Conformation Changes (conformation + change)

Distribution by Scientific Domains
Distribution within Chemistry

Selected Abstracts

Biochemical and Conformation Changes of Actomyosin from Threadfin Bream Stored in Ice

J. Yongswawatdigul
ABSTRACT: Biochemical and conformational changes of actomyosin stored in ice were investigated. The K-value of threadfin bream increased from 9% to 40% after storage for 12 d. Ca2+ -, EDTA-, Mg2+ -, and Mg2+ -Ca2+ -ATPase activities of actomyosin decreased, whereas Mg2+ -EGTA ATPase activities increased. Total SH content of actomyosin increased after 3 d and decreased thereafter. Surface hydrophobicity gradually increased within 6 d. Protein loss during washing increased with storage time. A significant reduction (50%) of breaking force of thrice-washed mince was observed in fish stored in ice for 6 d. There was no evidence of proteolysis of muscle proteins stored up to 9 d as shown with SDS-PAGE. [source]

Optical Detection of Mercury(II) in Aqueous Solutions by Using Conjugated Polymers and Label-Free Oligonucleotides,

X. Liu
A conjugated-polymer-based "mix-and-detect" optical sensor for mercury ions is fabricated by using a water-soluble poly[3-(3,- N,N,N -triethylamino-1,-propyloxy)-4-methyl-2,5-thiophene hydrochloride] (PMNT) and a label-free, mercury-specific oligonucleotide (MSO) probe. PMNT binds to the Hg2+ -free MSO and the Hg2+,MSO complex in different ways, and exhibits distinguishable and specific optical responses to the target-induced conformation change. [source]

A modified Ising model for the thermodynamic properties of local and global protein folding,unfolding observed by circular dichroism and small-angle X-ray scattering

Ying-Jen Shiu
Based on the mean-field approximation, we have applied a modified Ising model to describe general protein unfolding behavior at thermodynamic equilibrium with the free energy contributed by the subgroup units (amino acids or peptide bonds) of the protein. With the thermodynamic properties of the protein, this model can associate the stepwise change of an unfolding fraction ratio profile with the local and global conformation unfolding. Taking cytochrome c (cyt c) as a model protein, we have observed, using small-angle X-ray scattering and circular dichroism (CD), the global and local structure changes for the protein in three kinds of denaturant environments: acid, urea and guanidine hydrochloride. The small-angle X-ray scattering and CD results are mapped to the unfolding fractions as a function of the pH value or denaturant concentration, from which we have extracted local and global unfolding free energies of cyt c in different denaturant environments using a modified Ising model. Based on the characteristics of the thermodynamic properties deduced from the local and global protein folding,unfolding, we discuss the thermodynamic stabilities of the protein in the three denaturant environments, and the possible correlation between the global conformation change of the protein and the local unfolding activities of the S,Fe bond in the Met80-heme and the ,-helices. [source]

Functionally relevant motions of haloalkane dehalogenases occur in the specificity-modulating cap domains

Michal Otyepka
Abstract One-nanosecond molecular dynamics trajectories of three haloalkane dehalogenases (DhlA, LinB, and DhaA) are compared. The main domain was rigid in all three dehalogenases, whereas the substrate specificity-modulating cap domains showed considerably higher mobility. The functionally relevant motions were spread over the entire cap domain in DhlA, whereas they were more localized in LinB and DhaA. The highest amplitude of essential motions of DhlA was noted in the ,4,-helix-loop-,4-helix region, formerly proposed to participate in the large conformation change needed for product release. The highest amplitude of essential motions of LinB and DhaA was observed in the random coil before helix 4, linking two domains of these proteins. This flexibility is the consequence of the modular composition of haloalkane dehalogenases. Two members of the catalytic triad, that is, the nucleophile and the base, showed a very high level of rigidity in all three dehalogenases. This rigidity is essential for their function. One of the halide-stabilizing residues, important for the catalysis, shows significantly higher flexibility in DhlA compared with LinB and DhaA. Enhanced flexibility may be required for destabilization of the electrostatic interactions during the release of the halide ion from the deeply buried active site of DhlA. The exchange of water molecules between the enzyme active site and bulk solvent was very different among the three dehalogenases. The differences could be related to the flexibility of the cap domains and to the number of entrance tunnels. [source]

