Many Local Motions Cooperate to Produce the Adenylate Kinase Conformational Transition |
| |
| Authors: | Michael D Daily George N Phillips Qiang Cui |
| |
| Institution: | 1. Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA;2. Computation and Informatics in Biology and Medicine Training Program, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA;3. Department of Biochemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA;4. Department of Computer Sciences, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA;5. Theoretical Chemical Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA;1. Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA;2. Department of Physics, Freie Universität Berlin, Berlin 14195, Germany;3. Interfaculty Institute of Biochemistry, Eberhard Karls University Tübingen, Tübingen 72074, Germany;4. Laboratory of Physical Chemistry, ETH Zürich, Zürich 8093, Switzerland;1. Department of Chemistry, College of Sciences, Shiraz University, Shiraz, 71454, Iran;2. Nanotechnology Research Institute, Shiraz University, Shiraz, Iran;1. Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520, United States;2. Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas, Lawrence, KS 66045, United States;1. Department of Physics, Center for the Physics of Living Cells, Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois |
| |
| Abstract: | Conformational transitions are functionally important in many proteins. In the enzyme adenylate kinase (AK), two small domains (LID and NMP) close over the larger CORE domain; the reverse (opening) motion limits the rate of catalytic turnover. Here, using double-well Gō simulations of Escherichia coli AK, we elaborate on previous investigations of the AK transition mechanism by characterizing the contributions of rigid-body (Cartesian), backbone dihedral, and contact motions to transition-state (TS) properties. In addition, we compare an apo simulation to a pseudo-ligand-bound simulation to reveal insights into allostery. In Cartesian space, LID closure precedes NMP closure in the bound simulation, consistent with prior coarse-grained models of the AK transition. However, NMP-first closure is preferred in the apo simulation. In backbone dihedral space, we find that, as expected, backbone fluctuations are reduced in the O/C transition in parts of all three domains. Among these “quenching” residues, most in the CORE, especially residues 11–13, are rigidified in the TS of the bound simulation, while residues 42–44 in the NMP are flexible in the TS. In contact space, in both apo and bound simulations, one nucleus of closed-state contacts includes parts of the NMP and CORE; CORE–LID contacts are absent in the TS of the apo simulation but formed in the TS of the bound simulation. From these results, we predict mutations that will perturb the opening and/or closing transition rates by changing the entropy of dihedrals and/or the enthalpy of contacts. Furthermore, regarding allostery, the fully closed structure is populated in the apo simulation, but our contact results imply that ligand binding shifts the preferred O/C transition pathway, thus precluding a simple conformational selection mechanism. Finally, the analytical approach and the insights derived from this work may inform the rational design of flexibility and allostery in proteins. |
| |
| Keywords: | |
| 本文献已被 ScienceDirect 等数据库收录！ |
|
