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Loop Conformation (loop + conformation)
Selected AbstractsModeling of loops in protein structuresPROTEIN SCIENCE, Issue 9 2000András Fiser Abstract Comparative protein structure prediction is limited mostly by the errors in alignment and loop modeling. We describe here a new automated modeling technique that significantly improves the accuracy of loop predictions in protein structures. The positions of all nonhydrogen atoms of the loop are optimized in a fixed environment with respect to a pseudo energy function. The energy is a sum of many spatial restraints that include the bond length, bond angle, and improper dihedral angle terms from the CHARMM-22 force field, statistical preferences for the main-chain and side-chain dihedral angles, and statistical preferences for nonbonded atomic contacts that depend on the two atom types, their distance through space, and separation in sequence. The energy function is optimized with the method of conjugate gradients combined with molecular dynamics and simulated annealing. Typically, the predicted loop conformation corresponds to the lowest energy conformation among 500 independent optimizations. Predictions were made for 40 loops of known structure at each length from 1 to 14 residues. The accuracy of loop predictions is evaluated as a function of thoroughness of conformational sampling, loop length, and structural properties of native loops. When accuracy is measured by local superposition of the model on the native loop, 100, 90, and 30% of 4,, 8,, and 12,residue loop predictions, respectively, had <2 Ĺ RMSD error for the mainchain N, Ca, C, and O atoms; the average accuracies were 0.59 6 0.05, 1.16 6 0.10, and 2.61 6 0.16 Ĺ, respectively. To simulate real comparative modeling problems, the method was also evaluated by predicting loops of known structure in only approximately correct environments with errors typical of comparative modeling without misalignment. When the RMSD distortion of the main-chain stem atoms is 2.5 Ĺ, the average loop prediction error increased by 180, 25, and 3% for 4,, 8,, and 12,residue loops, respectively. The accuracy of the lowest energy prediction for a given loop can be estimated from the structural variability among a number of low energy predictions. The relative value of the present method is gauged by (1) comparing it with one of the most successful previously described methods, and (2) describing its accuracy in recent blind predictions of protein structure. Finally, it is shown that the average accuracy of prediction is limited primarily by the accuracy of the energy function rather than by the extent of conformational sampling. [source] Biochemical and structural characterization of residue 96 mutants of Plasmodium falciparum triosephosphate isomerase: active-site loop conformation, hydration and identification of a dimer-interface ligand-binding siteACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2009P. Gayathri Plasmodium falciparum TIM (PfTIM) is unique in possessing a Phe residue at position 96 in place of the conserved Ser that is found in TIMs from the majority of other organisms. In order to probe the role of residue 96, three PfTIM mutants, F96S, F96H and F96W, have been biochemically and structurally characterized. The three mutants exhibited reduced catalytic efficiency and a decrease in substrate-binding affinity, with the most pronounced effects being observed for F96S and F96H. The kcat values and Km values are (2.54 ± 0.19) × 105,min,1 and 0.39 ± 0.049,mM, respectively, for the wild type; (3.72 ± 0.28) × 103,min,1 and 2.18 ± 0.028,mM, respectively, for the F96S mutant; (1.11 ± 0.03) × 104,min,1 and 2.62 ± 0.042,mM, respectively, for the F96H mutant; and (1.48 ± 0.05) × 105,min,1 and 1.20 ± 0.056,mM, respectively, for the F96W mutant. Unliganded and 3-phosphoglycerate (3PG) complexed structures are reported for the wild-type enzyme and the mutants. The ligand binds to the active sites of the wild-type enzyme (wtPfTIM) and the F96W mutant, with a loop-open state in the former and both open and closed states in the latter. In contrast, no density for the ligand could be detected at the active sites of the F96S and F96H mutants under identical conditions. The decrease in ligand affinity could be a consequence of differences in the water network connecting residue 96 to Ser73 in the vicinity of the active site. Soaking of crystals of wtPfTIM and the F96S and F96H mutants resulted in the binding of 3PG at a dimer-interface site. In addition, loop closure at the liganded active site was observed for wtPfTIM. The dimer-interface site in PfTIM shows strong electrostatic anchoring of the phosphate group involving the Arg98 and Lys112 residues of PfTIM. [source] Structural characterization of the N-terminal mineral modification domains from the molluscan crystal-modulating biomineralization proteins, AP7 and AP24BIOPOLYMERS, Issue 5 2004Brandon A. Wustman Abstract The AP7 and AP24 proteins represent a class of mineral-interaction polypeptides that are found in the aragonite-containing nacre layer of mollusk shell (H. rufescens). These proteins have been shown to preferentially interfere with calcium carbonate mineral growth in vitro. It is believed that both proteins play an important role in aragonite polymorph selection in the mollusk shell. Previously, we demonstrated the 1,30 amino acid (AA) N-terminal sequences of AP7 and AP24 represent mineral interaction/modification domains in both proteins, as evidenced by their ability to frustrate calcium carbonate crystal growth at step edge regions. In this present report, using free N-terminal, C, -amide "capped" synthetic polypeptides representing the 1,30 AA regions of AP7 (AP7-1 polypeptide) and AP24 (AP24-1 polypeptide) and NMR spectroscopy, we confirm that both N-terminal sequences possess putative Ca (II) interaction polyanionic sequence regions (2 × ,DD, in AP7-1, ,DDDED, in AP24-1) that are random coil-like in structure. However, with regard to the remaining sequences regions, each polypeptide features unique structural differences. AP7-1 possesses an extended ,-strand or polyproline type II-like structure within the A11,M10, S12,V13, and