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 1,135 records · Page 63Linked to original sources
PubMed2003

Structural and functional consequences of binding site mutations in transferrin: crystal structures of the Asp63Glu and Arg124Ala mutants of the N-lobe of human transferrin.

Human transferrin is a serum protein whose function is to bind Fe(3+) with very high affinity and transport it to cells, for delivery by receptor-mediated endocytosis. Structurally, the transferrin molecule is folded into two globular lobes, representing its N-terminal and C-terminal halves, with each lobe possessing a high-affinity iron binding site, in a cleft between two domains. Central to function is a highly conserved set of iron ligands, including an aspartate residue (Asp63 in the N-lobe) that also hydrogen bonds between the two domains and an arginine residue (Arg124 in the N-lobe) that binds an iron-bound carbonate ion. To further probe the roles of these residues, we have determined the crystal structures of the D63E and R124A mutants of the N-terminal half-molecule of human transferrin. The structure of the D63E mutant, determined at 1.9 A resolution (R = 0.245, R(free) = 0.261), showed that the carboxyl group still binds to iron despite the larger size of the Glu side chain, with some slight rearrangement of the first turn of alpha-helix residues 63-72, to which it is attached. The structure of the R124A mutant, determined at 2.4 A resolution (R = 0.219, R(free) = 0.288), shows that the loss of the arginine side chain results in a 0.3 A displacement of the carbonate ion, and an accompanying movement of the iron atom. In both mutants, the iron coordination is changed slightly, the principal change being in each case a lengthening of the Fe-N(His249) bond. Both mutants also release iron more readily than the wild type, kinetically and in terms of acid lability of iron binding. We attribute this to more facile protonation of the synergistically bound carbonate ion, in the case of R124A, and to strain resulting from the accommodation of the larger Glu side chain, in the case of D63E. In both cases, the weakened Fe-N(His) bond may also contribute, consistent with protonation of the His ligand being an early intermediate step in iron release, following the protonation of the carbonate ion.

Amino Acid Substitution↗
PubMed2002

Structural basis of phospholipase A2 inhibition for the synthesis of prostaglandins by the plant alkaloid aristolochic acid from a 1.7 A crystal structure.

This is the first structural observation of a plant product showing high affinity for phospholipase A(2) and regulating the synthesis of arachidonic acid, an intermediate in the production of prostaglandins. The crystal structure of a complex formed between Vipera russelli phospholipase A(2) and a plant alkaloid aristolochic acid has been determined and refined to 1.7 A resolution. The structure contains two crystallographically independent molecules of phospholipase A(2) in the form of an asymmetric dimer with one molecule of aristolochic acid bound to one of them specifically. The most significant differences introduced by asymmetric molecular association in the structures of two molecules pertain to the conformations of their calcium binding loops, beta-wings, and the C-terminal regions. These differences are associated with a unique conformational behavior of Trp(31). Trp(31) is located at the entrance of the characteristic hydrophobic channel which works as a passage to the active site residues in the enzyme. In the case of molecule A, Trp(31) is found at the interface of two molecules and it forms a number of hydrophobic interactions with the residues of molecule B. Consequently, it is pulled outwardly, leaving the mouth of the hydrophobic channel wide open. On the other hand, Trp(31) in molecule B is exposed to the surface and moves inwardly due to the polar environment on the molecular surface, thus narrowing the opening of the hydrophobic channel. As a result, the aristolochic acid is bound to molecule A only while the binding site of molecule B is empty. It is noteworthy that the most critical interactions in the binding of aristolochic acid are provided by its OH group which forms two hydrogen bonds, one each with His(48) and Asp(49).

Animals↗
PubMed2004

Solution structure of human beta-parvalbumin and structural comparison with its paralog alpha-parvalbumin and with their rat orthologs.

