SEARCH · PubMed Health

Results for “Protein Structure, Tertiary”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 523 records · Page 29Linked to original sources

PubMed2002

Structure-function relationships of heterodimeric amino acid transporters.

Heterodimeric amino acid transporters mediate the transfer of amino acids between organs and between different cell types. Members of this particular family of amino acid transporters are constituted by a heavy chain and an associated light chain. The heavy chain is a type II membrane protein with an intracellular amino terminus, a single transmembrane helix, and a large extracellular domain. The light chain, in contrast, is a typical helix-bundle protein with 12 putative transmembrane helices. Two different heavy chains, designated 4F2hc and rbAT, and seven different light chains have been identified to date. Deletion studies indicate that the extracellular domain of the heavy chain has two subdomains. The carboxy-terminal tip of 4F2hc is critical for recognition of certain light chains, whereas the carboxy-terminal tip of rbAT is involved in substrate transport. Sequence alignments suggest that the major part of the extracellular domain forms an alpha/beta domain similar to bacterial alpha-amylases. A structural model of the rbAT extracellular domain is presented that is in agreement with experimental observations from several mutations and that aligns well with the alpha-amylase domain.

Amino Acid Transport Systems↗

PubMed2005

Structure-activity relationship within the serine protease inhibitors of the pacifastin family.

The members of the Pacifastin family are serine protease inhibitors found in insects and crustacean. They are either small inhibitors (made of one consensus cysteine-rich motif) or proteins (4-9 motifs). Some of these inhibitors are characterized by a species selectivity for the trypsin inhibition. Structural data discriminate the small inhibitors that apparently look very similar into two groups. Interestingly, the inhibitors that display species selectivity fall in the same structural group.

Amino Acid Sequence↗

PubMed2000

The [beta]2a subunit is a molecular groom for the Ca2+ channel inactivation gate.

Ca(2+) channel inactivation is a key element in controlling the level of Ca(2+) entry through voltage-gated Ca(2+) channels. Interaction between the pore-forming alpha(1) subunit and the auxiliary beta subunit is known to be a strong modulator of voltage-dependent inactivation. Here, we demonstrate that an N-terminal membrane anchoring site (MAS) of the beta(2a) subunit strongly reduces alpha(1A) (Ca(V)2.1) Ca(2+) channel inactivation. This effect can be mimicked by the addition of a transmembrane segment to the N terminus of the beta(2a) subunit. Inhibition of inactivation by beta(2a) also requires a link between MAS and another important molecular determinant, the beta interaction domain (BID). Our data suggest that mobility of the Ca(2+) channel I-II loop is necessary for channel inactivation. Interaction of this loop with other identified intracellular channel domains may constitute the basis of voltage-dependent inactivation. We thus propose a conceptually novel mechanism for slowing of inactivation by the beta(2a) subunit, in which the immobilization of the channel inactivation gate occurs by means of MAS and BID.

Animals↗

PubMed2005

Factor X Shanghai and disruption of translocation to the endoplasmic reticulum.

BACKGROUND AND OBJECTIVES: Most secreted proteins, including coagulation factor X (FX), are synthesized with a signal peptide, which is necessary for targeting the nascent polypeptide into the endoplasmic reticulum. Characterization of naturally occurring mutations may provide insights into the functional roles of the amino acids in the signal peptide. DESIGN AND METHODS: A 52-year old male patient with type I FX deficiency was studied. Mutations were searched for by FX gene (F10) sequencing. The wild-type and the mutant FX proteins were expressed in transfected cells and then immunological assays were performed. Pulse-chase experiments and cell-free expression studies were conducted to determine the cellular fate of the mutant FX molecules. RESULTS: The patient we studied was homozygous for a substitution of arginine for serine at codon -30 in the signal sequence of F10. Immunoassays detected low FX antigen levels in both the conditioned media and lysates of the cells expressing the mutant protein. Pulse-chase analysis showed that only trace amounts of the mutant FX protein were detectable in the conditioned media, and that the mutant molecules did not accumulate inside the cells either. The results of cell-free expression studies showed that although the transcription and translation of the mutant construct were normal, no post-translational processing, such as N-linked glycosylation, occurred in the presence of microsomes. INTERPRETATION AND CONCLUSIONS: These findings suggest that substitution of a neutral polar amino acid, serine by arginine, in the hydrophobic core of FX signal peptide severely impairs the ability of the protein to enter the endoplasmic reticulum and results in FX deficiency.

