosome exit tunnel. (pacb.com)
It is well established that proteins can fold cotranslationally outside the ribosome exit tunnel, whereas studies of folding inside the exit tunnel have so far detected only the formation of helical secondary structure and collapsed or partially structured folding intermediates. (pacb.com)
Thus, for small protein domains, the ribosome itself can provide the kind of sheltered folding environment that chaperones provide for larger proteins. (pacb.com)
Moreover, our examination of OpenFold's learning process sheds light on how it sequentially acquires spatial dimensions during protein folding. (cbirt.net)
Several lines of evidence suggest that the initial step in protein folding involves the collapse of a polypeptide chain. (elsevierpure.com)
Protein Folding and Neurodegeneration: Biophysics to the Rescue? (alzforum.org)
This does not change our view of protein folding in the least. (alzforum.org)

Identification of two N-terminal non-alpha-helical domain motifs important in the assembly of glial fibrillary acidic protein. (ox.ac.uk)
Supersecondary structures or motifs, are simple and frequent combinations of the secondary structure with a specific geometric arrangement. (vigyansarovar.com)

It may represent an accumulation of misfolded, damaged or unwanted proteins, awaiting or undergoing degradation. (biomedcentral.com)

Primary and Secondary Coordination Sphere Effects on the Structure and Function of S-Nitrosylating Azurin. (stanford.edu)
The global to expect complete eradication of elimination of congenital syphilis: ratio- aureus primary and secondary syphilis in nale and strategy for action. (cdc.gov)

Small details in the sequence, easily tunable by evolution, can yield to one or the other type of proteins. (irbbarcelona.org)
Ideally, the solution of these protein structures will also contribute to the understanding of protein sequence-structure relationships in general. (nih.gov)
The term 'motif' is also describes a consensus sequence of amino acids, i.e. a partial sequence common to a number of different proteins, which may or may not adopt similar conformations in the different proteins. (vigyansarovar.com)
1hxw is a 2 chain structure with sequence from 9hiv1 . (proteopedia.org)
Building upon prior deep learning work utilizing co-evolutionary data from multiple sequence alignments (MSAs) and homologous structures, AlphaFold2 has made remarkable strides in solving this problem for natural proteins with extensive MSAs. (cbirt.net)
3cyx is a 2 chain structure with sequence from Human immunodeficiency virus 1 . (proteopedia.org)
The primary amino acid sequence of a protein is a translated version from its gene sequence which carries important messages and information concealed therein. (springeropen.com)
The figure shows RBMS1 protein scanning the DNA in search of its target sequence and binding to the sequence's nucleotides in a specific manner. (neelsb.com)
Proteins search and bind specific sequence in the background of billions of bases in the genome. (neelsb.com)

Baldwin developed tools and designed rigorous experiments to show that instead of simply switching in binary fashion from their initial linear conformations into correctly folded final shapes, as had been postulated, proteins transition into their final shapes through short-lived intermediate structures. (stanford.edu)

Phoratoxin is an amphipathic molecule, a feature that is frequently found in membrane binding proteins. (wikipedia.org)
Matrix protein p17 has two main functions: in infected cell, it targets Gag and Gag-pol polyproteins to the plasma membrane via a multipartite membrane-binding signal, that includes its myristoylated N-terminus. (proteopedia.org)
They have been defined as monotropic integral membrane proteins located primarily in the endoplasmic reticulum (COX-1) and the perinuclear envelope (COX-2). (medscape.com)

Plant Dicer-like proteins (DCLs) are RNase III, double-stranded RNA (dsRNA)-specific endonucleases with specialized functions in producing short (s)RNAs of 21- to 24-nucleotides (nt), including micro (mi)RNAs and short interfering (si)RNAs of endogenous or viral origin. (biomedcentral.com)
It binds in the cytoplasm the human BAF protein which prevent autointegration of the viral genome, and might be included in virions at the ration of zero to 3 BAF dimer per virion. (proteopedia.org)
Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. (proteopedia.org)
We studied the course of infection by analysing the production of viral RNA, proteins and phage particles produced in the cell-free reactions. (fortunejournals.com)
The replication of the viral RNA was determined by RT-PCR, while the translation of the viral proteins was examined by radiolabelling, and the production of infectious phage particles was evaluated by double-layered plaque assays. (fortunejournals.com)
Specifically, the viral RNA was replicated, the viral proteins were translated, and infectious phage particles were produced in the cell-free infection systems. (fortunejournals.com)
The pattern of translation regulation of the viral proteins appeared similar to in vivo infection. (fortunejournals.com)