The aim of this research was to determine the structure of human beta-parvalbumin (109 amino acids) and to compare it with its paralog and ortholog proteins. The structure was determined in solution using multinuclear and multidimensional NMR methods and refined using substitution of the EF-hand Ca(2+) ion with a paramagnetic lanthanide. The resulting family of structures had a backbone rmsd of 0.50 A. Comparison with rat oncomodulin (X-ray, 1.3 A resolution) as well as with human (NMR, backbone rmsd of 0.49 A) and rat (X-ray, 2.0 A resolution) parvalbumins reveals small but reliable local differences, often but not always related to amino acid variability. The analysis of these structures has led us to propose an explanation for the different affinity for Ca(2+) between alpha- and beta-parvalbumins and between parvalbumins and calmodulins.

Amino Acid Sequence↗
PubMed1998

Solution structure of Ace-AMP1, a potent antimicrobial protein extracted from onion seeds. Structural analogies with plant nonspecific lipid transfer proteins.

The three-dimensional solution structure of Ace-AMP1, an antifungal protein extracted from onion seeds, was determined using 1H NMR spectroscopy and molecular modeling. This cationic protein contains 93 amino acid residues and four disulfide bridges. Its structure was determined from 1260 NOE-derived distance restraints and 173 dihedral restraints derived from NOEs and 3JCaHNH coupling constants. The global fold involves four helical segments connected by three loops and a C-terminal tail without regular secondary structures, except for a 3(10)-helix turn and a beta-turn. The most striking feature is the absence of any continuous cavity running through the whole molecule as found in recently determined structures of nonspecific transfer proteins extracted from wheat and maize seeds, although their global folds are very similar. Consistent with the absence of a cavity in the core of Ace-AMP1, it was found that this protein, in contrast to ns-LTPs, does not bind fluorescently labeled phospholipids in solution. On the other hand, Ace-AMP1 is able to interact with phospholipid membranes as shown by the release of carboxyfluorescein from the lumen of artificial liposomes and by the induction of alterations in fluorescence polarization of fluorescently labeled phospholipids embedded in artificial liposomes.

Amino Acid Sequence↗
PubMed2001

Poly(oxazoline)s with tapered minidendritic side groups as models for the design of synthetic macromolecules with tertiary structure. A demonstration of the limitations of living polymerization in the design of 3-D structures based on single polymer chains.

The synthesis and living cationic ring-opening polymerization of 2-[3,4-bis(n-alkan-1-yloxy)phenyl]-2-oxazolines with alkan being tetradecan and pentadecan, i.e., (3,4)nG1-Oxz with n = 14 and 15, is described. The structural analysis of the resulting polymers with well-defined molecular weights and narrow molecular weight distribution was carried out by a combination of techniques, including differential scanning calorimetry (DSC), thermal optical polarized microscopy (TOPM), and X-ray diffraction (XRD). At low molecular weights both polymers self-assemble into spherical supramolecules that self-organize into a Pm3n 3-D lattice while at high molecular weights they form cylindrical macromolecules that self-organize into a p6mm 2-D hexagonal columnar lattice. Both polymers exhibit a 3-D shape change as a function of their degree of polymerization as was reported for the first time in a previous publication from our laboratory (Percec, V.; Ahn, C.-H; Ungar, G.; Yeardley, D. J. P.; Möller, M.; Sheiko, S. S. Nature (London) 1998, 391, 161). Since these polymers can be obtained via a living polymerization, a detailed mechanistic investigation of the influence of the degree of polymerization and molecular weight distribution on the formation of a 3-D spherical macromolecule from a single polymer chain, i.e., a tertiary structure, was possible. The experimental results have demonstrated that the synthesis of nonbiological macromolecules exhibiting tertiary structure is possible in at most a few percent of all macromolecules via living polymerization. This is the case even when macromolecules with very narrow molecular weight distributions and well-defined molecular weights are used. Therefore, the design of synthetic macromolecules with tertiary structure requires not only chains with well-defined molecular weight but also, in particular, macromolecules with no distribution of their chain length.