Amino Acid Substitution↗

PubMed1989

The effects of near-UV radiation on human lens beta-crystallins: protein structural changes and the production of O2- and H2O2.

beta-Crystallins (beta 1-, beta 2- and beta 3-crystallin) comprise nearly half the protein of the human lens. The effect of near-UV radiation, which is one of the possible risk factors in cataract formation, on the beta-crystallins is investigated in this study. Protein intersubunit crosslinking, change in charge of the protein subunits to more acidic species and changes in protein tertiary structure (conformation) by 300 nm irradiation are reported. The fluorescence yield of protein tryptophan residues decreases by 300 nm irradiation. There is an increase in nontryptophan fluorescence (lambda cx 340 nm, lambda cm 400-600 nm), and in protein absorption at 340 nm, due to the formation of tryptophan photooxidation products. Both tryptophan and its oxidation products can be photoexcited by 300 nm irradiation and the latter are known to be good photosensitizers. The results provide evidence for the generation of H2O2 in the irradiated human beta-crystallin solutions by the Type I photosensitizing action of the chromophores absorbing at 300 nm. The H2O2 is generated via the intermediate production of O2 anion; the latter spontaneously dismutates to H2O2, presumably via O2- protein interactions. The amount of H2O2 generated per absorbed photon is compared for various solutions of beta 1-, beta 2- and beta 3-crystallins from human lenses of different age.

Circular Dichroism↗

PubMed1997

Progress in protein structure prediction.

If protein structure prediction methods are to make any impact on the impending onerous task of analyzing the large numbers of unknown protein sequences generated by the ongoing genome-sequencing projects, it is vital that they make the difficult transition from computational 'gedankenexperiments' to practical software tools. This has already happened in the field of comparative modelling and is currently happening in the threading field. Unfortunately, there is little evidence of this transition happening in the field of ab initio tertiary-structure prediction.

Algorithms↗

PubMed2006

Dominant pathways in protein folding.

We present a method to investigate the kinetics of protein folding and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. By writing the solution of the Fokker-Planck equation in terms of a path integral, we derive a Hamilton-Jacobi variational principle from which we are able to compute the most probable pathway of folding. The method is applied to the folding of the Villin headpiece subdomain simulated using a Go model. An initial collapsing phase driven by the initial configuration is followed by a rearrangement phase, in which secondary structures are formed and all computed paths display strong similarities. This completely general method does not require the prior knowledge of any reaction coordinate and is an efficient tool to perform simulations of the entire folding process with available computers.

Biophysics↗

PubMed2001

The N-terminal portion of mature aldehyde dehydrogenase affects protein folding and assembly.

