Conformational Entropy from Slowly Relaxing Local Structure
Analysis of N-15-H Relaxation in Proteins: Application to
Pheromone Binding to MUP-I in the 283-308 K Temperature Range

J 2017

Conformational Entropy from Slowly Relaxing Local Structure Analysis of N-15-H Relaxation in Proteins: Application to Pheromone Binding to MUP-I in the 283-308 K Temperature Range

ŽÍDEK, Lukáš and Eva MEIROVITCH

Basic information

Original name

Conformational Entropy from Slowly Relaxing Local Structure Analysis of N-15-H Relaxation in Proteins: Application to Pheromone Binding to MUP-I in the 283-308 K Temperature Range

Authors

ŽÍDEK, Lukáš (203 Czech Republic, guarantor, belonging to the institution) and Eva MEIROVITCH (376 Israel)

Edition

Journal of Physical Chemistry B, WASHINGTON, AMER CHEMICAL SOC, 2017, 1520-6106

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10403 Physical chemistry

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.146

RIV identification code

RIV/00216224:14310/17:00098087

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1021/acs.jpcb.7b06049

UT WoS

000411772100007

Keywords in English

MODEL-FREE APPROACH; MAGNETIC-RESONANCE RELAXATION; NMR RELAXATION; BACKBONE DYNAMICS; LIGAND-BINDING; ORDER PARAMETERS; DEPENDENCE; COMPLEX; DOMAIN; MOTIONS

Abstract

V originále

The slowly relaxing local structure (SRLS) approach is applied to N-15-H relaxation from the major urinary protein I (MUP-I), and its complex with pheromone 2-sec-butyl-4,5-dihydrothiazol. The objective is to elucidate dynamics, and binding-induced changes in conformational entropy. Experimental data acquired previously in the 283- 308 K temperature range are used. The N-H bond is found to reorient globally with correlation time, tau(1,0) and locally with correlation time, tau(2,0), where tau(1,0) >> tau(2,0). The local motion is restricted by the potential u =-c(0)(2)D(00)(2), where D-00(2) is the Wigner rotation matrix element for L = 2, K = 0, and c(0)(2) evaluates the strength of the potential. u yields straightforwardly the order parameter, < D-00(2)>, and the conformational entropy, S-k, both given by P-eq = exp(-u). The deviation of the local ordering/local diffusion axis from the N-H bond, given by the angle beta, is also determined. We find that c(0)(2) congruent to 18 +/- 4 and T-2,T-0 = 0-170 ps for ligand-free MUP-I, whereas c(0)(2) congruent to 15 +/- 4 and tau(2,0) = 20-270 ps for ligand-bound MUP-I beta is in the 0-10 degrees range. c(0)(2) and tau(2,0) decrease, whereas beta increases, when the temperature is increased from 283 to 308 K. Thus, SRLS provides physically well-defined structure-related (c(0)(2) and < D-00 >(2)), motion-related (tau(2,0)), geometry related (beta), and binding-related (S-k) local parameters, and their temperature-dependences. Intriguingly, upon pheromone binding the conformational entropy of MUP-I decreases at high temperature and increases at low temperature. The very same experimental data were analyzed previously with the model-free (MF) method which yielded "global" (in this context, "relating to the entire 283-308 K range") amplitude (S-2) and rate (tau(e)) of the local motion, and a phenomenological exchange term (R-ex). S-2 is found to decrease (implying implicitly "global" increase in S-k) upon pheromone binding.

Citovat

ŽÍDEK, Lukáš and Eva MEIROVITCH. Conformational Entropy from Slowly Relaxing Local Structure Analysis of N-15-H Relaxation in Proteins: Application to Pheromone Binding to MUP-I in the 283-308 K Temperature Range. Journal of Physical Chemistry B. WASHINGTON: AMER CHEMICAL SOC, 2017, vol. 121, No 37, p. 8684-8692. ISSN 1520-6106. Available from: https://dx.doi.org/10.1021/acs.jpcb.7b06049.