Calorimetry, Differential Scanning↗
PubMedDate not supplied

Structure-activity relationships for skin sensitization potential: development of structural alerts for use in knowledge-based toxicity prediction systems.

The development of qualitative structure-activity relationships for the prediction of skin sensitization potential, based on structural alerts (substructures associated with a toxicological mechanism), and suitable for incorporation as rules into a knowledge-based system is described. The structure dependence of the skin sensitization mechanism may be largely defined in terms of the presence or metabolic/nonmetabolic formation of protein reactive functional groups on the test compound and by the physicochemical requirements of significant skin penetration. The proposed structural alerts were tested on a data set of diverse chemicals. The results showed that the alerts have potential as preliminary indicators of skin sensitization potential for a wide range of low molecular weight chemicals.

Acylation↗
PubMedDate not supplied

Prediction of material properties from chemical structures. The clearing temperature of nematic liquid crystals derived from their chemical structures by artificial neural networks.

The prediction of properties of molecules just on the basis of their chemical structures is desirable to selectively make molecules that have the wanted properties, like biological activity, viscosity, or toxicity. Here, we present an example of a new way to predict a property from the chemical structure of a chemically heterogeneous class of compounds. The clearing temperatures of nematic liquid-crystalline phases of 17383 compounds were used to train neural networks to derive this material property directly from their chemical structure. The trained neural networks were subsequently tested with 4345 structural patterns of molecules unknown to the networks to assess their predictive value. The clearing temperatures were predicted by the best network with a standard deviation of 13 degrees.

Crystallization↗
PubMed2006

Tuning peptoid secondary structure with pentafluoroaromatic functionality: a new design paradigm for the construction of discretely folded peptoid structures.

Peptoids, or oligomers of N-substituted glycine, are an important class of non-native polymers whose close structural similarity to natural alpha-peptides and ease of synthesis offer significant advantages for the study of biomolecular interactions and the development of biomimetics. Peptoids that are N-substituted with alpha-chiral aromatic side chains have been shown to adopt either helical or "threaded loop" conformations, depending upon solvent and oligomer length. Elucidation of the factors that impact peptoid conformation is essential for the development of general rules for the design of peptoids with discrete and novel structures. Here, we report the first study of the effects of pentafluoroaromatic functionality on the conformational profiles of peptoids. This work was enabled by the synthesis of a new, alpha-chiral amine building block, (S)-1-(pentafluorophenyl)ethylamine (S-2), which was found to be highly compatible with peptoid synthesis (delivering (S)-N-(1-(pentafluorophenyl)ethyl)glycine oligomers). The incorporation of this fluorinated monomer unit allowed us to probe both the potential for pi-stacking interactions along the faces of peptoid helices and the role of side chain electrostatics in peptoid folding. A series of homo- and heteropeptoids derived from S-2 and non-fluorinated, alpha-chiral aromatic amide side chains were synthesized and characterized by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. Enhancement of pi-stacking by quadrupolar interactions did not appear to play a significant role in stabilizing the conformations of heteropeptoids with alternating fluorinated and non-fluorinated side chains. However, incorporation of (S)-N-(1-(pentafluorophenyl)ethyl)glycine monomers enforced helicity in peptoids that typically exhibit threaded loop conformations. Moreover, we found that the incorporation of a single (S)-N-(1-(pentafluorophenyl)ethyl)glycine monomer could be used to selectively promote looped or helical structure in this important peptoid class by tuning the electronics of nearby heteroatoms. The strategic installation of this monomer unit represents a new approach for the manipulation of canonical peptoid structure and the construction of novel peptoid architectures.

Amides↗
PubMed1975

Non-computer approach to structure-activity study. An expanded Fibonacci search applied to structurally diverse types of compounds.