Human liver cytosolic (ALDH1) and mitochondrial (ALDH2) aldehyde dehydrogenases are both encoded in the nucleus and synthesized in the cytosol. ALDH1 must fold in the cytosol, but ALDH2 is first synthesized as a precursor and must remain unfolded during import into mitochondria. The two mature forms share high identity (68%) at the protein sequence level except for the first 21 residues (14%); their tertiary structures were found to be essentially identical. ALDH1 folded faster in vitro than ALDH2 and could assemble to tetramers while ALDH2 remained as monomers. Import assay was used as a tool to study the folding status of ALDH1 and ALDH2. pALDH1 was made by fusing the presequence of precursor ALDH2 to the N-terminal end of ALDH1. Its import was reduced about 10-fold compared to the precursor ALDH2. The exchange of the N-terminal 21 residues from the mature portion altered import, folding, and assembly of precursor ALDH1 and precursor ALDH2. More of chimeric ALDH1 precursor was imported into mitochondria compared to its parent precursor ALDH1. The import of chimeric ALDH2 precursor, the counterpart of chimeric ALDH1 precursor, was reduced compared to its parent precursor ALDH2. Mature ALDH1 proved to be more stable against urea denaturation than ALDH2. Urea unfolding improved the import of precursor ALDH1 and the chimeric precursors but not precursor ALDH2, consistent with ALDH1 and the chimeric ALDHs being more stable than ALDH2. The N-terminal segment of the mature protein, and not the presequence, makes a major contribution to the folding, assembly, and stability of the precursor and may play a role in folding and hence the translocation of the precursor into mitochondria.

Aldehyde Dehydrogenase↗

PubMed1992

The organization of potato virus X coat proteins in virus particles studied by tritium planigraphy and model building.

Potato virus X particles containing the intact, undegraded Ps form of the coat protein and particles containing the in situ degraded Pf form of the coat protein, which is devoid of 19-21 amino acids from the N-terminus, were bombarded with thermally activated tritium atoms, and the intramolecular distribution of the tritium label was studied. The tritium planigraphy revealed that the N-terminal region of the coat protein is the most accessible region for both type of PVX particles. The C-terminal region of the coat protein in the intact virus particles is almost inaccessible to the hot tritium atoms, whereas in Pf particles this region becomes available for the tritium label. A model of PVX coat protein tertiary structure was built, taking into account the predicted secondary structure of the protein, the principles of packing alpha-helices and beta-structure in globular proteins, and known biochemical, immunological, and tritium bombardment data. In the model one beta-sheet consisting of beta-strands at regions 1-12, 14-22, and 24-33 flanks the molecule and forms the outside surface of the PVX particles.

Amino Acid Sequence↗

PubMed2004

Destabilization of the colicin E9 Endonuclease domain by interaction with negatively charged phospholipids: implications for colicin translocation into bacteria.

We have shown previously that the 134-residue endonuclease domain of the bacterial cytotoxin colicin E9 (E9 DNase) forms channels in planar lipid bilayers (Mosbahi, K., Lemaître, C., Keeble, A. H., Mobasheri, H., Morel, B., James, R., Moore, G. R., Lea, E. J., and Kleanthous, C. (2002) Nat. Struct. Biol. 9, 476-484). It was proposed that the E9 DNase mediates its own translocation across the cytoplasmic membrane and that the formation of ion channels is essential to this process. Here we describe changes to the structure and stability of the E9 DNase that accompany interaction of the protein with phospholipid vesicles. Formation of the protein-lipid complex at pH 7.5 resulted in a red-shift of the intrinsic protein fluorescence emission maximum (lambda(max)) from 333 to 346 nm. At pH 4.0, where the E9 DNase lacks tertiary structure but retains secondary structure, DOPG induced a blue-shift in lambda(max), from 354 to 342 nm. Changes in lambda(max) were specific for anionic phospholipid vesicles at both pHs, suggesting electrostatics play a role in this association. The effects of phospholipid were negated by Im9 binding, the high affinity, acidic, exosite inhibitor protein, but not by zinc, which binds at the active site. Fluorescence-quenching experiments further demonstrated that similar protein-phospholipid complexes are formed regardless of whether the E9 DNase is initially in its native conformation. Consistent with these observations, chemical and thermal denaturation data as well as proteolytic susceptibility experiments showed that association with negatively charged phospholipids destabilize the E9 DNase. We suggest that formation of a destabilizing protein-lipid complex pre-empts channel formation by the E9 DNase and constitutes the initial step in its translocation across the Escherichia coli inner membrane.

Acrylamide↗

PubMed2005

Structural genomics analysis of alternative splicing and application to isoform structure modeling.

