Local Conformation (local + conformation)

Distribution by Scientific Domains


Selected Abstracts


Probing the Local Conformation within ,-Conjugated One-dimensional Supramolecular Stacks using Frequency Modulation Atomic Force Microscopy

ADVANCED MATERIALS, Issue 41 2009
Benjamin Grévin
Frequency-modulation atomic force microscopy is used to investigate the local conformation within 1D stacks obtained by the self-assembly of ,-conjugated molecules from solution. The structural parameters extracted from the experimental data can be interpreted in terms of local molecular conformation, by comparison with models obtained by molecular mechanics and dynamics simulations. [source]


Surprising Effects on the Conformational Entropy due to Nonrandom Distributions of Local Conformations Along Unperturbed Chains

MACROMOLECULAR THEORY AND SIMULATIONS, Issue 7 2006
Wayne L. Mattice
Abstract Summary: Nonrandomness in the distribution of rotational isomeric states along a flexible unperturbed chain reduces its conformational entropy. Pairwise interdependence of the bonds is a necessary, but not sufficient, condition for a significant reduction. The reduction in conformational entropy from this source can be as severe as a factor of three. It is generally more severe for isotactic chains than for the syndiotactic chains constructed from the same monomer. Surprising effects are sometimes seen, such as the nearly identical reductions in conformational entropy for polydimethylsiloxane, a very flexible chain, and for poly(methyl methacrylate), a much stiffer chain. Fractional difference in conformational entropy due to nonrandomness versus probability of helix in helix-coil transition. [source]


Phosphorylation modulates the local conformation and self-aggregation ability of a peptide from the fourth tau microtubule-binding repeat

FEBS JOURNAL, Issue 19 2007
Jin-Tang Du
Phosphorylation of tau protein modulates both its physiological role and its aggregation into paired helical fragments, as observed in Alzheimer's diseased neurons. It is of fundamental importance to study paired helical fragment formation and its modulation by phosphorylation. This study focused on the fourth microtubule-binding repeat of tau, encompassing an abnormal phosphorylation site, Ser356. The aggregation propensities of this repeat peptide and its corresponding phosphorylated form were investigated using turbidity, thioflavin T fluorescence and electron microscopy. There is evidence for a conformational change in the fourth microtubule-binding repeat of tau peptide upon phosphorylation, as well as changes in aggregation activity. Although both tau peptides have the ability to aggregate, this is weaker in the phosphorylated peptide. This study reveals that both tau peptides are capable of self-aggregation and that phosphorylation at Ser356 can modulate this process. [source]


Nucleotide-binding domain 1 of cystic fibrosis transmembrane conductance regulator

FEBS JOURNAL, Issue 17 2000
Production of a suitable protein for structural studies
Cystic fibrosis is caused by mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR). This protein belongs to the large ATP-binding cassette (ABC) family of transporters. Most patients with cystic fibrosis bear a mutation in the nucleotide-binding domain 1 (NBD1) of CFTR, which plays a key role in the activation of the channel function of CFTR. Determination of the three dimensional structure of NBD1 is essential to better understand its structure,function relationship, and relate it to the biological features of CFTR. In this paper, we report the first preparation of recombinant His-tagged NBD1, as a soluble, stable and isolated domain. The method avoids the use of renaturing processes or fusion constructs. ATPase activity assays show that the recombinant domain is functional. Using tryptophan intrinsic fluorescence, we point out that the local conformation, in the region of the most frequent mutation ,F508, could differ from that of the nucleotide-binding subunit of histidine permease, the only available ABC structure. We have undertaken three dimensional structure determination of NBD1, and the first two dimensional 15N- 1H NMR spectra demonstrate that the domain is folded. The method should be applicable to the structural studies of NBD2 or of other NBDs from different ABC proteins of major biological interest, such as multidrug resistance protein 1 or multidrug resistance associated protein 1. [source]


Probing the Local Conformation within ,-Conjugated One-dimensional Supramolecular Stacks using Frequency Modulation Atomic Force Microscopy

ADVANCED MATERIALS, Issue 41 2009
Benjamin Grévin
Frequency-modulation atomic force microscopy is used to investigate the local conformation within 1D stacks obtained by the self-assembly of ,-conjugated molecules from solution. The structural parameters extracted from the experimental data can be interpreted in terms of local molecular conformation, by comparison with models obtained by molecular mechanics and dynamics simulations. [source]


