Literature DB >> 15051877

Biomolecular cryocrystallography: structural changes during flash-cooling.

Bertil Halle1.   

Abstract

To minimize radiation damage, crystal structures of biological macromolecules are usually determined after rapid cooling to cryogenic temperatures, some 150-200 K below the normal physiological range. The biological relevance of such structures relies on the assumption that flash-cooling is sufficiently fast to kinetically trap the macromolecule and associated solvent in a room-temperature equilibrium state. To test this assumption, we use a two-state model to calculate the structural changes expected during rapid cooling of a typical protein crystal. The analysis indicates that many degrees of freedom in a flash-cooled protein crystal are quenched at temperatures near 200 K, where local conformational and association equilibria may be strongly shifted toward low-enthalpy states. Such cryoartifacts should be most important for strongly solvent-coupled processes, such as hydration of nonpolar cavities and surface regions, conformational switching of solvent-exposed side chains, and weak ligand binding. The dynamic quenching that emerges from the model considered here can also rationalize the glass transition associated with the atomic fluctuations in the protein.

Entities:  

Mesh:

Year:  2004        PMID: 15051877      PMCID: PMC387327          DOI: 10.1073/pnas.0308315101

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  41 in total

Review 1.  Observation of unstable species in enzyme-catalyzed transformations using protein crystallography.

Authors:  G A Petsko; D Ringe
Journal:  Curr Opin Chem Biol       Date:  2000-02       Impact factor: 8.822

2.  Sequence-specific binding of counterions to B-DNA.

Authors:  V P Denisov; B Halle
Journal:  Proc Natl Acad Sci U S A       Date:  2000-01-18       Impact factor: 11.205

Review 3.  DNA-cation interactions: The major and minor grooves are flexible ionophores.

Authors:  N V Hud; M Polak
Journal:  Curr Opin Struct Biol       Date:  2001-06       Impact factor: 6.809

4.  Slaving: solvent fluctuations dominate protein dynamics and functions.

Authors:  P W Fenimore; H Frauenfelder; B H McMahon; F G Parak
Journal:  Proc Natl Acad Sci U S A       Date:  2002-11-20       Impact factor: 11.205

5.  The influence of temperature on lysozyme crystals. Structure and dynamics of protein and water.

Authors:  I V Kurinov; R W Harrison
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1995-01-01

Review 6.  Cold denaturation of proteins.

Authors:  P L Privalov
Journal:  Crit Rev Biochem Mol Biol       Date:  1990       Impact factor: 8.250

Review 7.  The 'glass transition' in protein dynamics: what it is, why it occurs, and how to exploit it.

Authors:  Dagmar Ringe; Gregory A Petsko
Journal:  Biophys Chem       Date:  2003-09       Impact factor: 2.352

8.  Solvent content of protein crystals.

Authors:  B W Matthews
Journal:  J Mol Biol       Date:  1968-04-28       Impact factor: 5.469

9.  On the interpretation of data from isothermal processes.

Authors:  R Lumry
Journal:  Methods Enzymol       Date:  1995       Impact factor: 1.600

10.  Dynamics of protein and peptide hydration.

Authors:  Kristofer Modig; Edvards Liepinsh; Gottfried Otting; Bertil Halle
Journal:  J Am Chem Soc       Date:  2004-01-14       Impact factor: 15.419

View more
  90 in total

Review 1.  Protein hydration dynamics in solution: a critical survey.

Authors:  Bertil Halle
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2004-08-29       Impact factor: 6.237

2.  Neutron frequency windows and the protein dynamical transition.

Authors:  Torsten Becker; Jennifer A Hayward; John L Finney; Roy M Daniel; Jeremy C Smith
Journal:  Biophys J       Date:  2004-09       Impact factor: 4.033

3.  Atomic-resolution structures of horse liver alcohol dehydrogenase with NAD(+) and fluoroalcohols define strained Michaelis complexes.

Authors:  Bryce V Plapp; S Ramaswamy
Journal:  Biochemistry       Date:  2012-05-01       Impact factor: 3.162

4.  Hyperquenching for protein cryocrystallography.

Authors:  Matthew Warkentin; Viatcheslav Berejnov; Naji S Husseini; Robert E Thorne
Journal:  J Appl Crystallogr       Date:  2006-12-01       Impact factor: 3.304

5.  Acoustic vibrations contribute to the diffuse scatter produced by ribosome crystals.

Authors:  Yury S Polikanov; Peter B Moore
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2015-09-26

6.  Relaxation kinetics and the glassiness of native proteins: coupling of timescales.

Authors:  Canan Baysal; Ali Rana Atilgan
Journal:  Biophys J       Date:  2004-12-13       Impact factor: 4.033

7.  Membrane protein dynamics and detergent interactions within a crystal: a simulation study of OmpA.

Authors:  Peter J Bond; José D Faraldo-Gómez; Sundeep S Deol; Mark S P Sansom
Journal:  Proc Natl Acad Sci U S A       Date:  2006-06-09       Impact factor: 11.205

8.  CIRSE: a solvation energy estimator compatible with flexible protein docking and design applications.

Authors:  David S Cerutti; Tushar Jain; J Andrew McCammon
Journal:  Protein Sci       Date:  2006-07       Impact factor: 6.725

9.  Salt bridges: geometrically specific, designable interactions.

Authors:  Jason E Donald; Daniel W Kulp; William F DeGrado
Journal:  Proteins       Date:  2011-01-05

10.  Simulations of a protein crystal: explicit treatment of crystallization conditions links theory and experiment in the streptavidin-biotin complex.

Authors:  David S Cerutti; Isolde Le Trong; Ronald E Stenkamp; Terry P Lybrand
Journal:  Biochemistry       Date:  2008-10-25       Impact factor: 3.162

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.