signal propagation in proteins and relation to equilibrium fluctuations在蛋白质和信号传播关系平衡的波动.pdfVIP

Signal Propagation in Proteins and Relation to Equilibrium Fluctuations * Chakra Chennubhotla, Ivet Bahar Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America Elastic network (EN) models have been widely used in recent years for describing protein dynamics, based on the premise that the motions naturally accessible to native structures are relevant to biological function. We posit that equilibrium motions also determine communication mechanisms inherent to the network architecture. To this end, we explore the stochastics of a discrete-time, discrete-state Markov process of information transfer across the network of residues. We measure the communication abilities of residue pairs in terms of hit and commute times, i.e., the number of steps it takes on an average to send and receive signals. Functionally active residues are found to possess enhanced communication propensities, evidenced by their short hit times. Furthermore, secondary structural elements emerge as efficient mediators of communication. The present findings provide us with insights on the topological basis of communication in proteins and design principles for efficient signal transduction. While hit/commute times are information-theoretic concepts, a central contribution of this work is to rigorously show that they have physical origins directly relevant to the equilibrium fluctuations of residues predicted by EN models. Citation: Chennubhotla C, Bahar I (2007) Signal propagation in proteins and relation to equilibrium fluctuations. PLoS Comput Biol 3(9): e172. doi:10.1371/journal.pcbi. 0030172 the Kirchhoff matrix of inter-residue contacts that underlie Introduction