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Protein Conformation (4):
Recent article
Protein Conformation
Biochimica et Biophysica Acta (1807)11 2011
Abstract
We have charted seven decades of research beginning with the discovery of CcP and leading to the latest functional and structural work, which has clarified the mechanism of the intermolecular ET, addressed the putative functional role of a low-affinity binding site, and identified lowly-populated in...
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PMID: 21820401
PDF is available here.
PDF is available here.
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Abstract
We present an application of in silico quantitative structure-activity relationship (QSAR) models to establish a new ligand-based computational approach for generating virtual libraries. The Free-Wilson methodology was applied to extract rules from two data sets containing compounds which were scree...
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PMID: 20981520
PDF is available here.
PDF is available here.
Abstract
Amyloid-β protein (Aβ) is the principal component of the neuritic plaques found in Alzheimer's disease. The predominant Aβ morphology in the plaques is fibrillar which has prompted substantial in vitro work to better understand the molecular organization of Aβ fibrils. In the current study, trypt...
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PMID: 21843498
PDF is available here.
PDF is available here.
Abstract
We found that the core ER-lumenal domain (cLD) of yeast Ire1 binds to unfolded proteins in yeast cells and to peptides primarily composed of basic and hydrophobic residues in vitro. Mutation of amino acid side chains exposed in a putative peptide-binding groove of Ire1 cLD impaired peptide binding....
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PMID: 21852455
PDF is available here.
PDF is available here.
FEBS Journal (278)19 2011
Abstract
Chromatin remodelling is the ATP-dependent change in nucleosome organisation driven by Snf2 family ATPases. The biochemistry of this process depends on the behaviours of ATP-dependent motor proteins and their dynamic nucleosome substrates, which brings significant technical and conce...
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PMID: 21810178
PDF is available here.
PDF is available here.
Abstract
We use cryo-electron microscopy to determine the subnanometre structures of Cascade before and after binding to a target sequence. These structures reveal a sea-horse-shaped architecture in which the crRNA is displayed along a helical arrangement of protein subunits that protect the crRNA from degra...
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PMID: 21938068
PDF is available here.
PDF is available here.
Abstract
We employed the new PMCA format with beads (PMCAb) to gain insight into the mechanism of prion amplification. Using a panel of six hamster prion strains, the effect of beads on amplification was found to be strain-specific, with the largest improvements in efficiency observed for strains with the hi...
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PMID: 21848309
PDF is available here.
PDF is available here.
Abstract
Abstract
In this paper, a pH-inductive protein-scaffold biosynthesis of shape-tunable crystalline gold nanoparticles at room temperature has been developed. By simple manipulation of the reaction solution's pH, anisotropic gold nanoparticles including spheres, triangles and cubes could be produced by incubati...
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PMID: 21828895
PDF is available here.
PDF is available here.
Abstract
We describe an energetic ion-assisted plasma process that can make any surface hydrophilic and at the same time enable it to covalently immobilize functional biological molecules. We show that the modification creates free radicals that migrate to the surface from a reservoir beneath. When they reac...
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PMID: 21844370
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1808)10 2011
Abstract
We aimed to determine how these two molecules modify pig kidney Na,K-ATPase. Oleic and linoleic acids did not modify reactions involving the E(1) (Na(+)) conformations of the Na,K-ATPase. In contrast, K(+) dependent reactions were strongly modified after treatment. Oleic and linoleic acids were foun...
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PMID: 21767529
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1808)10 2011
Abstract
Replacement of the glycine at position 117 by a cysteine in the melibiose permease creates an interesting phenotype: while the mutant transporter shows still transport activity comparable to the wild type its pre steady-state kinetic properties are drastically altered. The transient charge displaceme...
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PMID: 21801712
PDF is available here.
PDF is available here.
Abstract
We start by reproducing the trend in the measured change in catalysis upon mutations (which was assumed to arise as a result of a "dynamical knockout" caused by the mutations). This analysis is performed by calculating the change in the corresponding activation barriers without the need to invoke dy...
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PMID: 21831831
PDF is available here.
PDF is available here.
Abstract
We show here that DNA binding to the DNA-gate of gyrase and wrapping of DNA around the C-terminal domains of GyrA induces a narrowing of the N-gate. This half-closed state prepares capture of a T-segment in the upper cavity of gyrase. Subsequent N-gate closure upon binding of ATP then poises the rea...
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PMID: 21817063
PDF is available here.
PDF is available here.
Abstract
We report the crystal structure of a motor domain dimer in complex with its tail domain at 2.2 angstroms and compare it with a structure of the motor domain alone at 2.7 angstroms. These structures indicate that neither an induced conformational change nor steric blocking is the cause of inhibition....
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PMID: 21836017
PDF is available here.