Alternative splicing is a sophisticated nuclear process that regulates gene expression. It represents an important mechanism for enhancing the functional diversity of proteins. Our current knowledge of alternatively spliced variants is derived mainly from mRNA transcripts, and very little is known about their protein tertiary structures. We carried out a large-scale analysis of known alternatively spliced variants at both protein sequence and structure levels and have shown that threading is, in general, a viable approach for modeling structures of alternatively spliced variants. An examination of alternative splicing at the protein sequence level revealed that the size of splicing events follows the power law distribution and the majority of splicing isoforms harbor only one or two alternations. We examined alternative splicing in the context of protein 3D structures and found that the boundaries of alternative splicing events generally happen in coil regions of secondary structures and exposed residues and the majority of the sequences involved in splicing are located on the surface of proteins. In light of these findings, we then proceeded to demonstrate that threading represents a useful tool for structure prediction of alternative splicing isoforms and addressed the fold stability issue of threading-based structure prediction by molecular dynamics simulation. Our analysis and the insights gained have helped to establish a viable method for structure prediction of alternatively spliced isoforms at the genome scale.

Alternative Splicing↗

PubMed2003

Effects of disulfide bonds on compactness of protein molecules revealed by volume, compressibility, and expansibility changes during reduction.

To elucidate the effects of disulfide bonds on the compactness of protein molecules, the partial specific volume (v(o)) and coefficients of adiabatic compressibility (beta(s)(o)) and thermal expansibility (alpha) of five globular proteins (ovalbumin, beta-lactoglobulin, lysozyme, ribonuclease A, and bovine serum albumin) were measured in aqueous solutions with pH values of 7 and 2 at 25 degrees C when their disulfide bonds were totally reduced by carboxamidomethylation. Circular dichroism and fluorescence spectra show that the secondary and tertiary structures are partly disrupted by reduction, depending on the number of disulfide bonds in the proteins and the pH of the medium. The conformational changes are accompanied by decreases in v(o) and beta(s)(o) and by an increase in alpha, indicating that reduction decreases the internal cavity and increases surface hydration. The beta(s)(o) values of native or oxidized proteins decrease, and the effects of reduction on the volumetric parameters become more significant as the number of disulfide bonds increases and as they are formed over a larger distance in the primary structure. These results demonstrate that disulfide bonds play an important role, mainly via entropic forces, in the three-dimensional structure and compactness of protein molecules.

Animals↗

PubMed1996

A functional role for protein cavities in domain: domain motions.

Motions between individual domains are known to play an important role in protein function. Protein cavities at domain interfaces have been suggested to facilitate such movements. Consequently, the cavity morphology in a set of multi-domain proteins has been critically examined. The conformational changes were well characterised by atomic resolution tertiary structures prior to and after domain motions. The results showed that interdomain cavities play a number of specific functional roles by either facilitating, or being otherwise involved with, domain: domain motions. Correspondingly, a higher fraction of cavity surface is observed at domain interfaces as compared to that buried within individual domains. Furthermore, interdomain cavity-forming residues were found to be highly conserved in terms of amino acid residue sequence and volume within their aligned protein families, more so than residues exclusive to the domain interface and intradomain cavities. These results provide substantial evidence of cavities fulfilling a specific functional role in multi-domain proteins.

Amino Acid Sequence↗

PubMed1997

Applying experimental data to protein fold prediction with the genetic algorithm.