The kinetics of G-CSF folding

PROTEIN SCIENCE, Issue 10 2002
David N. Brems
Abstract The folding kinetics of G-CSF were determined by trp-fluorescence and far-UV circular dichroism. Folding and unfolding was achieved by rapid dilution and mixing of the denaturant, GdnHCl. G-CSF is a four-helical bundle protein with two long loops between the first and second helices and between the third and fourth helices. The entire conformational change expected by fluorescence was observed by stopped-flow technology, but due to rapid refolding kinetics only a portion was observed by circular dichroism. G-CSF contains two trp residues, and their contribution to the fluorescent-detected kinetics were deciphered through the use of single-site trp mutants. The trp moieties are probes of the local conformation surrounding their environment. One trp at residue 118 is located within the third helix while the other trp at residue 58 is part of the long loop between the first and second helices. The refolding results were most consistent with the following mechanism: U , I1 , I2 , N; where U represents the unfolded protein, I1 represents intermediate state 1, I2 represents intermediate state 2, and N represents the native state. I1 is characterized as having approximately one-half of the native-like helical structure and none of the native-like fluorescence. I2 has 100% of the native helical structure and most of the trp-118 and little of the trp-58 native-like fluorescence. Thus refolding occurs in distinct stages with half of the helix forming first followed by the remaining half of the helix including the third helix and finally the loop between the first and second helices folds. [source]


Near-atomic resolution crystal structure of an A-­DNA decamer d(CCCGATCGGG): cobalt hexammine interaction with A-DNA

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2003
Boopathy Ramakrishnan
The structure of the DNA decamer d(CCCGATCGGG) has been determined at 1.25,Ĺ resolution. The decamer crystallized in the tetragonal space group P43212, with unit-cell parameters a = b = 44.3, c = 24.8,Ĺ and one strand in the asymmetric unit. The structure was solved by the molecular-replacement method and refined to Rwork and Rfree values of 16.3 and 18.5%, respectively, for 5969 reflections. The decamer forms the A-form DNA duplex, with the abutting crystal packing typical of A-DNA. The crystal packing interactions seem to distort the local conformation: A5 adopts the trans/trans conformation for the torsion angles , and , instead of the usual gauche,/gauche+ conformations, yielding G*(G·C) base triplets. The highly hydrated [Co(NH3)6]3+ ion adopts a novel binding mode to the DNA duplex, binding directly to phosphate groups and connecting to N7 and O6 atoms of guanines by water bridges. Analysis of thermal parameters (B factors) shows that the nucleotides involved in abutting crystal packing are thermally more stable than other nucleotides in the duplex. [source]


Accurate prediction of proton chemical shifts.

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2001

Abstract Forty-five proton chemical shifts in 14 aromatic molecules have been calculated at several levels of theory: Hartree,Fock and density functional theory with several different basis sets, and also second-order Mřller,Plesset (MP2) theory. To obtain consistent experimental data, the NMR spectra were remeasured on a 500 MHz spectrometer in CDCl3 solution. A set of 10 molecules without strong electron correlation effects was selected as the parametrization set. The calculated chemical shifts (relative to benzene) of 29 different protons in this set correlate very well with the experiment, and even better after linear regression. For this set, all methods perform roughly equally. The best agreement without linear regression is given by the B3LYP/TZVP method (rms deviation 0.060 ppm), although the best linear fit of the calculated shifts to experimental values is obtained for B3LYP/6-311++G**, with an rms deviation of only 0.037 ppm. Somewhat larger deviations were obtained for the second test set of 4 more difficult molecules: nitrobenzene, azulene, salicylaldehyde, and o -nitroaniline, characterized by strong electron correlation or resonance-assisted intramolecular hydrogen bonding. The results show that it is possible, at a reasonable cost, to calculate relative proton shieldings in a similar chemical environment to high accuracy. Our ultimate goal is to use calculated proton shifts to obtain constraints for local conformations in proteins; this requires a predictive accuracy of 0.1,0.2 ppm. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1887,1895, 2001 [source]


