European Biophysics Journal

, Volume 24, Issue 1, pp 1–11 | Cite as

Structure and atomic fluctuation patterns of potato carboxypeptidase a inhibitor protein

A molecular dynamics study in water
  • B. Oliva
  • X. Daura
  • E. Querol
  • F. X. Avilés
  • O. Tapia
Article

Abstract

Molecular dynamics (MD) simulation methods were applied to the study of the structural and dynamic fluctuation properties of the potato carboxypeptidase A inhibitor protein (PCI) immersed in a bath of 1259 water molecules. A trajectory of 200 ps was generated at constant temperature and pressure. The crystallographic structure of PCI, as found in its complex with bovine carboxy-peptidase A (CPA), was used to seed the MD simulation. Analyses show that the structure of the PCI core is fairly rigid and stable in itself, and that little deformation is caused by the protein-protein interactions found in the PCI-CPA complex. The N-terminal tail fluctuates to approach the core structure and appears as a relatively disordered region. In contrast, the conformations of the C-terminal tail, which is involved in the inhibitory mechanism, fluctuates in the neighborhood of the X-ray structure in orientations which facilitate CPA binding. Comparison with the structural entries for PCI in water obtained from both 2D-NMR experiments and X-ray data shows that important features of the MD structural results fluctuates between the initial crystal values and those obtained from the NMR solution structure. This fluctuation is not uniform; minor regions move away from the X-ray conformation while they do not approach the NMR conformation. The results reported suggest that the trajectory is long enough to show a behavior that is consistent with the conformational space available to the protein in solution.

Key words

Carboxypeptidase inhibitor Molecular dynamics Computer simulation NMR/X-Ray comparison Solvent effects 

Abbreviations

CPA

Carboxypeptidase

DG

Distance Geometry

NMR

Nuclear Magnetic Resonance

NIS

Non Inertial Solvent

MD

Molecular Dynamics

PBC

Periodic Boundary Conditions

PCI

Potato Carboxypeptidase Inhibitor

RMSD

Root Mean Square Deviation

a.m.u.

Atomic mass units

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Copyright information

© Springer-Verlag 1995

Authors and Affiliations

  • B. Oliva
    • 1
  • X. Daura
    • 1
  • E. Querol
    • 1
  • F. X. Avilés
    • 1
  • O. Tapia
    • 2
  1. 1.Institut de Biologia Fonamental i Deparament de BioquímicaUniversitat Autònoma de BarcelonaBellaterra (Barcelona)Spain
  2. 2.Department of Physical ChemistryUniversity of UppsalaUppsalaSweden

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