PDF is available here.
Abstract
Abstract
We used high-speed atomic force microscopy to show that the rotorless F(1) still "rotates"; in the isolated α(3)β(3) stator ring, the three β subunits cyclically propagate conformational states in the counterclockwise direction, similar to the rotary shaft rotation in F(1). The structural basis o...
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PMID: 21817054
PDF is available here.
PDF is available here.
Abstract
Biochimica et Biophysica Acta (1812)8 2011
Abstract
We review key molecular aspects of transactivation by NRs with special emphasis on the recent advances in the molecular mechanisms responsible for receptor- and gene-specific transcriptional activation. This article is part of a Special Issue entitled: Translating nuclear receptors from health to di...
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PMID: 21193032
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1814)8 2011
Abstract
Biological function involves a series of chemical reactions of biological molecules, and during these reactions, there are numerous spectrally silent dynamic events that cannot be monitored by absorption or emission spectroscopic techniques. Such spectrally silent dynamics include changes in conforma...
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PMID: 21211575
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1814)8 2011
Abstract
We therefore summarise recent efforts to fundamentally improve this situation by decoupling the sampling of the energy landscape from the description of the kinetics of the process. Recent years have seen the emergence of many advanced sampling techniques, which permit efficient characterisation of...
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PMID: 20851219
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1814)8 2011
Abstract
We present examples of proteins where changes in stability results in changes in affinity and of proteins where stability and affinity are uncorrelated. We discuss the possibility for a relationship between stability and binding. From the data presented is it clear that there are specific sites (fle...
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PMID: 21094283
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1807)11 2011
Abstract
The cytochrome bc(1) complex is a key component in several respiratory pathways. One of the characteristics of the eukaryotic complex is the presence of a small acidic subunit, which is thought to guide the interaction of the complex with its electron acceptor and facilitate electron transfer. Paraco...
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PMID: 21856278
PDF is available here.
PDF is available here.
Abstract
We investigated an Austrian family with 16 affected individuals by exome sequencing. We found a missense mutation, c.1858G>A (p.Asp620Asn), in the VPS35 gene in all seven affected family members who are alive. By screening additional PD cases, we saw the same variant cosegregating with the disease i...
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PMID: 21763483
PDF is available here.
PDF is available here.
Abstract
We cloned 576 new HIV antibodies from four unrelated individuals. All four individuals produced expanded clones of potent broadly neutralizing CD4-binding-site antibodies that mimic binding to CD4. Despite extensive hypermutation, the new antibodies shared a consensus sequence of 68 immunoglobulin H...
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PMID: 21764753
PDF is available here.
PDF is available here.
Abstract
We investigated the function and calcium regulation of the COOH-terminal end segment of TnI. A TnI model molecule was labeled with Alexa fluor 532 at a Cys engineered at the COOH-terminal end and used to reconstitute tertiary troponin complex. A Ca(2+) -regulated conformational change in the COOH te...
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PMID: 21777381
PDF is available here.
PDF is available here.
Abstract
We dissect the folding mechanism of the α-helical molten-globular protein NCBD from three fundamentally different approaches: statistical-mechanical variable barrier model, Cα-based Gō-model and explicit water all-atom molecular dynamics (MD) simulations. We find that NCBD displays the characteri...
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PMID: 21732676
PDF is available here.
PDF is available here.
Abstract
We use molecular simulations of a coarse-grained model, which reproduces most of the salient features of the experimental melting profiles of PK and HP, to show that crowding enhances the stability of PK relative to HP in the wild type and in a mutant associated with dyskeratosis congenita. In monod...
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PMID: 21736319
PDF is available here.
PDF is available here.
Abstract
We combined methods of computer simulation and experiments based on circular dichroism (CD) to investigate the structural characteristics of CaM that influence its target recognition in crowded cell-like conditions. We developed a unique multiscale solution of charges computed from quantum chemistry...
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PMID: 21829336
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1814)7 2011
Abstract
We present the solution structure of GIP in membrane-mimicking environments by proton NMR spectroscopy and molecular modelling. GIP adopts an α-helical conformation between residues Phe(6)-Gly(31) and Ala(13)-Gln(29) for micellar and bicellar media, respectively. Previously we examined the effect o...
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PMID: 21539943
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1807)11 2011
Abstract
Cytochrome bd is a respiratory quinol:O(2) oxidoreductase found in many prokaryotes, including a number of pathogens. The main bioenergetic function of the enzyme is the production of a proton motive force by the vectorial charge transfer of protons. The sequences of cytochromes bd are not homologous...
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PMID: 21756872
PDF is available here.
PDF is available here.
