High-field EPR-detected shifts of magnetic tensor components of spin label side chains reveal protein conformational changes: The proton entrance channel of bacteriorhodopsin

2001 ◽  
Vol 21 (3-4) ◽  
pp. 441-452 ◽  
Author(s):  
C. Wegener ◽  
A. Savitsky ◽  
M. Pfeiffer ◽  
K. Möbius ◽  
H. J. Steinhoff
Keyword(s):  
Conformational Changes ◽  
Spin Label ◽  
High Field ◽  
Entrance Channel ◽  
Side Chains ◽  
Protein Conformational Changes

Interaction between Spin Labels and DPPC Vesicles

1986 ◽  
Vol 41 (7-8) ◽  
pp. 799-801
Author(s):  
W. Lohmann ◽  
B. Kiefer ◽  
W. Schmehl
Keyword(s):  
Spin Label ◽  
High Field ◽  
Spin Labels ◽  
Side Chains ◽  
Nmr Studies ◽  
H Nmr ◽  
Low Field ◽  
Head Groups ◽  
Vesicle Preparation ◽  
Stabilizing Effect

Abstract1H NMR studies on DPPC vesicles labeled with the spin labels (1,14) or (12,3) have shown that both of the spin labels influence the fatty acid side chains as well as the choline head groups. The spin label (12,3) affects, natural­ly, the head groups stronger than the spin label (1,14), while the reversed effect can be observed at the side chains. This effect progresses with time after vesicle preparation and is fully developed after about 24 h. Addition of Na- ascorbate, at this time, seems to reverse the effect indicat­ing a stabilizing effect of the vitamin on the membrane. These results could be confirmed by ESR investigations according to which the high-field signal seems to be indica­tive for changes occurring at the side chains, while the low-field signal seems to reflect modifications of the head groups. Since the spin label (1,14) affects considerably the head groups at temperatures <6 °C, in which case the spec­trum is very similar to that obtained with spin label (12,3) at 24 °C, one might conclude that there might be a phase transition in regard to the head groups.

scholarly journals Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER Distance Restraints

2021 ◽  
Vol 17 (6) ◽  
pp. e1009107
Author(s):  
Diego del Alamo ◽  
Kevin L. Jagessar ◽  
Jens Meiler ◽  
Hassane S. Mchaourab
Keyword(s):  
Conformational Changes ◽  
Spin Label ◽  
Protein Conformational Changes ◽  
Alternative Protein ◽  
Distance Distributions ◽  
Distance Restraints ◽  
Double Electron ◽  
The Time Domain ◽  
Double Electron Electron Resonance ◽  
Experimental Structure

We describe an approach for integrating distance restraints from Double Electron-Electron Resonance (DEER) spectroscopy into Rosetta with the purpose of modeling alternative protein conformations from an initial experimental structure. Fundamental to this approach is a multilateration algorithm that harnesses sets of interconnected spin label pairs to identify optimal rotamer ensembles at each residue that fit the DEER decay in the time domain. Benchmarked relative to data analysis packages, the algorithm yields comparable distance distributions with the advantage that fitting the DEER decay and rotamer ensemble optimization are coupled. We demonstrate this approach by modeling the protonation-dependent transition of the multidrug transporter PfMATE to an inward facing conformation with a deviation to the experimental structure of less than 2Å Cα RMSD. By decreasing spin label rotamer entropy, this approach engenders more accurate Rosetta models that are also more closely clustered, thus setting the stage for more robust modeling of protein conformational changes.

Infrared spectra of N-acetyl-L-α-amino-acid N'-methylamides with aliphatic side chains in non-polar solvents

1981 ◽  
Vol 46 (3) ◽  
pp. 772-780 ◽  
Author(s):  
Jorga Smolíková ◽  
Jan Pospíšek ◽  
Karel Bláha
Keyword(s):  
Amino Acid ◽  
Conformational Changes ◽  
Infrared Spectra ◽  
Room Temperature ◽  
Side Chains ◽  
Polar Solvents

Infrared spectra of the L-alanine (I), L-leucine (II), L-valine (III) and L-tert-leucine (IV) N-acetyl N'-methylamides were measured. Amides I-IV are not self associated in tetrachlormethane in the concentration 2 . 10-5 mol l-1 at room temperature and in tetrachloroethylene in the concentration 1.5 . 10-4 mol l-1 at temperatures above 65° C. True conformational changes are observable only with the least flexible amide IV which exists at room temperature in a C5 conformation. This conformational type is also highly populated in the valine derivative III, but is less important in the alanine and leucine derivatives I and II in which the intramolecularly bonded C7 and the distorted hydrogen-nonbonded conformations contribute seriously.

scholarly journals Protein conformational changes and myelin solubilization by anion-detergent solutions

FEBS Letters ◽  
1992 ◽  
Vol 309 (3) ◽  
pp. 376-380 ◽  
Author(s):  
Jaime Monreal ◽  
Pedro Carmona ◽  
Pilar Regueiro ◽  
Ricardo S. Diaz
Keyword(s):  
Conformational Changes ◽  
Protein Conformational Changes ◽  
Detergent Solutions

The interaction of ligands with chemically modified phosphorylase b

1976 ◽  
Vol 54 (5) ◽  
pp. 494-499
Author(s):  
D. Brooks ◽  
S. J. W. Busby ◽  
J. R. Griffiths ◽  
G. K. Radda ◽  
O. Avramovic-Zikic
Keyword(s):  
Conformational Changes ◽  
Spin Label ◽  
Native Enzyme ◽  
Carboxyl Groups ◽  
Chemically Modified ◽  
Allosteric Effector ◽  
Spin Resonance ◽  
Label Probe ◽  
Glycine Ethyl Ester ◽  
Modified Enzyme

Phosphorylase b which had been inactivated with 5-diazo-1H-tetrazole was specifically labelled with 4-iodoacetamidosalicylic acid (a fluorescent probe) or with N-(1-oxyl-2,2,6,6,-tetramethyl-4-piperidinyl)iodoacetamide (a spin label probe) so that the binding of ligands and accompanying conformational changes could be determined by fluorescence or electron spin resonance changes, respectively. The allosteric effector, AMP, causes conformational changes similar to those caused in the native enzyme. The affinity of binding of phosphate or AMP to the inhibited protein is the same as for the unmodified protein. The heterotropic interactions between glucose-1-phosphate or glycogen and AMP are much less in the inactivated enzyme than in unmodified phosphorylase. Using a light scattering assay, it is shown that the modified enzyme binds to glycogen less strongly than the native protein.Phosphorylase b which had been inactivated by carbodiimide in the presence of glycine ethyl ester, resulting in the modification of one or more carboxyl groups, was labelled with the spin label probe described above. The modified enzyme has an affinity for AMP similar to that of the native enzyme. AMP binding to the modified enzyme is tightened by glycogen, weakened by glucose-6-phosphate and is unaffected by glucose- 1-phosphate.The actions of 5-diazo-1H-tetrazole and carbodiimide on phosphorylase are discussed in the light of the above observations.

Protein conformational changes revealed by optical spectroscopic reflectometry in porous silicon multilayers

2008 ◽  
Vol 21 (3) ◽  
pp. 035115 ◽  
Author(s):  
Edoardo De Tommasi ◽  
Ilaria Rea ◽  
Ivo Rendina ◽  
Lucia Rotiroti ◽  
Luca De Stefano
Keyword(s):  
Porous Silicon ◽  
Conformational Changes ◽  
Protein Conformational Changes ◽  
Spectroscopic Reflectometry
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