His discoveries laid the groundwork for our understanding of how a newborn protein accurately folds up into its adult shape within milliseconds - an insight that's informed molecular biology ever since. (stanford.edu)
The traditional discrete view of protein universe as a set of separate folds has been criticized in the light of growing evidence that almost any arrangement of secondary structures is possible and the whole protein space can be traversed through a path of similar structures. (elsevierpure.com)
This approach aimed to systematically assess OpenFold's capability to extrapolate to unfamiliar protein folds. (cbirt.net)
unreadable] DESCRIPTION (provided by applicant): How a protein folds into its native structure is one of the most important and challenging problems in biological science today. (elsevierpure.com)

Unlike HTH proteins, the actual DNA-binding motif of the HLH proteins is a stretch of about 13 "basic" amino acids adjacent to the HLH whose main role is in protein dimerization. (vigyansarovar.com)

We found that the complexity of the effect of polymers on protein structure cannot be ascribed solely to macromolecular crowding since the behavior of proteins in solutions containing polymers is dependent on protein and polymer structure. (usf.edu)

Instead of adopting one defined oligomerization state, some proteins exist as equilibrium of several distinctly sized species. (fu-berlin.de)

Here, using a combination of cotranslational nascent chain force measurements, inter-subunit fluorescence resonance energy transfer studies on single translating ribosomes, molecular dynamics simulations, and cryoelectron microscopy, we show that a small zinc-finger domain protein can fold deep inside the vestibule of the ribosome exit tunnel. (pacb.com)

Capsid protein p24 forms the conical core that encapsulates the genomic RNA-nucleocapsid complex in the virion. (proteopedia.org)
The core is constituted by capsid protein hexamer subunits. (proteopedia.org)

Proteins have segments of their polypeptide chain/chains that can be repeatedly coiled or folded into helix and pleated structures, respectively. (stackexchange.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)

His fields of research comprise RNA-mediated gene silencing processes with a focus on epigenetic phenomena, including studies on RNA-directed DNA methylation, the characterization of virus silencing suppressor proteins, the development of plant bioreactor platforms and viroid research. (degruyter.com)

This FOA encourages applications to establish partnerships between researchers interested in a biological problem of significant scope and researchers providing high-throughput structure determination capabilities through the NIGMS PSI:Biology network. (nih.gov)
Applicants to this FOA should propose work to solve a substantial biological problem for which the determination of many protein structures is necessary. (nih.gov)
It is expected that these awards will lead to new collaborations between researchers emphasizing biological function and researchers emphasizing biological structure. (nih.gov)
proteins could carry out their biological functions. (lu.se)
It can cover an unusually wide range of specimens from hard inorganic materials (oxides, metals and semiconductors) to soft materials (biological, colloidal systems, proteins). (lu.se)

Direct imaging of crystal structures and nanoparticles down to 0.86 Å resolution can be performed, as well as electron diffraction and element mapping/point analyses. (lu.se)

Structure, modes of action, stability, and resistance to these plant compounds will be discussed as well as their application in food industries and possible technologies by which they can be delivered. (hindawi.com)

An assembly intermediate is modeled with the maturation factor Atp25, providing insight into the biogenesis of the mitoribosomal large subunit and translation regulation. (nature.com)
Finally, we describe a bL9m-lacking assembly intermediate complexed with the maturation factor Atp25 that is formed as a result of protein splitting. (nature.com)

Hydrophobicity-dependent Effects of Polymers on Different Protein Conf" by Amanda E. Sales, Leonid Breydo et al. (usf.edu)

mRNAs are transported along microtubules (MTs) by different kinesins and cytoplasmic dynein and get anchored at the actin cortex, intermediate filaments or unknown structures (1, 3). (europa.eu)

50% in the transition state, although most regions do have some very weak structure. (au.dk)
The structure of the transition state appears to be an expanded form of the native state in which secondary and tertiary elements have been partly formed concurrently. (au.dk)

abstract = "Recently, the nature of protein structure space has been widely discussed in the literature. (elsevierpure.com)

Crystal structures of this novel transcarbamylase complexed with carbamyl phosphate and N-succinyl-L-norvaline, as well as sulfate and N-succinyl-L-norvaline have been determined and refined to 2.9 and 2.8 A resolution, respectively. (nih.gov)

At the time there were a number of critical, unanswered questions about proteins," said Paul Berg, PhD, emeritus professor of biochemistry and a member of that original group. (stanford.edu)
When we're taught biochemistry, we see proteins in their physiologically active forms. (alzforum.org)

