Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Structure”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 19 recordsLinked to original sources
PubMed1992

The refined 1.9-A X-ray crystal structure of D-Phe-Pro-Arg chloromethylketone-inhibited human alpha-thrombin: structure analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure-function relationships.

Thrombin is a multifunctional serine proteinase that plays a key role in coagulation while exhibiting several other key cellular bioregulatory functions. The X-ray crystal structure of human alpha-thrombin was determined in its complex with the specific thrombin inhibitor D-Phe-Pro-Arg chloromethylketone (PPACK) using Patterson search methods and a search model derived from trypsinlike proteinases of known spatial structure (Bode, W., Mayr, I., Baumann, U., Huber, R., Stone, S.R., & Hofsteenge, J., 1989, EMBO J. 8, 3467-3475). The crystallographic refinement of the PPACK-thrombin model has now been completed at an R value of 0.156 (8 to 1.92 A); in particular, the amino- and the carboxy-termini of the thrombin A-chain are now defined and all side-chain atoms localized; only proline 37 was found to be in a cis-peptidyl conformation. The thrombin B-chain exhibits the characteristic polypeptide fold of trypsinlike serine proteinases; 195 residues occupy topologically equivalent positions with residues in bovine trypsin and 190 with those in bovine chymotrypsin with a root-mean-square (r.m.s.) deviation of 0.8 A for their alpha-carbon atoms. Most of the inserted residues constitute novel surface loops. A chymotrypsinogen numbering is suggested for thrombin based on the topological equivalences. The thrombin A-chain is arranged in a boomeranglike shape against the B-chain globule opposite to the active site; it resembles somewhat the propeptide of chymotrypsin(ogen) and is similarly not involved in substrate and inhibitor binding. Thrombin possesses an exceptionally large proportion of charged residues. The negatively and positively charged residues are not distributed uniformly over the whole molecule, but are clustered to form a sandwichlike electrostatic potential; in particular, two extended patches of mainly positively charged residues occur close to the carboxy-terminal B-chain helix (forming the presumed heparin-binding site) and on the surface of loop segment 70-80 (the fibrin[ogen] secondary binding exosite), respectively; the negatively charged residues are more clustered in the ringlike region between both poles, particularly around the active site. Several of the charged residues are involved in salt bridges; most are on the surface, but 10 charged protein groups form completely buried salt bridges and clusters. These electrostatic interactions play a particularly important role in the intrachain stabilization of the A-chain, in the coherence between the A- and the B-chain, and in the surface structure of the fibrin(ogen) secondary binding exosite (loop segment 67-80).(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Chloromethyl Ketones↗
PubMed1978

[Rule of antibody structure: the primary structure of a human monoclonal IgA1-immunoglobulin (myeloma protein Tro), V. The arrangement of the tryptic peptides and a discussion of the complete primary structure of the H-chain (author's transl)].

This communication deals with the sequence work done with tryptic and chymotryptic peptides and some cyanogen bromide splitting products. With these peptides, and if necessary with their splitting peptides, the whole primary structure of the alpha1-H-chain of myeloma protein Tro is established. The position of the amides is determined by electrophoresis and digestion with aminopeptidase M. The alpha1-chain Tro comprises 475 amino acid residues. Because of its specific exchanges and deletions the variable part of alpha1-chain Tro belongs to subgroup III of variable parts of H-chains. The switch from the variable to the constant part occurs at position 119/120 and is analogous to other chains which have been sequenced up to now. The large number of cysteine residues in the alpha-chain which may influence the tertiary structure, especially in the hinge and the subsequent CH2-region, is noteworthy. Furthermore, myeloma protein Tro is compared with the other alpha1-chain Bur[5] sequenced in the meantime, and protein But[6], which is an IgA2 molecule of the allotype A2m(2).

Amino Acid Sequence↗
PubMed1976

[The rule of antibody structure. The primary structure of a monoclonal IgG1 immunoglobulin (myeloma protein Nie). III. The chymotryptic peptides of the H-chain, alignment of the tryptic peptides and discussion of the complete structure].

