Domain mobility in proteins from NMR/SRLS. 2009

Yury E Shapiro, and Edith Kahana, and Eva Meirovitch
The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel. shapiro@nmrsgi4.ls.biu.ac.il

Enhanced internal mobility in proteins is typically functional. Domain motion in enzymes, necessarily related to catalysis, is a prototype in this context. Experimental (15)N spin relaxation data from E. coli adenylate kinase report qualitatively on nanosecond motion experienced by the domains AMPbd and LID. Previous quantitative analysis based on the mode-coupling slowly relaxing local structure approach confirmed nanosecond mobility but yielded unduly small local ordering and local geometry not interpretable directly in terms of the local protein structure. Here, we show that these features ensue from having assumed axial local ordering and highly axial local diffusion. After eliminating these simplified second-rank tensor properties, a physically sound picture, with the local motion interpretable as domain motion, is obtained. Rhombic local ordering, with components given by <Sxx> = 0.471, <Syy> = -0.952 and <Szz> = 0.481, and main ordering axis, Y(M), lying along C(alpha)(i-1) - C(alpha)(i), has been determined. The associated rhombic potential is given by axial (rhombic) coefficients of <c(2)(0)> = -3.3 (<c(2)(2)> = 17.8). The average correlation time for domain motion is 10.4 (6.4) ns at 288 (302) K; the corresponding correlation time for global motion is 20.6 (14.9) ns. The rates for domain motion exhibit noteworthy Arrhenius-type temperature-dependence, yielding activation energies of 63.8 +/- 7.0 (53.0 +/- 9.1) kJ/mol for the AMPbd (LID) domain. The traditional model-free analysis ignores mode-coupling and simplifies tensor properties. Within its scope, the AKeco backbone emerges as largely rigid, <Szz> approximately = 0.94; the main ordering axis, Z(M), lies along N-H, <c(2)(0)> approximately = 16 (c(2)(2) = 0); and the slow local motional correlation time lies at the low end of the nanosecond time scale.

UI MeSH Term Description Entries
D007700 Kinetics The rate dynamics in chemical or physical systems.
D008956 Models, Chemical Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment. Chemical Models,Chemical Model,Model, Chemical
D008962 Models, Theoretical Theoretical representations that simulate the behavior or activity of systems, processes, or phenomena. They include the use of mathematical equations, computers, and other electronic equipment. Experimental Model,Experimental Models,Mathematical Model,Model, Experimental,Models (Theoretical),Models, Experimental,Models, Theoretic,Theoretical Study,Mathematical Models,Model (Theoretical),Model, Mathematical,Model, Theoretical,Models, Mathematical,Studies, Theoretical,Study, Theoretical,Theoretical Model,Theoretical Models,Theoretical Studies
D008968 Molecular Conformation The characteristic three-dimensional shape of a molecule. Molecular Configuration,3D Molecular Structure,Configuration, Molecular,Molecular Structure, Three Dimensional,Three Dimensional Molecular Structure,3D Molecular Structures,Configurations, Molecular,Conformation, Molecular,Conformations, Molecular,Molecular Configurations,Molecular Conformations,Molecular Structure, 3D,Molecular Structures, 3D,Structure, 3D Molecular,Structures, 3D Molecular
D009682 Magnetic Resonance Spectroscopy Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING). In Vivo NMR Spectroscopy,MR Spectroscopy,Magnetic Resonance,NMR Spectroscopy,NMR Spectroscopy, In Vivo,Nuclear Magnetic Resonance,Spectroscopy, Magnetic Resonance,Spectroscopy, NMR,Spectroscopy, Nuclear Magnetic Resonance,Magnetic Resonance Spectroscopies,Magnetic Resonance, Nuclear,NMR Spectroscopies,Resonance Spectroscopy, Magnetic,Resonance, Magnetic,Resonance, Nuclear Magnetic,Spectroscopies, NMR,Spectroscopy, MR
D011506 Proteins Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein. Gene Products, Protein,Gene Proteins,Protein,Protein Gene Products,Proteins, Gene
D002384 Catalysis The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction. Catalyses
D004926 Escherichia coli A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc. Alkalescens-Dispar Group,Bacillus coli,Bacterium coli,Bacterium coli commune,Diffusely Adherent Escherichia coli,E coli,EAggEC,Enteroaggregative Escherichia coli,Enterococcus coli,Diffusely Adherent E. coli,Enteroaggregative E. coli,Enteroinvasive E. coli,Enteroinvasive Escherichia coli
D000263 Adenylate Kinase An enzyme that catalyzes the phosphorylation of AMP to ADP in the presence of ATP or inorganic triphosphate. EC 2.7.4.3. Myokinase,AMP Kinase,ATP-AMP Phosphotransferase,ATP-AMP Transphosphorylase,Adenylokinase,ATP AMP Phosphotransferase,ATP AMP Transphosphorylase,Kinase, AMP,Kinase, Adenylate,Phosphotransferase, ATP-AMP,Transphosphorylase, ATP-AMP
D013696 Temperature The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms. Temperatures

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