title: Strain analysis of protein structures and low dimensionality of mechanical allosteric couplings.
abstract: In many proteins, especially allosteric proteins that communicate regulatory states from allosteric to active sites, structural deformations are functionally important. To understand these deformations, dynamical experiments are ideal but challenging. Using static structural information, although more limited than dynamical analysis, is much more accessible. Underused for protein analysis, strain is the natural quantity for studying local deformations. We calculate strain tensor fields for proteins deformed by ligands or thermal fluctuations using crystal and NMR structure ensembles. Strains-primarily shears-show deformations around binding sites. These deformations can be induced solely by ligand binding at distant allosteric sites. Shears reveal quasi-2D paths of mechanical coupling between allosteric and active sites that may constitute a widespread mechanism of allostery. We argue that strain-particularly shear-is the most appropriate quantity for analysis of local protein deformations. This analysis can reveal mechanical and biological properties of many proteins.
authors.affiliation: Laboratory of Living Matter, The Rockefeller University, New York, NY 10065; Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10065; mich.r.mitchell@gmail.com tsvitlusty@gmail.com livingmatter@rockefeller.edu.
authors.forename: Michael R
authors.identifier: 0000-0003-2127-4820
authors.initials: MR
authors.lastname: Mitchell
authors.affiliation: The Simons Center for Systems Biology, School of Natural Sciences, Institute for Advanced Study, Princeton, NJ 08540; Center for Soft and Living Matter, Institute for Basic Science, Ulsan 689-798, South Korea; Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 689-798, South Korea mich.r.mitchell@gmail.com tsvitlusty@gmail.com livingmatter@rockefeller.edu.
authors.forename: Tsvi
authors.initials: T
authors.lastname: Tlusty
authors.affiliation: Laboratory of Living Matter, The Rockefeller University, New York, NY 10065; Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10065; The Simons Center for Systems Biology, School of Natural Sciences, Institute for Advanced Study, Princeton, NJ 08540; mich.r.mitchell@gmail.com tsvitlusty@gmail.com livingmatter@rockefeller.edu.
authors.forename: Stanislas
authors.initials: S
authors.lastname: Leibler
mesh_terms: D000494:Allosteric Regulation; D000495:Allosteric Site; D020134:Catalytic Domain; D004926:Escherichia coli / Q000201:enzymology; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D009169:Mycobacterium tuberculosis / Q000201:enzymology; D010455:Peptides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*
chemical_list: D008024:Ligands; D010455:Peptides; D011506:Proteins
keywords: elasticity; protein allostery; protein mechanics; strain