[NMR paper] (15)N-H-Related Conformational Entropy Changes Entailed By Plexin-B1 RBD Dimerization: A Combined Molecular Dynamics/NMR Relaxation Approach.

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(15)N-H-Related Conformational Entropy Changes Entailed By Plexin-B1 RBD Dimerization: A Combined Molecular Dynamics/NMR Relaxation Approach.

Related Articles (15)N-H-Related Conformational Entropy Changes Entailed By Plexin-B1 RBD Dimerization: A Combined Molecular Dynamics/NMR Relaxation Approach.

J Phys Chem B. 2017 Mar 10;:

Authors: Zerbetto M, Meirovitch E

Abstract
We report on a new method for determining function-related conformational entropy changes in proteins. Plexin-B1 RBD dimerization serves as example, and internally-mobile N-H bonds serve as probes. Sk (entropy in units of kBT) is given by -?(Peq lnPeq)d?, where Peq= exp(-u) is the probability density for probe orientation, and u the local potential. Previous SRLS analyses of (15)N-H relaxation in proteins determined linear combinations of D(2)00(?) and (D(2)02(?) + D(2)0-2(?)) (D(L)0K(?) - Wigner rotation matrix element in uniaxial local medium) as "best-fit" form of u. SRLS also determined the "best-fit" orientation of the related ordering tensor. On the basis of this information the coefficients (in the linear combination) of the terms specified above are determined with molecular dynamics (MD) simulations. With the explicit expression for u thus in hand, Sk is calculated. We find that in general Sk decreases, i.e., the local order increases, upon plexin-B1 RBD dimerization. The largest decrease in Sk occurs in the helices ?1 and ?2, followed by the L4 loop. Only the relatively small peripheral ?2 strand, ?2/?1 loop, and ?3/?4 loop, become more disordered. That ?-helices dominate ?Sk = Sk(dimer) - Sk(monomer), a few peripheral outliers apparently counterbalance the overall decrease in Sk, and the probability density function, Peq has rhombic symmetry given that the underlying potential, u, has rhombic symmetry, are interesting features. We also derive S(2) (the proxy of u in the simple "model-free" limit of SRLS) with MD. Its conversion into a potential requires assumptions and adopting a simple axial form of u. Ensuing ?Sk(MF) profiles are u-dependent and differ from ?Sk(SRLS). A method that provides consistent, general and accurate Sk, atomistic/mesoscopic in nature, has been developed. Its ability to provide new insights in protein research has been illustrated.


PMID: 28281763 [PubMed - as supplied by publisher]



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