In this final paper the complete primary structure of the H-chain of immunoglobulin Nie (IgG1, Gm1+, 17+) is established by overlapping tryptic fragments with chymotryptic peptides. The preceding papers dealt with the purification of the protein, the characterization of the light and heavy chains, the purification and characterization of the cyanogen bromide cleavage products, the location of the disulfide bonds, the isolation of the tryptic peptides and their sequence determination. The gamma1-chain Nie comprises 448 amino acid residues. When the protein is compared with other H-chains, the switch from the variable to the constant part occurs at position 119/120. Based on the amino acid sequence of the variable part, protein Nie belongs to subgroup III of the H-chains. It was the first protein of this subgroup to be sequenced. In the meantime several other proteins are known which have been assigned to the same subgroup on the basis of linked amino acid exchanges in comparison to members of other subgroups. This confirms the evolutionary origin of antibody variability and hence the genetically fixed antibody specific. Furthermore protein Nie is the first completely determined chain with the genetic factors Gm1+, 17+. These factors are inherited codominantly and are localized on the constant part of the gamma1-chain. By comparison with protein Eu, which is Gml-, 4+ and therefore an allele of Nie, these serologically defined factors are correlated with Eu. Besides the amino acid exchanges caused by the Gm-factors we elucidated a series of differences to the constant part of the protein Eu. These differences include 6 amide postions and the sequence from residues 387 to 391. Using the structure of IgG1 Nie as an example some rules for the evolution of immunoglobulin sequences have been described. In particular the "elongation-rule" and the "Disulfide-rule" are discussed. While chain-elongation of the H-chains can simply be explained by repeated gene duplications of a basic unit containing ca 110 amino acids, the location of disulfide bonds is determined partly by gene duplication, which implies multiplication of evolutionary "old" cystein residues and partly by the relatively recent acquisition of "new" cystein in appropriate sites. Most evident is the origin of the "hindge-region" by partial gene duplication on the C-terminal residues of the first homology region.

Amino Acid Sequence↗
PubMed1992

The solution structure of eglin c based on measurements of many NOEs and coupling constants and its comparison with X-ray structures.

A high-precision solution structure of the elastase inhibitor eglin c was determined by NMR and distance geometry calculations. A large set of 947 nuclear Overhauser (NOE) distance constraints was identified, 417 of which were quantified from two-dimensional NOE spectra at short mixing times. In addition, a large number of homonuclear 1H-1H and heteronuclear 1H-15N vicinal coupling constants were used, and constraints on 42 chi 1 and 38 phi angles were obtained. Structure calculations were carried out using the distance geometry program DG-II. These calculations had a high convergence rate, in that 66 out of 75 calculations converged with maximum residual NOE violations ranging from 0.17 A to 0.47 A. The spread of the structures was characterized with average root mean square deviations ( ) between the structures and a mean structure. To calculate the unbiased toward any single structure, a new procedure was used for structure alignment. A canonical structure was calculated from the mean distances, and all structures were aligned relative to that. Furthermore, an angular order parameter S was defined and used to characterize the spread of structures in torsion angle space. To obtain an accurate estimate of the precision of the structure, the number of calculations was increased until the and the angular order parameters stabilized. This was achieved after approximately 40 calculations. The structure consists of a well-defined core whose backbone deviates from the canonical structure ca. 0.4 A, a disordered N-terminal heptapeptide whose backbone deviates by 0.8-12 A, and a proteinase-binding loop whose backbone deviates up to 3.0 A. Analysis of the angular order parameters and inspection of the structures indicates that a hinge-bending motion of the binding loop may occur in solution. Secondary structures were analyzed by comparison of dihedral angle patterns. The high precision of the structure allows one to identify subtle differences with four crystal structures of eglin c determined in complexes with proteinases.

Amino Acid Sequence↗
PubMedDate not supplied

[Stereochemical theory of the 3-dimensional structure of globular proteins. I. Highly helical intermediate structures].