When bound to phage GA coat protein, the bulged adenine loops out of the helix and occupies a binding pocket on the surface of the protein, forming a nucleation complex for phage assembly. (rcsb.org)
These helix-turn-helix structure found in many proteins(transcription factors). (vigyansarovar.com)
Its major function is in DNA recognition, as α 3 helix is involved in the recognition and is known as " recognization helix " while another one stabilizes the interaction between DNA and Protein. (vigyansarovar.com)
Large number of prokaryotic repressors belong to the helix-turn-helix family of proteins. (vigyansarovar.com)
My guess is that one structure (either a helix or pleated structure) is lower in potential energy compared to the other (because one structure likely maximises the number of hydrogen bonds that can form, compared to the other), which begs the question, why do both structures form, if they are largely a result of hydrogen bonds in the polypeptide backbone, rather than only one structure forming? (stackexchange.com)
I assume it wasn't what you intended to say because not the hydrogen bonds form helix/pleated structures, but the proteins. (stackexchange.com)

Baldwin propelled leaps in scientists' understanding of how proteins assemble themselves into the three-dimensional shapes that are essential to their function. (stanford.edu)

Presumably, this process involves the interaction between the host's bromodomain-containing viroid RNA-binding protein 1 (VIRP1) and the viroid's TR domain (6). (degruyter.com)
This requires an efficient and highly specific interaction between protein and DNA that control some of the most important processes pertaining to cell survival and growth. (neelsb.com)

Cleavages take place as an ordered, step-wise cascade to yield mature proteins. (proteopedia.org)
These results illustrate that using side-chain chemical shift data in conjunction with MD simulations can provide quantitative information about the free energy landscapes of proteins and yield detailed insights into their functional mechanisms. (ox.ac.uk)
Yet, the local yield a set of mean atomic positions r 0 density, averaged over volume elements of 0.1-1 nm3, varies k r k that define the ``ground-state'' protein structure, or, if resolution permits, a small substantially within a protein (14, 17, 18). (lu.se)

Evolutionary analysis comparing mitoribosomes from different species with bacterial counterparts, illustrates that the exit tunnel evolves via deletions in the rRNA and extensions of mitoribosomal proteins. (nature.com)
In order to determine which helicases facilitate DNA replication across these barriers, we analyzed fork progression through them in wild-type and mutant yeast cells, using 2-dimensional gel-electrophoretic analysis of the replication intermediates. (uthscsa.edu)
All three conservation analysis returned intermediate score near to "0" which suggest a neither close nor distant conservation relationship between two residuese. (tu-muenchen.de)
We used immunohistochemical and Western blot analysis to determine the distribution and amount of this protein in the frontal and temporal cortices of diseased and control subjects. (biomedcentral.com)

Glycine and alanine are both small amino acids, but glycine prefers turns while alanine prefers helices, and glycine is extremely flexible and intermediate while alanine is hydrophobic. (wikipedia.org)

Pospiviroidae's type species, potato spindle tuber viroid (PSTVd), has a rod-like secondary structure ∼360-nt-long genome that can be functionally and structurally divided into five domains: (i) terminal left, (ii) pathogenicity (P), (iii) central (C) containing the conserved central region, (iv) variable (v) and (5) terminal right (TR) (5). (degruyter.com)

Anatomy2

Organisms8

Diseases1

Chemicals and Drugs74

Analytical, Diagnostic and Therapeutic Techniques and Equipment59

Psychiatry and Psychology1

Phenomena and Processes85

Disciplines and Occupations13

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture4

Information Science34

Health Care13

Structural19

Metabolism4

Conformational5

Pathways3

Interactions9

Molecules7

Spectroscopy6

Tertiary structures2

Partially folded5

Residues7

Chemistry1

Amyloid4

Kinetics2

Biosynthesis3

Complexes4

Catalytic2

MRNA10

Aggregation2

Cytochrome2

Neuronal1

Copper proteins1

Mechanism3

Nucleic acid2

Sequences2

Folding15

Motifs2

Degradation1

Primary and secondary2

Sequence9

Conformations1

Membrane3

Viral7

Folds4

Dimerization1

Macromolecular1

Equilibrium1

Fluorescence1

Capsid2

Polypeptide chain1

Myoglobin1

Characterization1

Biological5

Electron1

Stability1

Maturation2

Polymers1

Filaments1

Transition2

Abstract1

Crystal structures1

Biochemistry2

Helix6

Assemble1

Interaction2

Yield3

Analysis4

Hydrophobic1

Genome1