The Fibonacci search technique, first applied to a structure-activity study by Bustard, has been expanded to allow the analysis of a broad class of structural types of compounds. The compounds are first arranged in order of increasing value of a molecular property of the analogs such as log P, Sigmapi, Sigmasigma, or Rm. A successful Fibonacci search of the compounds will find the most active analog in a small, predetermined number of steps. Examples are given where insight as to mechanism of action is indicated by the combination of various parameters such as log P and pKa. Additional examples illustrate the use of Fibonacci search to establish the parabolic dependence of the biological activity of lipophilicity and sigma, where such dependency had not been observed initially. This technique allows the treatment of a variety of structurally diverse types of compounds simultaneously. It is to be stressed that Fibonacci search can be applied to structure-activity studies without the use of a computer.

Antifungal Agents↗
PubMed2003

Total synthesis of the reputed structure of alcyonin and reassignment of its structure.

Introduction of the C4 hydroxyl group by an epoxy ester rearrangement is a pivotal step in the first total synthesis of the purported structure of alcyonin. As the spectral data for diol acetate 3 do not match those reported for alcyonin, the structure of this marine diterpene must be revised. Reexamination of NMR spectra, MS data, and chemical transformations of natural alcyonin suggests that the structure of this marine metabolite is allylic peroxide 15.[structure: see text]

Acetylation↗
PubMed1998

Prediction of the secondary structure contents of globular proteins based on three structural classes.

The prediction of the secondary structural contents (those of alpha-helix and beta-strand) of a globular protein is of great use in the prediction of protein structure. In this paper, a new prediction algorithm has been proposed based on Chou's database [Chou (1995), Proteins 21, 319-344]. The new algorithm is an improved multiple linear regression method, taking into account the nonlinear and coupling terms of the frequencies of different amino acids and the length of the protein. The prediction is also based on the structural classes of proteins, but instead of four classes, only three classes are considered, the alpha class, beta class, and the mixed alpha+beta and alpha/beta class or simply the alphabeta class. Thus the ambiguity that usually occurs between alpha+beta proteins and alpha/beta proteins is eliminated. A resubstitution examination for the algorithm shows that the average absolute errors are 0.040 and 0.035 for the prediction of alpha-helix content and beta-strand content, respectively. An examination of cross-validation, the jackknife analysis, shows that the average absolute errors are 0.051 and 0.045 for the prediction of alpha-helix content and beta-strand content, respectively. Both examinations indicate the self-consistency and the extrapolating effectiveness of the new algorithm. Compared with other methods, ours has the merits of simplicity and convenience for use, as well as high prediction accuracy. By incorporating the prediction of the structural classes, the only input of our method is the amino acid composition and the length of the protein to be predicted.

Algorithms↗
PubMed2003

Structure and function of the vacuolar H+-ATPase: moving from low-resolution models to high-resolution structures.

In the absence of a high-resolution structure for the vacuolar H+-ATPase, a number of approaches can yield valuable information about structure/function relationships in the enzyme. Electron microscopy can provide not only a representation of the overall architecture of the complex, but also a low-resolution map onto which structures solved for individually expressed subunits can be fitted. Here we review the possibilities for electron microscopy of the Saccharomyces V-ATPase and examine the suitability of V-ATPase subunits for expression in high yield prokaryotic systems, a key step towards high-resolution structural studies. We also review the role of experimentally-derived structural models in understanding structure/function relationships in the V-ATPase, with particular reference to the complex of proton-translocating 16 kDa proteolipids in the membrane domain of the V-ATPase. This model in turn makes testable predictions about the sites of binding of bafilomycins and the functional interactions between the proteolipid and the single-copy membrane subunit Vph1p, with implications for the constitution of the proton translocation pathway.

Cell Membrane↗
PubMed1994

Crystal structure of PvuII endonuclease reveals extensive structural homologies to EcoRV.

The crystal structure of the dimeric PvuII restriction endonuclease (R.PvuII) has been determined at a resolution of 2.4A. The protein has a mixed alpha/beta architecture and consists of two subdomains. Despite a lack of sequence homology, extensive structural similarities exist between one R.PvuII subdomain and the DNA-binding subdomain of EcoRV endonuclease (R.EcoRV); the dimerization subdomains are unrelated. Within the similar domains, flexible segments of R.PvuII are topologically equivalent to the DNA-binding turns of R.EcoRV; potential catalytic residues can be deduced from the structural similarities to R.EcoRV. Conformational flexibility is important for the interaction with DNA. A possible classification of endonuclease structures on the basis of the positions of the scissile phosphates is discussed.