The authors analyze the physical prerequisites on which the proposed stereochemical theory of the three-dimensional structure of globular proteins is based. The theory represents a stereochemical modelling of the mechanism of protein self-organization suggested earlier by one of the authors. According to this mechanism, a highly helical intermediate structure(s) is formed at first and then it passes into the native one. In the highly-helical intermediate structure the arrangement of the polypeptide chain in space is the same as in the native structure. These two structures differ mainly by the secondary structure of the chain. The transition into the native structure proceeds under the effect of long-range interactions which transform the excess alpha-helices into beta-structural and irregular conformations. The so-called s-helices are considered (the alpha-helix, whose hydrophobic groups form a separate cluster on its surface). s-Helices can be obtained on the greater part of the polypeptide chain of any globular protein. In the unfolded protein chain they are the most stable and rapidly formed structures. It has been shown that namely s-helices are the initial blocks for the formation of the highly-helical intermediate structure. Stereochemical principles of the s-helix packing that permit to predict the three-dimensional structure of highly helical proteins have been found. According to these principles the highly helical structure represents the packing of hydrophobic surfaces and s-helices. In their turn, hydrophobic surfaces are formed as a result of complementary interaction of borders of hydrophobic clusters of two s-helices according to the "knob-hole" principle.

Models, Chemical↗
PubMedDate not supplied

[Investigation of the structure of magnesium and lithium salts of T2 phage DNA by the method of x-ray diffraction. The possible mechanisms of the participation of cations in the structural transformation of double-stranded DNA].

The secondary structure of DNA is known to be largely determined by the kind of counterion bound to it. We have used the X-ray diffraction method to study the structure of magnesium and lithium salts of T2 phage DNA in oriented fibres. The structural behaviour of this glucosylated DNA in the form of magnesium and lithium salts was shown to be identical to the behaviour of the same salts of "normal" calf thymus DNA throughout the studied range of relative humidities (44-95%). However these two DNAs in the form of sodium salt are known to behave quite differently. One can presume that Mg2+ and Li+ influence the structural behaviour of double-stranded DNA so effectively as to be able to "ignore" the fact that T2 phage DNA contains glucoside residues. The results of this work and the already known facts concerning the structure of DNA in the form of various cation salts (in solution and in "solid" fibres) indicate that the structural behaviour of double-stranded DNA is mainly determined by the cation located in the region of the narrow groove of the double helix. If cations are graded according to the efficiency of their influence on the structural behaviour of DNA in fibres, the scale will coincide with that of their DNA-binding strength in water solution, that is: Mg2+ greater than Li+ greater than Na+ greater than K+ greater than Rb+. A qualitative consideration of electrostatic interaction between the cations and the negatively charged DNA strands leads one to suppose that this interaction must obstruct the transition of individual DNA molecules from the B-form to the A-form. Aggregation of self-aggregation of DNA molecules is presumed necessary to enable them to adopt the A-conformation.

Cations, Monovalent↗
PubMed2026

Dynamic Protein Structure Paradox: An Integrative Framework for Endpoint-Conditioned Evidentiary Sufficiency in Structure-to-Function Claims.

Accurate coordinates for a represented protein state do not, by themselves, establish activity or any other condition-specific function. This article defines the Dynamic Protein Structure Paradox (DPSP) as the apparent conflict between structural accuracy and functional underdetermination and develops it as an integrative evidentiary assessment framework rather than a new theory or paradigm. The underlying problem has been longstanding, since structural genomics, function annotation, allostery, and disorder research each established that fold does not determine function and that function does not determine fold. DPSP consolidates those results into one endpoint-conditioned rule. Once a measurable endpoint is defined, it assesses four coupled dimensions: relevant-state completeness, context completeness, ensemble or kinetic dependence, and chemical dependence. A rubric rates each dimension as adequate, uncertain, or missing, and a materiality test determines which gaps influence the stated decision. The outcome is one of three mutually exclusive modes of utilization: geometry-led, conditional, or function-measured. The deliverable is a concise evidence statement delineating what the structure supports, which decisive variable remains unmeasured, and what corroboration is necessary. DPSP complements, rather than replaces, existing structural, ensemble, and computational approaches. The framework remains unvalidated, its thresholds are provisional, and the studies necessary to confirm or refute it are specified.

Proteins↗
PubMed1976

The effects of deoxyribonucleic acid secondary structure on tertiary structure.

