Temperature effects on protein motions: A molecular dynamics study of RNase-Sa

R Dvorsky, J Sevcik, L S D Caves, R E Hubbard, C S Verma

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Abstract

The dynamics of the enzyme ribonuclease-Sa as a function of temperature has been explored through a series of molecular dynamics simulations. Long-range expansion and short-range contraction of the structure lends the protein a solidlike core and a liquidlike exterior as the temperature is increased. The trend in magnitudes of fluctuations of atoms are biphasic across the 150-200K region and are increasingly non-Brownian in character as the temperature is increased. The mobility of solvent molecules is much higher than the protein atoms, even though the solvent mobility displays behavior which is dampened relative to behavior in bulk water. The region of the active site that binds the base of the nucleotide ligand shows low plasticity relative to regions that interact with the sugar-phosphate part. This suggests that the enzyme is preorganized dynamically: regions with low plasticity confer specificity while the more flexible regions have the fluidity to facilitate energetically inexpensive conformational rearrangements such as those required to achieve the transition state. Below 200K the dynamics are characterized by low amplitude harmonic motions that involve concerted motions that involve small groups of atoms. Above 200K, the dynamics are dominated by large amplitude anharmonic motions which involve long-range correlations including breathing and twisting modes such as those required for ligand binding/release/activation. The temperature-dependent transition in the character of the dynamics at similar to 200K reflects the ease with which the system hops among barriers giving rise to enhanced diffusion across phase space. This enhanced plasticity is catalyzed by a significant increase in the mobility of solvent water molecules and the associated increase in frequency of different hydrogen bond arrangements and may facilitate the onset of significantly enhanced functionality above the transition temperature.

Original languageEnglish
Pages (from-to)10387-10397
Number of pages11
JournalJournal of Physical Chemistry B
Volume104
Issue number44
DOIs
Publication statusPublished - 9 Nov 2000

Keywords

  • HIV-1 REVERSE-TRANSCRIPTASE
  • NEUTRON-SCATTERING DATA
  • ALPHA-LYTIC PROTEASE
  • COLLECTIVE MOTIONS
  • GLASS-TRANSITION
  • STREPTOMYCES-AUREOFACIENS
  • GLOBULAR-PROTEINS
  • NORMAL-MODE
  • SUPERCOOLED LIQUIDS
  • ATOMIC FLUCTUATIONS

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