Bacterial Proteins↗
PubMed1999

Structure of the subunit c oligomer in the F1Fo ATP synthase: model derived from solution structure of the monomer and cross-linking in the native enzyme.

The structure of the subunit c oligomer of the H+-transporting ATP synthase of Escherichia coli has been modeled by molecular dynamics and energy minimization calculations from the solution structure of monomeric subunit c and 21 intersubunit distance constraints derived from cross-linking of subunits. Subunit c folds in a hairpin-like structure with two transmembrane helices. In the c12 oligomer model, the subunits pack to form a compact hollow cylinder with an outer diameter of 55-60 A and an inner space with a minimal diameter of 11-12 A. Phospholipids are presumed to pack in the inner space in the native membrane. The transmembrane helices pack in two concentric rings with helix 1 inside and helix 2 outside. The calculations strongly favor this structure versus a model with helix 2 inside and helix 1 outside. Asp-61, the H+-transporting residue, packs toward the center of the four transmembrane helices of two interacting subunits. From this position at the front face of one subunit, the Asp-61 carboxylate lies proximal to side chains of Ala-24, Ile-28, and Ala-62, projecting from the back face of a second subunit. These interactions were predicted from previous mutational analyses. The packing supports the suggestion that a c-c dimer is the functional unit. The positioning of the Asp-61 carboxyl in the center of the interacting transmembrane helices, rather than at the periphery of the cylinder, has important implications regarding possible mechanisms of H+-transport-driven rotation of the c oligomer during ATP synthesis.

Alanine↗
PubMed1996

Structure-function relationships of the Saccharomyces cerevisiae fatty acid synthase. Three-dimensional structure.

The three-dimensional structure of the Saccharomyces cerevisie fatty acid synthase was computed from electron microscopy of stain images. The barrel-shaped structure (point group symmetry 32) has major and minor axes of approximately 245 x 220 A, respectively, and consists of two different subunits organized in an alpha6beta6 complex (Mr = 2.5 x 10(6)). Two sets of three beta subunits form triangle-shaped caps that enclose the ends of the barrel. The wall of the barrel appears to consist of three N-shaped alpha subunit pairs each with an over and underlying arch-shaped beta subunit. Inside the molecule there are three major interconnected cavities that are tilted approximately 20 degrees with respect to its major axis. An axle-shaped structure extends the length of the cavity on the 3-fold axis and is connected to the two ends of the barrel. The cavities are partially divided on the equator of the molecule by three spokes that extend from the axle on the 2-fold axis to the exterior wall. We propose that these six cavities constitute the six equivalent sites of fatty acid synthesis resulting in an extraordinary structure-function relationship with the 42 catalytic sites involved in fatty acid synthesis inside the molecule. The six cavities each have two funnel-shaped openings ( approximately 20 A in diameter) which may serve to permit the diffusion of substrates and products in and out of these functional units. The subunits appear to be arranged in a manner that affords extensive intermolecular interactions contributing to the stability of this macromolecular complex.

Fatty Acid Synthases↗
PubMed1997

Domain structure of Thermus thermophilus UvrB protein. Similarity in domain structure to a helicase.