Specific residue interactions as revealed from a few and readily available experiments can be quite important in shaping a protein's tertiary topology by complementing basic and general folding principles. This experimental information is employed in structure prediction (mainchain topology) based on sequence knowledge and the genetic algorithm with its ability to optimize simultaneously many parameters. Examples investigated include the distribution of cysteinyl S-S bonds, protein side-chain ligands to iron-sulfur cages, cofactor-ligands, crosslinks amongst side-chains, and conserved hydrophobic and catalytic residues. Such interactions yield an improvement in the predicted topology (0.4-6.6 A root mean square deviation in the positions of the backbone C alpha-atoms relative to those observed) compared with those resulting from simulations relying only on basic protein folding principles. For several examples the resultant topology depended critically on knowledge of the few and specific interactions such that the relationship between predicted and observed C alpha-positions was near random without their use. The combined methodology (experimental data and the genetic algorithm) should prove helpful in settings where experiment and theory can cooperate in successive steps to elucidate an unknown structure.

Algorithms↗

PubMed1996

Ab initio tertiary-fold prediction of helical and non-helical protein chains using a genetic algorithm.

In this study, protein structures were predicted using a genetic algorithm. Optimal structures were selected according to basic protein-building principles. Having previously applied this approach to proteins with helical topology, this paper reports preliminary results on 3 proteins with mixed topology (helical and non-helical, e.g. sheet). The method seems to be generally applicable to protein-fold prediction since topology predictions close to the observed experimental structures are obtained.

Algorithms↗

PubMed1999

Extending the concept of template-assembled synthetic proteins.

The creation of native-like macromolecules in copying nature's way represents a fascinating challenge in protein chemistry today. In the absence of a detailed knowledge of the complex folding pathway the ultimate goal in protein de novo design, the construction of artificial proteins with predetermined three-dimensional structure and tailor-made functions based on a defined, generally valid set of rules, appears to be still out of reach. With progress in synthesis strategies and biostructural characterization methods, topological templates have become a versatile tool for inducing and stabilizing secondary and tertiary structures, such as protein loops, beta-turns, alpha-helices, beta-sheets and a variety of folding motifs. In this article, we extend the concept of template-assembled synthetic proteins for the construction of protein-like topologies with multiply bridged, oligocyclic chain architectures termed locked-in tertiary folds that exhibit unique physicochemical and folding properties because of the highly confined conformational space. Furthermore, we show that some fundamental questions in protein assembly can be approached applying the template concept. Using covalent template trapping of self-associated peptide assemblies in aqueous solution the structural and physical forces guiding protein folding, supramolecular assembly and molecular recognition processes can be studied on a molecular level.

Chromatography, High Pressure Liquid↗

PubMed2004

Predicted role for the archease protein family based on structural and sequence analysis of TM1083 and MTH1598, two proteins structurally characterized through structural genomics efforts.

Recently, the structures of two proteins belonging to the archease family, TM1083 from Thermotoga maritima and MTH1598 from Methanobacterium thermoautotrophicum, have been solved independently by two Protein Structure Initiative structural genomics pilot centers using X-ray crystallography and NMR, respectively. The archease protein family is a good example of one of the paradoxes of structural genomics: Approximately one third of protein structures produced by structural genomics centers have no known function and are still annotated as "hypothetical proteins" in the Protein Data Bank. In the case of archeases, despite the existence of two protein structures and abundant sequence information, there is still no function assigned to this protein family. Here, our group predicts, based on structural similarity, sequence conservation, and gene context analyses, that members of this protein family might function as chaperones or modulators of proteins involved in DNA/RNA processing. The conservation of genomic context for this protein family is constant from Archaea and Bacteria to humans, and suggests that unannotated open reading frames contiguous to them could be novel RNA/DNA binding proteins.

Amino Acid Motifs↗

PubMed2005

New method for protein secondary structure assignment based on a simple topological descriptor.

A simple, five-element descriptor, derived from the Delaunay tessellation of a protein structure in a single point per residue representation, can be assigned to each residue in the protein. The descriptor characterizes main-chain topology and connectivity in the neighborhood of the residue and does not explicitly depend on putative hydrogen bonds or any geometric parameter, including bond length, angles, and areas. Rules based on this descriptor can be used for accurate, robust, and computationally efficient secondary structure assignment that correlates well with the existing methods.

Algorithms↗