A 13C solid-state NMR analysis of steroid compounds

MAGNETIC RESONANCE IN CHEMISTRY, Issue 8 2008
Jen-Hsien Yang
Abstract 13C CP/MAS solid-state NMR spectroscopy has been utilized to analyze six steroid compounds, namely testosterone (Tes), hydrocortisone (Cor), trans -dehydroandrosterone (Adr), prednisolone (Prd), prednisone (Pre) and estradiol (Est). Among them, Tes displays a doublet pattern for all residues, whereas Prd, Pre and Est, exhibit exclusively singlets. For Cor and Adr, the 13C spectra contain both doublet and singlet patterns. The 13C doublet signal, with splittings of 0.2,1.5 ppm, are ascribed to local differences in the ring conformations associated with polymorphism. We have assigned all of the 13C resonances to the different residues in these steroid compounds on the basis of solution NMR data. The C-7, C-8, C-10, C-15 and C-16 residues of Tes, Cor and Adr consistently give rise to singlets or doublets with splittings of less than 0.5 ppm, indicating similar local conformations. Accompanying hydration and dehydration processes, a reversible phase transformation between ,- and ,-crystal forms has been observed in Tes, corresponding to singlet and doublet13C patterns, respectively. To further characterize the ring conformations in the ,-form, we have successfully extracted chemical shift tensor elements for the 13C doublets. It is demonstrated that 13C solid-state NMR spectroscopy provides a reliable and sensitive means of characterizing polymorphism in steroids. Copyright © 2008 John Wiley & Sons, Ltd. [source]


Proline-40 is Essential to Maintaining Cytochrome b5, s Stability and Its Electron Transfer with Cytochrome c

CHINESE JOURNAL OF CHEMISTRY, Issue 11 2002
Zhi-Qian Wang
Abstract In order to illustrate the roles played by Pro40 in the structure, properties and functions of Cytochrome b5, three mutated genes, P40V, P40Y, P40G were constructed in this work. Only the P40V gene was successfully expressed into holoprotein in E. coli JM83. According to the results of X-ray crystallographic analysis and various kinds of spectroscopy studies, it is evident that substituting valine for Pro40 does not result in significant alterations in the protein,s overall structure; however, local conformational perturbations in the proximity of the heme do occur. The redox potential of the P40V mutant is 40 mV lower than that of the wild type protein. Its stability towards heat, urea, acid and ethanol were significantly decreased. The mutation leads to a decrease in the hydrophobicity of the heme pocket, which is probably the major factor contributing to the above changes. Binding constants and electron transfer rates between cytochrome bs and cytochrome c were determined using UV-visible spectroscopy and stopped-flow techniques for both the wild type and the mutant. The results showed that the substitution of Pro40 by valine does not influence the binding constant of cytochrome b5 to cytochrome c; however, the electron transfer rate between them decreased significantly. This indicates that proline-40 is essential to maintaining cytochrome bss stability and its electron transfer with cytochrome c. These studies also provided a good example that property and functional changes of a protein do not necessarily require large overall structural alterations; in most cases, only perturbations on the local conformations are sufficient to induce significant changes in protein,s properties and functions. [source]


Structures of Cytochrome b5 Mutated at the Charged Surface-Residues and Their Interactions with Cytochrome c,

CHINESE JOURNAL OF CHEMISTRY, Issue 11 2002
Jlan Wu
Abstract Glu44, Glu48, Ghi56 and Asp60 are the negatively charged residues located at the molecular surface of cytochrome b5. Two mutants of cytochrome b5 were prepared, in which two or all of these four residues were mutated to alanines. The mutations give rise to slightly positive shifts of the redox potentials of cytochrome b5 and obvious decrease of the cytochrome b5 -cytochrome c binding constants and electron transfer rates. The crystal structures of the two mutants were determined at 0.18 nm resolution, showing no alteration in overall structures and exhibiting slight changes in the local conformations around the mutation sites as compared with the wild-type protein. Based on the crystal structure of the quadruple-site mutant, a model for the binding of this mutant with cytochrome c is proposed, which involves the salt bridges from Glu37, Glu38 and heme propionate of cytochrome b5 to three lysines of cytochrome c and can well account for the properties and behaviors of this mutant. [source]