Packing interface energetics in different crystal forms of the λ Cro dimer

Authors

  • Logan S. Ahlstrom,

    1. Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona
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  • Osamu Miyashita

    Corresponding author
    1. Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona
    2. RIKEN Advanced Institute for Computational Science, Minatojima-minami-machi, Chuo-ku, Japan
    • Correspondence to: Osamu Miyashita, RIKEN Advanced Institute for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan. E-mail: osamu.miyashita@riken.jp

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  • Logan S. Ahlstrom's current address is Department of Chemistry, The University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109.

ABSTRACT

Variation among crystal structures of the λ Cro dimer highlights conformational flexibility. The structures range from a wild type closed to a mutant fully open conformation, but it is unclear if each represents a stable solution state or if one may be the result of crystal packing. Here we use molecular dynamics (MD) simulation to investigate the energetics of crystal packing interfaces and the influence of site-directed mutagenesis on them in order to examine the effect of crystal packing on wild type and mutant Cro dimer conformation. Replica exchange MD of mutant Cro in solution shows that the observed conformational differences between the wild type and mutant protein are not the direct consequence of mutation. Instead, simulation of Cro in different crystal environments reveals that mutation affects the stability of crystal forms. Molecular Mechanics Poisson-Boltzmann Surface Area binding energy calculations reveal the detailed energetics of packing interfaces. Packing interfaces can have diverse properties in strength, energetic components, and some are stronger than the biological dimer interface. Further analysis shows that mutation can strengthen packing interfaces by as much as ∼5 kcal/mol in either crystal environment. Thus, in the case of Cro, mutation provides an additional energetic contribution during crystal formation that may stabilize a fully open higher energy state. Moreover, the effect of mutation in the lattice can extend to packing interfaces not involving mutation sites. Our results provide insight into possible models for the effect of crystallization on Cro conformational dynamics and emphasize careful consideration of protein crystal structures. Proteins 2014; 82:1128–1141. © 2013 Wiley Periodicals, Inc.

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