The secondary structure of supercoiled DNA was varied by changes in ionic strength. For I = 0.075-0.4 the structure remained in the previously established branched form with only minor alterations in molecular dimensions. In 4M-NaCl, which induces linear DNA to change its secondary structure to the C structure and brings about an increase in the superhelix density of the molecule, no extra branches were observed on the molecules. The limiting factors that dictate supercoil structure seem to be the number and position of potential branch points and the proximity with which the two intertwining DNA strands can approach each other on the arms of the branches. This value is close to 10nm under the conditions described, and is 14-15nm at I = 0.2. It is suggested that such values should be borne in mind when models of chromosome structure are being constructed.

Bacteriophages↗
PubMed1977

The structure of postsynaptic densities isolated from dog cerebral cortex. II. Characterization and arrangement of some of the major proteins within the structure.

An attempt was made to identify some of the proteins of the postsynaptic density (PSD) fraction isolated from dog cerebral cortex. The major protein has been tentatively labeled "neurofilament" protein, on the basis of its 51,000 mol wt correspondence to a protein found in neurofilament preparations. Other proteins are akin to some dog myofibrillar proteins, on the basis if immunological crossreaction and equal sodium dodecyl sulfate (SDS)-gel electrophoretic mobilities. While a protein similar to dog muscle myosin is not present in the PSD fraction, a major protein present is actin, as evident from reactivity with antiactin serum, from SDS-gel mobility, and from amino acid composition. Only very little tubulin may be present in the PSD fraction, as determined by gel electrophoresis. Various treatments of the PSD fraction were attempted in order to extract some proteins, as revealed by gel electrophoresis, and to observe the structural changes of the PSD fraction residue after extraction of these proteins. The PSD is remarkably resistant to various extraction conditions, with only 4 M guanidine being found to extract most of the proteins, except the 51,000 mol wt protein. Disulfide reducing agents such as dithiothreitol (DTT), blocking agents such as p-chloromercuribenzoate (PCMB) (both in the presence of deoxycholate [DOC]), a Ca++ extractor, ethylene glycol-bis (beta- aminoethyl ether) N,N,N',N'-tetraacetate (EGTA), and guanidine caused an opening up of the native dense PSD structure, revealing approximately 10-nm filaments, presumably consisting of "neurofilament" protein. Both DTT-DOC and PCMB-DOC removed chiefly actin but also some other proteins. EGTA, in greatly opening up the structure, as observed in the electron microscope, revealed both 10-nm and 3- to 5-nm filaments; the later could be composed of actin, since actin was still in the residue after the treatment. EGTA removed a major 18,000 mol wt component and two minor proteins of 68,000 and 73,000 mol wt. Based on the morphological and biochemical evidence, a picture is presented of the PSD as a structure partly made up of 10-nm and 3- to 5-nm filaments, held together through Ca++ interaction and by bonds amendable to breakage by sulfhydrylblocking and disulfide-reducing reagents; either removal of Ca++ and/or rupture of these disulfide bonds opens up the structure. On the basis of the existence of filamentous proteins and the appearance of the PSD after certain treatments as a closed or open structure, a theory is presented with envisages the PSD to function as a modulator in the conduction of the nerve impulse, by movements of its protein relative.

Actins↗
PubMed1975

Crystal structure of human erythrocyte carbonic anhydrase B. Three-dimensional structure at a nominal 2.2-A resolution.

The three-dimensional structure of carbonic anhydrase B (EC 4,2,1,1; carbonate hydro-lyase) from human erythrocytes has been determined to high resolution. Parallel and antiparallel pleated sheet makes up the predominant secondary structure of the enzyme. The tertiary structure is unique for its folding and is very similar to the structure is unique for its folding and is very similar to the structure of the isoenzyme, human erythrocyte carbonic anhydrase C. The essential metal ion, zinc, is firmly bound to the enzyme through three histidyl ligands and located at the bottom of a 12-A deep conical cavity. The zinc ligands are involved in a number of hydrogen bond formations with residues in the immediate vicinity of the active site cavity. Some of the similarities and differences in the sidechain orientation and active site topography of the two isoenzymes are also discussed.

Binding Sites↗
PubMed1977

Predicted secondary structure of snake venom toxins from their primary structures.

