N-15-H relaxation parameters from ribonuclease HI (RNase H), acquired in previous work at magnetic fields of 14.1 and 18.8 T, and at 300 K, are analyzed with the mode-coupling slowly relaxing local structure (SRLS) approach. In accordance with standard theoretical treatments of restricted motions, SRLS approaches N-H bond dynamics from a tensorial perspective. As shown previously, a physically adequate description of this phenomenon has to account for the asymmetry of the local spatial restrictions. So far, we used rhombic local ordering tensors; this is straightforward but computationally demanding. Here, we propose substantiating the asymmetry of the local spatial restrictions in terms of tilted axial local ordering (S) and local diffusion (D-2) tensors. Although less straightforward, this description provides physically sound structural and dynamic information and is efficient computationally. We find that the local order parameter, S-0(2) is on average 0.89 (0.84, and may be as small as 0.6) for the secondary structure elements (loops). The main local ordering axis deviates from the C-i-1(alpha)-C-i(alpha) axis by less than 6 degrees. At 300 K, D-2,(perpendicular to) is virtually the same as the global diffusion rate, D-1 = 1.8 x 10(7) s(-1). The correlation time 1/6D(2,II) ranges from 3-125 (208-344) ps for the secondary structure elements (loops) and is on average 125 ps for the C-terminal segment. The main local diffusion axis deviates from the N-H bond by less than 2 degrees (10 degrees) for the secondary structure elements (loops). An effective data-fitting protocol, which leads in most cases to unambiguous results with limited uncertainty, has been devised. A physically sound and computationally effective methodology for analyzing N-15 relaxation in proteins, that provides a new picture of N-H bond structural dynamics in proteins, has been set forth.

SRLS Analysis of15N Spin Relaxation fromE. coliRibonuclease HI: The Tensorial Perspective

ZERBETTO, MIRCO;POLIMENO, ANTONINO
2012

Abstract

N-15-H relaxation parameters from ribonuclease HI (RNase H), acquired in previous work at magnetic fields of 14.1 and 18.8 T, and at 300 K, are analyzed with the mode-coupling slowly relaxing local structure (SRLS) approach. In accordance with standard theoretical treatments of restricted motions, SRLS approaches N-H bond dynamics from a tensorial perspective. As shown previously, a physically adequate description of this phenomenon has to account for the asymmetry of the local spatial restrictions. So far, we used rhombic local ordering tensors; this is straightforward but computationally demanding. Here, we propose substantiating the asymmetry of the local spatial restrictions in terms of tilted axial local ordering (S) and local diffusion (D-2) tensors. Although less straightforward, this description provides physically sound structural and dynamic information and is efficient computationally. We find that the local order parameter, S-0(2) is on average 0.89 (0.84, and may be as small as 0.6) for the secondary structure elements (loops). The main local ordering axis deviates from the C-i-1(alpha)-C-i(alpha) axis by less than 6 degrees. At 300 K, D-2,(perpendicular to) is virtually the same as the global diffusion rate, D-1 = 1.8 x 10(7) s(-1). The correlation time 1/6D(2,II) ranges from 3-125 (208-344) ps for the secondary structure elements (loops) and is on average 125 ps for the C-terminal segment. The main local diffusion axis deviates from the N-H bond by less than 2 degrees (10 degrees) for the secondary structure elements (loops). An effective data-fitting protocol, which leads in most cases to unambiguous results with limited uncertainty, has been devised. A physically sound and computationally effective methodology for analyzing N-15 relaxation in proteins, that provides a new picture of N-H bond structural dynamics in proteins, has been set forth.
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11577/2510901
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