@article{1394037,
   author = {Žídek, Lukáš and Meirovitch, Eva},
   article_location = {WASHINGTON},
   article_number = {37},
   doi = {http://dx.doi.org/10.1021/acs.jpcb.7b06049},
   keywords = {MODEL-FREE APPROACH; MAGNETIC-RESONANCE RELAXATION; NMR RELAXATION; BACKBONE DYNAMICS; LIGAND-BINDING; ORDER PARAMETERS; DEPENDENCE; COMPLEX; DOMAIN; MOTIONS},
   language = {eng},
   issn = {1520-6106},
   journal = {Journal of Physical Chemistry B},
   title = {Conformational Entropy from Slowly Relaxing Local Structure Analysis of N-15-H Relaxation in Proteins: Application to Pheromone Binding to MUP-I in the 283-308 K Temperature Range},
   url = {http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b06049},
   volume = {121},
   year = {2017}
}

TY  - JOUR
ID  - 1394037
AU  - Žídek, Lukáš - Meirovitch, Eva
PY  - 2017
TI  - Conformational Entropy from Slowly Relaxing Local Structure Analysis of N-15-H Relaxation in Proteins: Application to Pheromone Binding to MUP-I in the 283-308 K Temperature Range
JF  - Journal of Physical Chemistry B
VL  - 121
IS  - 37
SP  - 8684-8692
EP  - 8684-8692
PB  - AMER CHEMICAL SOC
SN  - 15206106
KW  - MODEL-FREE APPROACH
KW  - MAGNETIC-RESONANCE RELAXATION
KW  - NMR RELAXATION
KW  - BACKBONE DYNAMICS
KW  - LIGAND-BINDING
KW  - ORDER PARAMETERS
KW  - DEPENDENCE
KW  - COMPLEX
KW  - DOMAIN
KW  - MOTIONS
UR  - http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b06049
L2  - http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b06049
N2  - The slowly relaxing local structure (SRLS) approach is applied to N-15-H relaxation from the major urinary protein I (MUP-I), and its complex with pheromone 2-sec-butyl-4,5-dihydrothiazol. The objective is to elucidate dynamics, and binding-induced changes in conformational entropy. Experimental data acquired previously in the 283- 308 K temperature range are used. The N-H bond is found to reorient globally with correlation time, tau(1,0) and locally with correlation time, tau(2,0), where tau(1,0) >> tau(2,0). The local motion is restricted by the potential u =-c(0)(2)D(00)(2), where D-00(2) is the Wigner rotation matrix element for L = 2, K = 0, and c(0)(2) evaluates the strength of the potential. u yields straightforwardly the order parameter, < D-00(2)>, and the conformational entropy, S-k, both given by P-eq = exp(-u). The deviation of the local ordering/local diffusion axis from the N-H bond, given by the angle beta, is also determined. We find that c(0)(2) congruent to 18 +/- 4 and T-2,T-0 = 0-170 ps for ligand-free MUP-I, whereas c(0)(2) congruent to 15 +/- 4 and tau(2,0) = 20-270 ps for ligand-bound MUP-I beta is in the 0-10 degrees range. c(0)(2) and tau(2,0) decrease, whereas beta increases, when the temperature is increased from 283 to 308 K. Thus, SRLS provides physically well-defined structure-related (c(0)(2) and < D-00 >(2)), motion-related (tau(2,0)), geometry related (beta), and binding-related (S-k) local parameters, and their temperature-dependences. Intriguingly, upon pheromone binding the conformational entropy of MUP-I decreases at high temperature and increases at low temperature. The very same experimental data were analyzed previously with the model-free (MF) method which yielded "global" (in this context, "relating to the entire 283-308 K range") amplitude (S-2) and rate (tau(e)) of the local motion, and a phenomenological exchange term (R-ex). S-2 is found to decrease (implying implicitly "global" increase in S-k) upon pheromone binding.
ER  -

ŽÍDEK, Lukáš and Eva MEIROVITCH. Conformational Entropy from Slowly Relaxing Local Structure Analysis of N-15-H Relaxation in Proteins: Application to Pheromone Binding to MUP-I in the 283-308 K Temperature Range. \textit{Journal of Physical Chemistry B}. WASHINGTON: AMER CHEMICAL SOC, 2017, vol.~121, No~37, p.~8684-8692. ISSN~1520-6106. Available from: https://dx.doi.org/10.1021/acs.jpcb.7b06049.

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