Raman signatures of ligand binding and allosteric conformation change in hexameric insulin

BIOPOLYMERS, Issue 5 2001
Davide Ferrari
Abstract Hexameric insulin is an allosteric protein that undergoes transitions between three conformational states (T6, T3R3, and R6). These allosteric states are stabilized by the binding of ligands to the phenolic pockets and by the coordination of anions to the His B10 metal sites. Raman difference (RD) spectroscopy is utilized to examine the binding of phenolic ligands and the binding of thiocyanate, p -aminobenzoic acid (PABA), or 4-hydroxy-3-nitrobenzoic acid (4H3N) to the allosteric sites of T3R3 and R6. The RD spectroscopic studies show changes in the amide I and III bands for the transition of residues B1,B8 from a meandering coil to an , helix in the T,R transitions and identify the Raman signatures of the structural differences among the T6, T3R3, and R6 states. Evidence of the altered environment caused by the ,30 displacement of phenylalanine (Phe) B1 is clearly seen from changes in the Raman bands of the Phe ring. Raman signatures arising from the coordination of PABA or 4H3N to the histidine (His) B10 Zn(II) sites show these carboxylates give distorted, asymmetric coordination to Zn(II). The RD spectra also reveal the importance of the position and the type of substituents for designing aromatic carboxylates with high affinity for the His B10 metal site. 2001 John Wiley & Sons, Inc. Biopolymers (Biospectroscopy) 62: 249,260, 2001 [source]

Structural and Biophysical Characterization of XIAP BIR3 G306E Mutant: Insights in Protein Dynamics and Application for Fragment-Based Drug Design

Cathy D. Moore
Previous reports describe modulators of X-linked inhibitor of apoptosis (XIAP),caspase interaction designed from the AVPI N-terminal peptide sequence of second mitochondria-derived activator of caspase. A fragment-based drug design strategy was initiated to identify therapeutic non-peptidomimetic antagonists of X-linked inhibitor of apoptosis protein,protein interactions. Fragments that bind to the AVPI binding site of BIR3 (bacculoviral inhibitory repeat) were identified, and to further localize the fragment binding within the AVPI binding site, a point mutation was designed which alters the dynamics of flexible loops and blocks PI region of the binding cleft, thus enabling definition of weakly bound small molecules in the AV portion of the binding cleft. Nuclear magnetic resonance analysis confirmed the G306E mutation stabilizes the AV pocket. Biophysical characterization of the mutant confirms conformation change within the PI sub-pocket as evidenced by a significant diminishment in binding affinity of AVPI mimetics, yet the binding affinity of the smaller AV mimetics is maintained or slightly improved in the mutant compared with wild-type. Additional data from non-covalent mass spectrometry analysis shows enhanced binding of AV mimetics to the G306E mutant over the wild-type. The presented data outline a protein engineering strategy that allowed mapping of AV-replacements with better sensitivity and precision. [source]

Inhibition Mechanism of TbIII on Horseradish Peroxidase Activity

Shaofen Guo
Abstract The inhibition mechanism of TbIII on horseradish peroxidase (HRP) in vitro was discussed. The results from MALDI-TOF/MS and X-ray photoelectron spectroscopy (XPS) showed that TbIII mainly interacts with the O-containing groups of the amides in the polypeptide chains of the HRP molecules and forms the complex of TbIII,HRP, and, in the complex, the molar ratio TbIII/HRP is 2,:,1. The results from CD and atomic force microscopy (AFM) indicated that the coordination effect between TbIII and HRP can lead to the conformation change in the HRP molecule, in which the contents of , -helix and , -sheet conformation in the peptide of the HRP molecules is decreased, and the content of the random coil conformation is increased. Meanwhile, the coordination effect also leads to the decrease in the content of inter- and intrapeptide-chain H-bonds in the HRP molecules, resulting in the HRP molecular looseness and/or aggregation. Thus, the conformation change in the HRP molecules can significantly decrease the electrochemical reaction of HRP and its electrocatalytic activity for the reduction of H2O2. [source]

