ACCESSIBILITY TO INTERNAL CAVITIES AND LIGAND-BINDING SITES MONITOREDBY PROTEIN CRYSTALLOGRAPHIC THERMAL FACTORS

Protein structures are flexible both in solution and in the solid stat e. X-ray crystallographically determined thermal factors monitor the f lexibility of protein atoms. A method utilizing such factors is propos ed to delineate protein regions through which a ligand can exchange be tween binding site and bulk solvent. It is based on the assumption tha t thermally excited protein regions are excellent candidates for openi ng a ligand channel. Computationally simple and inexpensive, the metho d analyzes directions from which thermal factors can propagate within the protein, resulting in thermal motion paths (TMPs). Applications to engineered T4 lysozymes, where an artificial internal cavity can host hydrophobic molecules, and to sperm whale myoglobins, where the activ e site is completely buried, yielded results in agreement with other i ndependent structural observations and with previous hypotheses. Furth er new features could also be suggested. The proposed TMP analysis cou ld aid molecular dynamics simulation studies as well as time-resolved and site-directed mutagenesis experimental studies, especially given i ts modest computational expense and its direct roots in experimental r esults based on thermal factors determined in high-resolution crystall ographic studies. (C) 1998 Wiley-Liss, Inc.