We have predicted the secondary structure of 38 snake venom toxins using the method of Chou and Fasman. Our predictions indicate that beta-chain and random coil structures predominate in these proteins. The conformations of long neurotoxins, short neurotoxins and cytotoxins are less similar than previously believed. Cytotoxins contain 40--50% of beta-structure and they form a notably homogeneous group. Short neurotoxins contain less beta-structure (13--30%) and more random coil than cytotoxins, and they also form a more heterogeneous group in terms of secondary structure. The characteristics of long neurotoxins are intermediate to the above mentioned groups. Experimental evidence supporting these propositions is discussed.

Amino Acid Sequence↗
PubMedDate not supplied

[Stereochemical theory of the 3-dimensional structure of globular proteins. III. Prediction of the tertiary structure].

A prediction is made of the tertiary structure of parvalbumin, the variable part of the immunoglobulin molecule, carboxypeptidase and the trypsin inhibitor. The structures obtained theoretically coincide completely with the native ones. In the case of the trypsin inhibitor molecule, the theoretical sequence of disulfide bridge formation completely coincides with the experimental data. Elements of symmetry were found in highly helical intermediate structures of the four proteins studied. The theory developed can be successfully applied for assembling the quaternary protein structure. Proceeding from this theory the mechanisms of the increased rate of assembly of protein spatial structure in conditions in vivo as compared with their assembly in vitro are analysed.

Animals↗
PubMed1977

Threonyl-transfer ribonucleic acid synthetase from Escherichia coli: subunit structure and genetic analysis of the structural gene by means of a mutated enzyme and of a specialized transducing lambda bacteriophage.

Threonyl-transfer ribonucleic acid synthetase (ThrRS) has been purified from a strain of Escherichia coli that shows a ninefold overproduction of this enzyme. Determination of the molecular weight of the purified, native enzyme by gel chromatography and by polyacrylamide gel electrophoresis at different gel concentrations yielded apparent molecular weight values of 150,000 and 161,000, respectively. Polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate yields a single protein band of 76,000-dalton size. From these results an alpha(2) subunit structure can be inferred. A mutant with a structurally altered ThrRS, which had been obtained by selection for resistance against the antibiotic borrelidin, was used to map the position of the ThrRS structural gene (thrS) by P1 transductions. It was found that thrS is located in the immediate neighborhood of pheS and pheT, which are the structural genes for the alpha and beta subunits of phenylalanyl-transfer ribonucleic acid (tRNA) synthetase, the gene order being aroD-pheT-pheS-thrS. A lambda phage that was previously shown to specifically transduce pheS, pheT, and also the structural gene for the translation initiation factor IF3 can complement the defect of the altered ThrRS of the borrelidin-resistant strain. This phage also stimulates the synthesis of the 76,000, molecular-weight polypeptide of ThrRS in ultraviolet light-irradiated. E. coli cells. These results indicate that the genes for ThrRS, alpha and beta subunits of phenylalanyl-tRNA synthetase, and initiation factor IF3 are immediately adjacent on the E. coli chromosome.

Amino Acyl-tRNA Synthetases↗
PubMedDate not supplied

[Optical properties and molecular structure of nucleic acids and their components. X. Infrared spectra and molecular structure of denatured DNA with different water content and degree of protonation].

IR-spectra (4000-900 cm-minus-1) of heat denatured DNA (d-DNA) of calf thymus have been obtained in the range of relative humidity of 0-93% and of the guota of protoned bases alpha of 0-0,5. fron these spectra the diagram of d-DNA states is plotted as the relationships of intensities and the location of some bands with and relative humidity. At alpha approximately 0,2 a compact structure S2-1 with firm hydrogen bonds between protoned and unprotoned bases which is similar to those observed earlier while protoning homopolynucleotides poly-A and poly-C. At G1'-large values of alpha S2-1-conformation destroyed and a loose structure (alpha approximately 0,35) appears. the latter is characterized by a minimum H-binding of the base and increased hydration. Further increase of alpha brings about the formation of sufficiently compact G2-1-STRUCTURE WHICH IS CHARACTERIZED BY SOLID H-bonds between PO2-groups and protoned bases. A specific effect of the structures found on the state of absorbed water and the structure of hydrate envelope is revealed.

Animals↗