Protein-water interactions in ribonuclease A and angiogenin: A molecular dynamics study

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2004-06, Vol.55 (4), p.915-923
• Main Authors: Sanjeev, B. S., Vishveshwara, S.
• Format: Article
• Language: English
• Subjects: Binding Sites; Computer Simulation; Hydrogen Bonding; invariant waters; maximum residence time; Models, Molecular; protein-water networks; Ribonuclease, Pancreatic - chemistry; Ribonuclease, Pancreatic - metabolism; Water - chemistry
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.20114

It is known that water molecules play an important role in the biological functioning of proteins. The members of the ribonuclease A (RNase A) family of proteins, which are sequentially and structurally similar, are known to carry out the obligatory function of cleaving RNA and individually perform other diverse biological functions. Our focus is on elucidating whether the sequence and structural similarity lead to common hydration patterns, what the common hydration sites are and what the differences are. Extensive molecular dynamics simulations followed by a detailed analysis of protein–water interactions have been carried out on two members of the ribonuclease A superfamily—RNase A and angiogenin. The water residence times are analyzed and their relationship with the characteristic properties of the protein polar atoms, such as their accessible surface area and mean hydration, is studied. The capacity of the polar atoms to form hydrogen bonds with water molecules and participate in protein–water networks are investigated. The locations of such networks are identified for both proteins. Proteins 2004. © 2004 Wiley‐Liss, Inc.