Characterization of Protein Conformational States by Normal-Mode Frequencies

2007 ◽  
Vol 129 (37) ◽  
pp. 11394-11401 ◽  
Author(s):  
Benjamin A. Hall ◽  
Samantha L. Kaye ◽  
Andy Pang ◽  
Rafael Perera ◽  
Philip C. Biggin
Keyword(s):  
Normal Mode ◽  
Conformational States

scholarly journals Rapid Characterization of Allosteric Networks with Ensemble Normal Mode Analysis

2016 ◽  
Vol 120 (33) ◽  
pp. 8276-8288 ◽  
Author(s):  
Xin-Qiu Yao ◽  
Lars Skjærven ◽  
Barry J. Grant
Keyword(s):  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Rapid Characterization

Spectroscopic Characterization of Nonnative Conformational States of Cytochromec

2002 ◽  
Vol 106 (25) ◽  
pp. 6566-6580 ◽  
Author(s):  
Silke Oellerich ◽  
Hainer Wackerbarth ◽  
Peter Hildebrandt
Keyword(s):  
Spectroscopic Characterization ◽  
Conformational States

Characterization of unstable rock slopes using ambient vibration analysis

2020 ◽  
Author(s):  
Donat Fäh ◽  
Mauro Häusler ◽  
Franziska Glueer ◽  
Jan Burjanek ◽  
Ulrike Kleinbrod
Keyword(s):  
Seismic Response ◽  
Normal Mode ◽  
Wave Velocity ◽  
Ambient Vibration ◽  
Mode Analysis ◽  
Permafrost Degradation ◽  
Rock Slopes ◽  
Spectral Ratios ◽  
S Wave

<p>Earthquake-induced landslides can have serious social impacts, causing many casualties and significant damage to infrastructure. They are the most destructive secondary hazards related to earthquakes. The impact of strong seismic events is not limited just to triggering of catastrophic slope failures, it also involves weakening of intact rock masses and reactivation of dormant slides. Hazard mitigation of potentially catastrophic landslides requires a thorough understanding of the mechanisms driving slope movements and seismic response.</p><p>We present an overview of the investigations on more than 25 instabilities. The results show that ambient vibration measurements allow for a rapid and objective characterization of potential slope instabilities. It is possible to distinguish unstable from stable areas, to identify slope eigen-frequencies, local amplification levels due to weak excitation, local deformation directions and properties of the internal slope structure. The ambient vibration techniques include single-station H/V ratios and polarization analyses, site-to-reference spectral ratios, array methods to identify surface-wave dispersion curves, and/or normal mode analysis using enhanced frequency domain decomposition. We analyse the seismic response of the rock slopes in different frequency bands together with its spatial and azimuthal variability, which is a fingerprint of the slope’s internal structure at different scales (tenth of meters to hundred meters). Normal mode behaviour is typically observed in structures with distinct sub-volumes, where the wave field at the resonance frequencies is oriented perpendicular to the deep persistent fractures. These structures show maximum amplification at their resonance frequency. Normal mode behaviour is also observed for rock towers, similar to what can be observed for buildings. In contrast, a highly fractured rock mass without dominant cracks is characterized by an S-wave velocity gradient with shear-wave velocity being significantly reduced close to the surface. Generally, normal modes do not develop, but surface waves propagate in such structures, which can be used for the determination of the S-wave profile. This is typical for large deep seated landslides with a layered structure. Without strong S-wave velocity contrast at depth, H/V spectral ratios show no clear peak and are not conclusive to characterize structures with highly fractured material. However, frequency-dependent ground-motion amplification from standard spectral ratios is directly related to the S-wave velocity profile and damping. Therefore, wave amplification can be a measure for the disintegration of the rock.</p><p>Repeated measurements on slopes allow for the detection of possible changes in their properties. Semi-permanent installations on instabilities of interest allow for a continuous assessment of the dynamic response in order to understand variations due to weather conditions and potential long-term changes. This includes the measurement of site-amplification during earthquakes derived from empirical spectral modelling. When measuring in the same season and weather condition, the seismic response of rock instabilities in general remains unchanged over years, as long a no external trigger affects the instability, including a strong earthquake, partial failure of the slope or permafrost degradation.</p>

Characterization of Ligand-Induced Conformational States in the β2Adrenergic Receptor

1999 ◽  
Vol 19 (1-4) ◽  
pp. 293-300 ◽  
Author(s):  
Brian Kobilka ◽  
Ulrik Gether ◽  
Roland Seifert ◽  
Sansan Lin ◽  
Pejman Ghanouni
Keyword(s):  
Conformational States

scholarly journals Characterization of the Multiple Conformational States of Free Monomeric and Trimeric Human Immunodeficiency Virus Envelope Glycoproteins after Fixation by Cross-Linker

2006 ◽  
Vol 80 (14) ◽  
pp. 6725-6737 ◽  
Author(s):  
Wen Yuan ◽  
Jessica Bazick ◽  
Joseph Sodroski
Keyword(s):  
Human Immunodeficiency Virus ◽  
Receptor Binding ◽  
Neutralizing Antibodies ◽  
Conformational Flexibility ◽  
Envelope Glycoproteins ◽  
Conformational States ◽  
Immunodeficiency Virus ◽  
Hiv 1 ◽  
Trimeric Envelope

ABSTRACT The human immunodeficiency virus type 1 (HIV-1) gp120 exterior and gp41 transmembrane envelope glycoproteins assemble into trimers on the virus surface that represent potential targets for antibodies. Potent neutralizing antibodies bind the monomeric gp120 glycoprotein with small changes in entropy, whereas unusually large decreases in entropy accompany gp120 binding by soluble CD4 and less potent neutralizing antibodies. The high degree of conformational flexibility in the free gp120 molecule implied by these observations has been suggested to contribute to masking the trimer from antibodies that recognize the gp120 receptor-binding regions. Here we use cross-linking and recognition by antibodies to investigate the conformational states of gp120 monomers and soluble and cell surface forms of the trimeric HIV-1 envelope glycoproteins. The fraction of monomeric and trimeric envelope glycoproteins able to be recognized after fixation was inversely related to the entropic changes associated with ligand binding. In addition, fixation apparently limited the access of antibodies to the V3 loop and gp41-interactive surface of gp120 only in the context of trimeric envelope glycoproteins. The results support a model in which the unliganded monomeric and trimeric HIV-1 envelope glycoproteins sample several different conformations. Depletion of particular fixed conformations by antibodies allowed characterization of the relationships among the conformational states. Potent neutralizing antibodies recognize the greatest number of conformations and therefore can bind the virion envelope glycoproteins more rapidly and completely than weakly neutralizing antibodies. Thus, the conformational flexibility of the HIV-1 envelope glycoproteins creates thermodynamic and kinetic barriers to neutralization by antibodies directed against the receptor-binding regions of gp120.

scholarly journals Biochemical characterization of different conformational states of the Sf9 cell-purified p53His175 mutant protein

FEBS Letters ◽  
1999 ◽  
Vol 463 (1-2) ◽  
pp. 179-184 ◽  
Author(s):  
Pascale A. Cohen ◽  
Ted R. Hupp ◽  
David P. Lane ◽  
Dion A. Daniels
Keyword(s):  
Biochemical Characterization ◽  
Mutant Protein ◽  
Conformational States
Sign in / Sign up

Export Citation Format

Share Document