Thermal Behavior of Tetrahydropyran-Intercalated VOPO4: Structural and Dynamics Study

Klra Melnov
Abstract The thermal behavior of tetrahydropyran-(THP-)intercalated VOPO4 was probed by an extensive combination of experimental methods (XRD, DSC, FTIR, solid-state NMR) and quantum chemical calculations. Two temperature-induced transitions were detected and all polymorphs exhibit a high degree of molecular order and tight packing of THP in VOPO4. The first reversible thermal transition at around 100 C was attributed to boat/chair conformation changes of the THP molecules. Most probably, a low-temperature boat conformation of the guest molecules present in the interlayer space of VOPO4 changes to a high-temperature chair conformation. This rearrangement of the THP molecules was confirmed by variable-temperature 13C CP/MAS NMR spectroscopy. Quantum chemical calculations using a B3LYP functional and 6-31G(d) basis set also support this idea. The second change at around 140 C is probably caused by a weakening of the donor,acceptor bond between the oxygen molecule of THP and the vanadium atom of the host and the formation of a disorder in packing of the THP molecules. ( Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source]

E2F1-mediated transcriptional inhibition of the plasminogen activator inhibitor type 1 gene

FEBS JOURNAL, Issue 18 2001
Magdalena Koziczak
,Gene expression of the plasminogen activation system is cell-cycle dependent. Previously, we showed that ectopic expression of E2F1 repressed the plasminogen activator inhibitor type 1 (PAI-1) promoter in a manner dependent on the presence of DNA-binding and transactivation domains of E2F1 but independent of binding to pocket-binding proteins, suggesting a novel mechanism for E2F-mediated negative gene regulation [Koziczak, M., Krek, W. & Nagamine, Y. (2000) Mol. Cell. Biol.20, 2014,2022]. However, it remains to be seen whether endogenous E2F can exert a similar effect. We report here that down-regulation of PAI-1 gene expression correlates with an increase in endogenous E2F activity. When cells were treated with a cdk2/4-specific inhibitor, which maintains E2F in an inactive state, the decline of serum-induced PAI-1 mRNA levels was suppressed. In mutant U2OS cells expressing a temperature-sensitive retinoblastoma protein (pRB), a shift to a permissive temperature induced PAI-1 mRNA expression. In U2OS cells stably expressing an E2F1-estrogen receptor chimeric protein that could be activated by tamoxifen, PAI-1 gene transcription was markedly reduced by tamoxifen even in the presence of cycloheximide. These results all indicate that endogenous E2F can directly repress the PAI-1 gene. DNase I hypersensitive-site analysis of the PAI-1 promoter suggested the involvement of conformation changes in chromatin structure of the PAI-1 promoter. 5, deletion analysis of the PAI-1 promoter showed that multiple sites were responsible for the E2F negative regulation, some of which were promoter dependent. Interestingly, one of these sites is a p53-binding element. [source]

Combined homology modelling and evolutionary significance evaluation of missense mutations in blood clotting factor VIII to highlight aspects of structure and function

HAEMOPHILIA, Issue 4 2009
Summary., Most small lesions in the factor VIII (FVIII) gene that cause haemophilia A (HA) are single nucleotide substitutions resulting in amino acid replacing (missense) mutations and leading to various phenotypes, ranging from mild to severe. We took a combined approach of homology modelling and quantitative evaluation of evolutionary significance of amino acid replacing alterations using the Grantham Matrix Score (GMS) to assess their structural effects and significance of pathological expression. Comparative homology models of all amino acid substitutions summarized in the FVIII mutations database plus these identified and reported lately by us or by our collaborators were evaluated. Altogether 640 amino acid replacing mutations were scored for potential distant or local conformation changes, influence on the molecular stability and predicted contact residues, using available FVIII domain models. The average propensity to substitute amino acid residues by mutation was found comparable to the overall probability of de novo mutations. Missense changes reported with various HA phenotypes were all confirmed significant using GMS. The fraction of these, comprising residues apparently involved in intermolecular interactions, exceeds the average proportion of such residues for FVIII. Predicted contact residues changed through mutation were visualized on the surface of FVIII domains and their possible functional implications were verified from the literature and are discussed considering available structural information. Our predictive modelling adds on the current view of domain interface molecular contacts. This structural insight could aid in part to the design of engineered FVIII constructs for therapy, to possibly enhance their stability and prolong circulating lifetime. [source]