S28,I27 sequence regions, with the remaining sequence regions adopting a random-coil-like structure, a trait common to other polyelectrolyte mineral-associated polypeptide sequences. Conversely, AP24-1 possesses random coil-like structure within A1,S9 and Q14,N16 sequence regions, and evidence for turn-like, bend, or loop conformation within the G10,N13, Q17,N24, and M29,F30 sequence regions, similar to the structures identified within the putative elastomeric proteins Lustrin A and sea urchin spicule matrix proteins. The similarities and differences in AP7 and AP24 N-terminal domain structure are discussed with regard to joint AP7,AP24 protein modification of calcium carbonate growth. © 2004 Wiley Periodicals, Inc. Biopolymers 2004 [source] ,-Hairpin folding and stability: molecular dynamics simulations of designed peptides in aqueous solutionJOURNAL OF PEPTIDE SCIENCE, Issue 9 2004Clara M. Santiveri Abstract The structural properties of a 10-residue and a 15-residue peptide in aqueous solution were investigated by molecular dynamics simulation. The two designed peptides, SYINSDGTWT and SESYINSDGTWTVTE, had been studied previously by NMR at 278 K and the resulting model structures were classified as 3:5 ,-hairpins with a type I + G1 ,-bulge turn. In simulations at 278 K, starting from the NMR model structure, the 3:5 ,-hairpin conformers proved to be stable over the time period evaluated (30 ns). Starting from an extended conformation, simulations of the decapeptide at 278 K, 323 K and 353 K were also performed to study folding. Over the relatively short time scales explored (30 ns at 278 K and 323 K, 56 ns at 353 K), folding to the 3:5 ,-hairpin could only be observed at 353 K. At this temperature, the collapse to ,-hairpin-like conformations is very fast. The conformational space accessible to the peptide is entirely dominated by loop structures with different degrees of ,-hairpin character. The transitions between different types of ordered loops and ,-hairpins occur through two unstructured loop conformations stabilized by a single side-chain interaction between Tyr2 and Trp9, which facilitates the changes of the hydrogen-bond register. In agreement with previous experimental results, ,-hairpin formation is initially driven by the bending propensity of the turn segment. Nevertheless, the fine organization of the turn region appears to be a late event in the folding process. Copyright © 2004 European Peptide Society and John Wiley & Sons, Ltd. [source] Pseudosymmetry, high copy number and twinning complicate the structure determination of Desulfovibrio desulfuricans (ATCC 29577) flavodoxinACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2009Megan Guelker The crystal structure of oxidized flavodoxin from Desulfovibrio desulfuricans (ATCC 29577) was determined by molecular replacement in two crystal forms, P3121 and P43, at 2.5 and 2.0,Ĺ resolution, respectively. Structure determination in space group P3121 was challenging owing to the presence of pseudo-translational symmetry and a high copy number in the asymmetric unit (8). Initial phasing attempts in space group P3121 by molecular replacement using a poor search model (46% identity) and multi-wavelength anomalous dispersion were unsuccessful. It was necessary to solve the structure in a second crystal form, space group P43, which was characterized by almost perfect twinning, in order to obtain a suitable search model for molecular replacement. This search model with complementary approaches to molecular replacement utilizing the pseudo-translational symmetry operators determined by analysis of the native Patterson map facilitated the selection and manual placement of molecules to generate an initial solution in the P3121 crystal form. During the early stages of refinement, application of the appropriate twin law, (,h, ,k, l), was required to converge to reasonable R -factor values despite the fact that in the final analysis the data were untwinned and the twin law could subsequently be removed. The approaches used in structure determination and refinement may be applicable to other crystal structures characterized by these complicating factors. The refined model shows flexibility of the flavin mononucleotide coordinating loops indicated by the isolation of two loop conformations and provides a starting point for the elucidation of the mechanism used for protein-partner recognition. [source] Modeling and Selection of Flexible Proteins for Structure-Based Drug Design: Backbone and Side Chain Movements in p38 MAPKCHEMMEDCHEM, Issue 2 2008Jyothi Subramanian Abstract Receptor rearrangement upon ligand binding (induced fit) is a major stumbling block in docking and virtual screening. Even though numerous studies have stressed the importance of including protein flexibility in ligand docking, currently available methods provide only a partial solution to the problem. Most of these methods, being computer intensive, are often impractical to use in actual drug discovery settings. We had earlier shown that ligand-induced receptor side-chain conformational changes could be modeled statistically using data on known receptor,ligand complexes. In this paper, we show that a similar approach can be used to model more complex changes like backbone flips and loop movements. We have used p38 MAPK as a test case and have shown that a few simple structural features of ligands are sufficient to predict the induced variation in receptor conformations. Rigorous validation, both by internal resampling methods and on an external test set, corroborates this finding and demonstrates the robustness of the models. We have also compared our results with those from an earlier molecular dynamics simulation study on DFG loop conformations of p38 MAPK, and found that the results matched in the two cases. Our statistical approach enables one to predict the final ligand-induced conformation of the active site of a protein, based on a few ligand properties, prior to docking the ligand. We can do this without having to trace the step-by-step process by which this state is arrived at (as in molecular dynamics simulations), thereby drastically reducing computational effort. [source] | ||||||||||