Abstract
We assess the impact of the F610A mutation on the functionality of AcrB by means of computational techniques, using doxorubicin as substrate. We found that the compound slides deeply inside the binding pocket after mutation, increasing the strength of the interaction. During subsequent conformationa...
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PMID: 21707050
PDF is available here.
PDF is available here.
Abstract
We applied molecular dynamics simulations and potential of mean force calculations to examine the structures and the free energies associated with these putative drug binding sites in an M2-lipid bilayer system. We found that, at biological pH (∼7.4), the pore binding site is more thermodynamicall...
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PMID: 21711026
PDF is available here.
PDF is available here.
Abstract
We identified a novel mutation in SIX1 (p.E125K) in a Tunisian family with variable HI and preauricular pits. This mutation is located at the same position as the mutation identified in the Catwhesel (Cwe) mouse. No renal and branchial defects were observed in our family nor in Cwe/+ mice. A homolog...
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PMID: 21700001
PDF is available here.
PDF is available here.
Abstract
We propose a medium sized model to test the ability of a variety of quantum chemistry approaches to provide reasonable geometric parameters and energetics for this system. Although our model is large enough to include the main polarizing groups of the active site, it is small enough to be used withi...
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PMID: 21667951
PDF is available here.
PDF is available here.
Abstract
The charge recombination lifetime of photosynthetic reaction centers (RCs) increases significantly upon lengthy illumination, revealing nonequilibrium structural transitions in the protein-cofactor system. This paper analyzes the charge recombination kinetics measured in isolated RCs following a syst...
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PMID: 21671683
PDF is available here.
PDF is available here.
Abstract
We compare the functional immunologic consequences of "conventional" complement deficiencies with these newly described developmental roles....
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PMID: 21664996
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1810)9 2011
Abstract
Flexibility is a common feature of proteins. For human aldose reductase, a variety of conformers have been observed in crystalline complexes with different inhibitors.
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PMID: 21684320
PDF is available here.
PDF is available here.
Abstract
We have investigated complexes of CK2 protein kinase with halogenated inhibitors by means of the advanced semiempirical quantum mechanical (SQM) PM6 method (called PM6-DH2X), which describes various types of noncovalent interactions including halogen bonding well. The PM6-DH2X method provides reliab...
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PMID: 21648479
PDF is available here.
PDF is available here.
Abstract
We show that FrsA converts pyruvate to acetaldehyde and carbon dioxide in a cofactor-independent manner and that its pyruvate decarboxylation activity is enhanced by the dephosphorylated form of IIA(Glc) (d-IIA(Glc)). Crystal structures of FrsA and its complex with d-IIA(Glc) revealed residues requi...
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PMID: 21623357
PDF is available here.
PDF is available here.
Abstract
Interleukin-1beta (IL-1beta) is an important cytokine in the immune system. Mammalian and avian IL-1betas share only 31-35% sequence identity, and the function of avian IL-1betas is less well understood by comparison. Although chicken and mammalian IL-1betas have similar tertiary str...
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PMID: 20820827
PDF is available here.
PDF is available here.
Abstract
We have characterized the binding properties between sialic acid, methyl 3'sialyllactoside, methyl 6'sialyllactoside and the H5N1 influenza virus neuraminidase using molecular docking and molecular dynamics simulations. Obtained molecular dynamics trajectories were analyzed in terms of ligand confor...
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PMID: 20853123
PDF is available here.
PDF is available here.
Abstract
To investigate the molecular scavenging capabilities of the larvae of Hermetia illucens, two serine proteases (SPs) were cloned and characterized. Multiple sequence alignments and phylogenetic tree analysis of the deduced amino acid sequences of Hi-SP1 and Hi-SP2 were suggested that...
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PMID: 21699751
PDF is available here.
PDF is available here.
Abstract
We report the isolation of N-aryl peptoid oligomers that adopt chiral folds, despite the absence of chiral centers. Peptoid monomers incorporating ortho-substituted N-aryl side chains are identified that exhibit axial chirality. We observe significant energy barriers to rotation about the stereogeni...
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PMID: 21634437
PDF is available here.
PDF is available here.
Abstract
We bring this 'bottom-up' approach alongside the current NGS-driven genetic study of genetic variations and disease aetiology. We describe experimental and computational techniques for assessing genetic variants and their deleterious effects on protein structure and function....
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PMID: 21350909
PDF is available here.
PDF is available here.
Abstract
Our results make the case that these two strategies greatly enhance the sampling of the conformational space near the native state. A detailed comparative analysis shows that our approach performs as well as state-of-the-art ab initio structure prediction protocols....
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PMID: 21714131
PDF is available here.
PDF is available here.
Abstract
We analyzed the possible relationship between the protein folding rates and the corresponding mRNA sequences. The content of guanine and cytosine (GC content) of palindromes in protein coding sequence was introduced as a new parameter and added in the Gromiha's model of predicting protein folding ra...
