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Conformational Fluctuations (conformational + fluctuation)

Distribution by Scientific Domains

Chemistry	100%

Selected Abstracts

Response of native and denatured hen lysozyme to high pressure studied by 15N/1H NMR spectroscopy

FEBS JOURNAL, Issue 6 2001
Yuji O. Kamatari
High-pressure 15N/1H NMR techniques were used to characterize the conformational fluctuations of hen lysozyme, in its native state and when denatured in 8 m urea, over the pressure range 30,2000 bar. Most 1H and 15N signals of native lysozyme show reversible shifts to low field with increasing pressure, the average pressure shifts being 0.069 ± 0.101 p.p.m. (1H) and 0.51 ± 0.36 p.p.m. (15N). The shifts indicate that the hydrogen bonds formed to carbonyl groups or water molecules by the backbone amides are, on average, shortened by ,,0.02 Å as a result of pressure. In native lysozyme, six residues in the , domain or at the ,/, domain interface have anomalously large nonlinear 15N and 1H chemical-shift changes. All these residues lie close to water-containing cavities, suggesting that there are conformational changes involving these cavities, or the water molecules within them, at high pressure. The pressure-induced 1H and 15N shifts for lysozyme denatured in 8 m urea are much more uniform than those for native lysozyme, with average backbone amide shifts of 0.081 ± 0.029 p.p.m. (1H) and 0.57 ± 0.14 p.p.m. (15N). The results show that overall there are no significant variations in the local conformational properties of denatured lysozyme with pressure, although larger shifts in the vicinity of a persistent hydrophobic cluster indicate that interactions in this part of the sequence may rearrange. NMR diffusion measurements demonstrate that the effective hydrodynamic radius of denatured lysozyme, and hence the global properties of the denatured ensemble, do not change detectably at high pressure. [source]

Temperature-induced reversible conformational change in the first 100 residues of ,-synuclein

PROTEIN SCIENCE, Issue 3 2006
Brian C. McNulty
Abstract Natively disordered proteins are a growing class of anomalies to the structure,function paradigm. The natively disordered protein ,-synuclein is the primary component of Lewy bodies, the cellular hallmark of Parkinson's disease. We noticed a dramatic difference in dilute solution 1H- 15N Heteronuclear Single Quantum Coherence (HSQC) spectra of wild-type ,-synuclein and two disease-related mutants (A30P and A53T), with spectra collected at 35°C showing fewer cross-peaks than spectra acquired at 10°C. Here, we show the change to be the result of a reversible conformational exchange linked to an increase in hydrodynamic radius and secondary structure as the temperature is raised. Combined with analytical ultracentrifugation data showing ,-synuclein to be monomeric at both temperatures, we conclude that the poor quality of the 1H- 15N HSQC spectra obtained at 35°C is due to conformational fluctuations that occur on the proton chemical shift time scale. Using a truncated variant of ,-synuclein, we show the conformational exchange occurs in the first 100 amino acids of the protein. Our data illustrate a key difference between globular and natively disordered proteins. The properties of globular proteins change little with solution conditions until they denature cooperatively, but the properties of natively disordered proteins can vary dramatically with solution conditions. [source]

Flexibility of the MHC class II peptide binding cleft in the bound, partially filled, and empty states: A molecular dynamics simulation study

BIOPOLYMERS, Issue 1 2009
Rakina Yaneva
Abstract Major histocompatibility (MHC) Class II cell surface proteins present antigenic peptides to the immune system. Class II structures in complex with peptides but not in the absence of peptide are known. Comparative molecular dynamics (MD) simulations of a Class II protein (HLA-DR3) with and without CLIP (invariant chain-associated protein) peptide were performed starting from the CLIP-bound crystal structure. Depending on the protonation of acidic residues in the P6 peptide-binding pocket the simulations stayed overall close to the start structure. The simulations without CLIP showed larger conformational fluctuations especially of ,-helices flanking the binding cleft. Largest fluctuations without CLIP were observed in a helical segment near the peptide C-terminus binding region matching a segment recognized by antibodies specific for empty Class II proteins. Simulations on a Val86Tyr mutation that fills the peptide N-terminus binding P1 pocket or of a complex with a CLIP fragment (dipeptide) bound to P1 showed an unexpected long range effect. In both simulations the mobility not only of P1 but also of the entire binding cleft was reduced compared to simulations without CLIP. It correlates with the experimental finding that the CLIP fragment binding to P1 is sufficient to prevent antibody recognition specific for the empty form at a site distant from P1. The results suggest a mechanism how a local binding event of small peptides or of an exchange factor near P1 may promote peptide binding and exchange through a long range stabilization of the whole binding cleft in a receptive (near bound) conformation. © 2008 Wiley Periodicals, Inc. Biopolymers 91: 14,27, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source]

Review fluorescence correlation spectroscopy for probing the kinetics and mechanisms of DNA hairpin formation

BIOPOLYMERS, Issue 1 2008
Alan Van Orden
Abstract This article reviews the application of fluorescence correlation spectroscopy (FCS) and related techniques to the study of nucleic acid hairpin conformational fluctuations in free aqueous solutions. Complimentary results obtained using laser-induced temperature jump spectroscopy, single-molecule fluorescence spectroscopy, optical trapping, and biophysical theory are also discussed. The studies cited reveal that DNA and RNA hairpin folding occurs by way of a complicated reaction mechanism involving long- and short-lived reaction intermediates. Reactions occurring on the subnanoseconds to seconds time scale have been observed, pointing out the need for experimental techniques capable of probing a broad range of reaction times in the study of such complex, multistate reactions. © 2007 Wiley Periodicals, Inc. Biopolymers 89: 1,16, 2008. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source]

Single-Molecule Spectroscopy on a Ladder-Type Conjugated Polymer: Electron,Phonon Coupling and Spectral Diffusion

CHEMPHYSCHEM, Issue 14 2009
Richard Hildner Dr.
Abstract We employ low-temperature single-molecule spectroscopy combined with pattern recognition techniques for data analysis on a methyl-substituted ladder-type poly(para -phenylene) (MeLPPP) to investigate the electron,phonon coupling to low-energy vibrational modes as well as the origin of the strong spectral diffusion processes observed for this conjugated polymer. The results indicate weak electron,phonon coupling to low-frequency vibrations of the surrounding matrix of the chromophores, and that low-energy intrachain vibrations of the conjugated backbone do not couple to the electronic transitions of MeLPPP at low temperatures. Furthermore, these findings suggest that the main line-broadening mechanism of the zero-phonon lines of MeLPPP is fast, unresolved spectral diffusion, which arises from conformational fluctuations of the side groups attached to the MeLPPP backbone as well as of the surrounding host material. [source]