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Water penetration and escape in proteins
1Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, New Mexico 87545, USA. angel@+10.lanl.gov
Proteins
|March 14, 2000
Summary
Molecular dynamics simulations reveal how water molecules penetrate and escape the protein cytochrome c (cyt c). Some internal water molecules exhibit restricted motion, while others diffuse, indicating varied binding sites and energy barriers for water exchange.
Area of Science:
- Biophysics
- Computational Biology
- Protein Dynamics
Background:
- Cytochrome c (cyt c) is a crucial protein involved in electron transport.
- Understanding water dynamics within proteins is essential for elucidating their function.
- Previous studies have explored protein hydration, but detailed kinetic analysis of internal water is limited.
Purpose of the Study:
- To investigate the kinetics of water penetration and escape within cytochrome c.
- To characterize the behavior and residence times of internal water molecules.
- To determine the energy landscape governing water exchange in cyt c.
Main Methods:
- Molecular dynamics (MD) simulations were performed at various temperatures (300 K, 360 K, 430 K).
- Water molecule entry and exit were tracked by monitoring coordination numbers.
- Mean square displacements (MSD) and survival time correlation functions were analyzed.
Main Results:
- Over 200 water penetration events were observed at 300 K, with some molecules residing inside for extended periods (up to 500 ps).
- Internal water molecules exhibited diverse behaviors, from structural water-like MSD to diffusion in transient cavities.
- Analysis revealed a broad distribution of energy barriers for water escape, suggesting complex interactions.
Conclusions:
- The entropy of interior water molecules in cyt c is comparable to bulk water.
- Water exchange kinetics are governed by a distribution of activation energy barriers.
- MD simulations provide valuable insights into the dynamic hydration of proteins.