UvrB protein plays an essential role in the prokaryotic excision repair system. UvrB protein shows cryptic ATPase activity, DNA binding, helicase-like activity, and incision activity by interacting with UvrA or UvrC proteins. To reveal the structure-function relationship of this multifunctional protein, the domain structure of Thermus thermophilus UvrB protein (ttUvrB) was studied by limited proteolysis and denaturation experiments. Proteolytic profiles indicated that ttUvrB consists of four domains: the N domain (residues 2-105), M domain (106-455), C1 domain (456-590), and C2 domain (591-665). The properties of the proteolytic fragments indicated the involvement of the respective domains in the functions of the protein as follows: the N and C1 domains are necessary for ATPase activity, the C1 domain is indispensable for DNA binding, and the N and/or M domains are involved in UvrA binding. The structural stability of the C1 and C2 domains was higher than that of the N and M domains, which supports the proposed domain nature of ttUvrB. Based on these results and the crystal structure of PcrA helicase (Subramanya, H. S., Bird, L. E., Brannigan, J. A., and Wigley, D. B. (1996) Nature 384, 379-383), the domain organization of ttUvrB was proposed.

Adenosine Triphosphatases↗
PubMed1997

The solution structure of the pleckstrin homology domain of human SOS1. A possible structural role for the sequential association of diffuse B cell lymphoma and pleckstrin homology domains.

A large subset of pleckstrin homology (PH) domains are immediately to the C terminus of diffuse B cell lymphoma (Dbl) homology (DbH) domains. Dbl domains are generally considered to be GTPase-exchange factors; many are proto-oncogenes. PH domains appear to function as membrane-recruitment factors, or have specific protein-protein interactions. Since dual domain (DbH/PH) constructs are known to have significant properties in other pathways, it is possible that a defined interdomain relationship is required for DbH/PH function. We determined the solution structure of the human SOS1 PH domain for a construct partially extended into the preceding DbH domain. There are specific structural contacts between the PH and the vestigial DbH domain. This appears to involve structural elements common to this subfamily of PH domains, and to DbH domains. The human SOS1 PH domain binds to inositol 1,4,5-triphosphate with a approximately 60 mu M affinity. Using chemical shift titration, the binding site is identified to be essentially identical to that observed crystallographically for the inositol 1,4,5-triphosphate complex with the PH domain of phospholipase Cdelta. This site may serve as an interdomain regulator of DbH or other domains' functions. While the overall fold of the human SOS1 PH domain is similar to other PH domains, the size and position of the intrastrand loops and the presence of an N-terminal alpha-helix of the vestigial DbH domain suggest that the subfamily of PH domains associated with DbH domains may be a well defined structural group in which the PH domain is a membrane recruiter and modulator.

Amino Acid Sequence↗
PubMed1999

Novel insight into the copper-ligand geometry in the crystal structure of Ulva pertusa plastocyanin at 1.6-A resolution. Structural basis for regulation of the copper site by residue 88.

The crystal structure of plastocyanin from a green alga, Ulva pertusa, has been determined at 1.6-A resolution. At its copper site, U. pertusa plastocyanin has a distorted tetrahedral coordination geometry similar to other plastocyanins. In comparison with structures of plastocyanins reported formerly, a Cu(II)-Sdelta(Met92) bond distance (2.69 A) is shorter by about 0.2 A and a Cu(II)-Sgamma(Cys84) distance is longer by less than 0.1 A in U. pertusa plastocyanin. These subtle but significant differences are caused by the structural change at a His-Met loop (His87-Met92) due to an absence of a O(Asp85)-Ogamma(Ser88) hydrogen bond which is found in Enteromorpha prolifera plastocyanin. In addition, poplar and Chlamydomonas reinhardtii plastocyanins with a glutamine at residue 88 have a weak cation-pi interaction with Tyr83. This interaction lengthens the Cu(II)-Sdelta(Met92) bond of poplar and C. reinhardtii plastocyanins by 0.14 and 0.20 A, respectively. As a result of structural differences, U. pertusa plastocyanin has a less distorted geometry than the other plastocyanins. Thus, the cupric geometry is finely tuned by the interactions between residues 85 and 88 and between residues 83 and 88. This result implies that the copper site is more flexible than reported formerly and that the rack mechanism would be preferable to the entatic theory. The His-Met loop may regulate the electron transfer rate within the complex between plastocyanin and cytochrome f.

Amino Acid Sequence↗