title: Capturing Invisible Motions in the Transition from Ground to Rare Excited States of T4 Lysozyme L99A.
abstract: Proteins commonly sample a number of conformational states to carry out their biological function, often requiring transitions from the ground state to higher-energy states. Characterizing the mechanisms that guide these transitions at the atomic level promises to impact our understanding of functional protein dynamics and energy landscapes. The leucine-99-to-alanine (L99A) mutant of T4 lysozyme is a model system that has an experimentally well characterized excited sparsely populated state as well as a ground state. Despite the exhaustive study of L99A protein dynamics, the conformational changes that permit transitioning to the experimentally detected excited state (∼3%, ΔG ∼2 kcal/mol) remain unclear. Here, we describe the transitions from the ground state to this sparsely populated excited state of L99A as observed through a single molecular dynamics (MD) trajectory on the Anton supercomputer. Aside from detailing the ground-to-excited-state transition, the trajectory samples multiple metastates and an intermediate state en route to the excited state. Dynamic motions between these states enable cavity surface openings large enough to admit benzene on timescales congruent with known rates for benzene binding. Thus, these fluctuations between rare protein states provide an atomic description of the concerted motions that illuminate potential path(s) for ligand binding. These results reveal, to our knowledge, a new level of complexity in the dynamics of buried cavities and their role in creating mobile defects that affect protein dynamics and ligand binding.
authors.affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California.
authors.forename: Jamie M
authors.initials: JM
authors.lastname: Schiffer
authors.affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California; Drug Design Data Resource, University of California, San Diego, La Jolla, California. Electronic address: vfeher@ucsd.edu.
authors.forename: Victoria A
authors.initials: VA
authors.lastname: Feher
authors.affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California; National Biomedical Computation Resource, University of California, San Diego, La Jolla, California.
authors.forename: Robert D
authors.initials: RD
authors.lastname: Malmstrom
authors.affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California; Centro de Enseñanza Técnica y Superior (CETYS) Campus Ensenada, Camino a Microondas Trinidad, Ensenada, Baja Califiornia, Mexico.
authors.forename: Roxana
authors.initials: R
authors.lastname: Sida
authors.affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California; National Biomedical Computation Resource, University of California, San Diego, La Jolla, California; Drug Design Data Resource, University of California, San Diego, La Jolla, California. Electronic address: ramaro@ucsd.edu.
authors.forename: Rommie E
authors.initials: RE
authors.lastname: Amaro
mesh_terms: D019943:Amino Acid Substitution; D017122:Bacteriophage T4 / Q000201:enzymology*; D056004:Molecular Dynamics Simulation; D009068:Movement; D009113:Muramidase / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D009154:Mutation; D011487:Protein Conformation
chemical_list: D009113:Muramidase