Thermoresponsive transport through porous membranes with grafted PNIPAM gates

AICHE JOURNAL, Issue 4 2003
Liang-Yin Chu
Both thermoresponsive flat membranes and core-shell microcapsule membranes, with a porous membrane substrate and grafted poly(N-isopropylacrylamide) (PNIPAM) gates, were successfully prepared using a plasma-graft pore-filling polymerization method. PNIPAM was proven to be grafted homogeneously onto the porous membrane substrates, in the direction of both the membrane thickness and surface. Regardless of the solute molecular size, temperature had an opposite effect on diffusion coefficients of the solute across the PNIPAM-grafted membranes with low graft yields as opposed to those with high graft yields. The PE-g-PNIPAM membranes change from positive thermo-response to negative thermoresponse types with increasing pore-filling ratios at around 30%. Phenomenological models were developed for predicting the diffusion coefficient of the solute across PNIPAM-grafted membranes at temperatures, both above and below the lower critical solution temperature (LCST). Predicted diffusional coefficients of solutes across both the PNIPAM-grafted flat and PNIPAM-grafted microcapsule membranes fit the experimental values. To obtain an ideal result for the diffusional thermoresponsive controlled release through PNIPAM-grafted membranes, the substrates strong enough to prevent any conformation changes are more suitable for preparing thermoresponsive membranes than weak ones. [source]

Assessing predictions of protein,protein interaction: The CAPRI experiment

Jol Janin
Abstract The Critical Assessment of PRedicted Interactions (CAPRI) experiment was designed in 2000 to test protein docking algorithms in blind predictions of the structure of protein,protein complexes. In four years, 17 complexes offered by crystallographers as targets prior to publication, have been subjected to structure prediction by docking their two components. Models of these complexes were submitted by predictor groups and assessed by comparing their geometry to the X-ray structure and by evaluating the quality of the prediction of the regions of interaction and of the pair wise residue contacts. Prediction was successful on 12 of the 17 targets, most of the failures being due to large conformation changes that the algorithms could not cope with. Progress in the prediction quality observed in four years indicates that the experiment is a powerful incentive to develop new procedures that allow for flexibility during docking and incorporate nonstructural information. We therefore call upon structural biologists who study protein,protein complexes to provide targets for further rounds of CAPRI predictions. [source]

Macromolecular recognition in the Protein Data Bank

Jol Janin
Crystal structures deposited in the Protein Data Bank illustrate the diversity of biological macromolecular recognition: transient interactions in protein,protein and protein,DNA complexes and permanent assemblies in homodimeric proteins. The geometric and physical chemical properties of the macromolecular interfaces that may govern the stability and specificity of recognition are explored in complexes and homodimers compared with crystal-packing interactions. It is found that crystal-packing interfaces are usually much smaller; they bury fewer atoms and are less tightly packed than in specific assemblies. Standard-size interfaces burying 1200,2000,2 of protein surface occur in protease,inhibitor and antigen,antibody complexes that assemble with little or no conformation changes. Short-lived electron-transfer complexes have small interfaces; the larger size of the interfaces observed in complexes involved in signal transduction and homodimers correlates with the presence of conformation changes, often implicated in biological function. Results of the CAPRI (critical assessment of predicted interactions) blind prediction experiment show that docking algorithms efficiently and accurately predict the mode of assembly of proteins that do not change conformation when they associate. They perform less well in the presence of large conformation changes and the experiment stimulates the development of novel procedures that can handle such changes. [source]