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PMID: 21613670
PDF is available here.
PDF is available here.
Abstract
A high-throughput screening of natural product libraries identified (-)-gambogic acid (1), a component of the exudate of Garcinia harburyi, as a potential Hsp90 inhibitor, in addition to the known Hsp90 inhibitor celastrol (2). Subsequent testing established that 1 inhibited cell proliferation, broug...
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PMID: 21486005
PDF is available here.
PDF is available here.
Abstract
We could only predict the structure of the main domain, which had central barrel of eight beta-strands surrounded by eight alpha-helices. Superimposition of the 2NPD region of ER domain of Mycobacterium tuberculosis H37Rv on to the corresponding region of 2UVA_G revealed a good structural alignment...
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PMID: 21793307
PDF is available here.
PDF is available here.
Abstract
I and II chaperonins, mainly in the molecular rearrangements that take place during the functional cycle. These differences are evident for the most complex chaperonin, the eukaryotic cytosolic CCT, which highlights the uniqueness of this important molecular machine.
Copyright © 201...
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PMID: 21723731
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1808)10 2011
Abstract
We have solved the structure of the naturally occurring peptide in detergent micelles at a neutral pH. The structure has an overall kinked helix motif, with residues 7-17 and 21-28 in a helical conformation, and with a 3(10) helix from Gly 33-Asn 35. In addition, the angle between the N- and C-termi...
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PMID: 21723249
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1807)9 2011
Abstract
ATP synthases are part of the sophisticated cellular metabolic network and therefore multiple interactions have to be considered. As discussed in this review, ATP synthases form various supramolecular structures. These include dimers and homooligomeric species, but also interactions...
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PMID: 21679683
PDF is available here.
PDF is available here.
Abstract
We propose the existence of a dynamic DNA readout mechanism, wherein distant segments modulate conformational preferences, flexibility or spacing of the DNA binding motifs or serve as competitive partners. Despite their low sequence similarity, these intrinsically disordered regions are often conser...
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PMID: 21620710
PDF is available here.
PDF is available here.
Cancer Cell (19)5 2011
Abstract
We investigate the mechanisms by which ETS fusions mediate their effects, and find that the product of the predominant ETS gene fusion, TMPRSS2:ERG, interacts in a DNA-independent manner with the enzyme poly (ADP-ribose) polymerase 1 (PARP1) and the catalytic subunit of DNA protein kinase (DNA-PKcs)...
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PMID: 21575865
PDF is available here.
PDF is available here.
Abstract
We highlight here our efforts to elucidate the influence of iron heme spin state and secondary structure of human cyt P450s on voltammetric and biocatalytic properties, using methodologies to quantitatively describe the dynamics of these processes in thin films. We also describe the first cyt P450/r...
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PMID: 21591685
PDF is available here.
PDF is available here.
Abstract
We determined three X-ray structures: R-HPP with inert cobalt-containing enzyme (Co(II)-HppE) at 2.1 Å resolution; R-HPP with active iron-containing enzyme (Fe(II)-HppE) at 3.0 Å resolution; and S-HPP-Fe(II)-HppE in complex with dioxygen mimic NO at 2.9 Å resolution. These structures, along with...
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PMID: 21682308
PDF is available here.
PDF is available here.
Abstract
A dinucleating macrocycle, H(2)PIM, containing phenoxylimine metal-binding units has been prepared. Reaction of H(2)PIM with [Fe(2)(Mes)(4)] (Mes = 2,4,6-trimethylphenyl) and sterically hindered carboxylic acids, Ph(3)CCO(2)H or Ar(Tol)CO(2)H (2,6-bis(p-tolyl)benzoic acid), afforded...
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PMID: 21682286
PDF is available here.
PDF is available here.
Abstract
Microperoxidase-11 has for the first time been successfully immobilized into a mesoporous metal-organic framework (MOF) consisting of nanoscopic cages and it demonstrates superior enzymatic catalysis performances compared to its mesoporous silica counterpart.
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PMID: 21682253
PDF is available here.
PDF is available here.
Abstract
Simulated annealing of chemical potential located the highest affinity positions of eight organic probes and water on eight static structures of hen egg white lysozyme (HEWL) in various conformational states. The location of the highest affinity binding site for at least six of the o...
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PMID: 21682273
PDF is available here.
PDF is available here.
Abstract
We provide evidence that the oxidation state of the disulfide bond within a loop domain peptide determines its activity. The oxidized (closed) form inhibits fusion, while the reduced (opened) form enhances hemifusion. These opposite activities reach 60% difference in viral fusion. Both forms of the...
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PMID: 21429941
PDF is available here.
PDF is available here.