Functional and structural characterization of a protein based on analysis of its hydrogen bonding network by hydrogen bonding plot

Knowledge of the relationship between protein's structure and its dynamic behavior is essential for understanding protein function. In this study, the description of a protein three-dimensional structure as a network of hydrogen bonding interactions (HB plot) is introduced as a tool for exploring protein structure and function. HB plot offers a simple way of analyzing protein secondary and tertiary structure. Moreover, hydrogen bonds stabilizing secondary structural elements and those formed between distant amino residues-defined as tertiary hydrogen bonds-can be easily distinguished in HB plot, thus, amino acid residues involved in stabilizing protein structure and function can be easily identified. By analyzing the network of tertiary interactions the possible spread of information within a protein can be investigated as well. The alteration in tertiary hydrogen bonding network during conformational transitions were investigated through case studies; and showed the applicability of HB plot in exploring mechanistic details in proteins. (C) 2007 Elsevier Inc. All rights reserved.