Proteinin içsel normal modları ve farklı protein konformasyonları arasındaki ilişki

Proteins are indispensible components of cellular functions. Although proteinstructure is determined as a static picture for most of the proteins, the dynamics or thetime-dependent behavior of proteins act as main contributors to protein function. Inaddition to ligand induced structural motions proteins also bear intrinsic motions arisingfrom thermal energy they contain. These ligand-independent motions possess functionalimportance according to experimental evidences for a large number of proteins and alink between these motions and functional motions are established both in terms ofstructure and timescale. These intrinsic fluctuations are revealed by low-frequencyindividual modes of proteins which are determined using a simplified version of normalmode analysis termed as Anisotropic Network Model (ANM). In this study, we applymodal analysis to eleven proteins including enzymes, antibodies and signal proteins.We investigate a kinetic relation between modal analysis and protein motions. For thispurpose we employ eigenvalues of Hessian matrix which carry information about thevibrational frequencies of these modes. In ANM studies these eigenvalues are used todetermine the low and high frequency modes of protein. Our findings imply acorrespondence between eigenvalues and kinetic/thermodynamic properties of proteinmotions. These intrinsic motions establish a dynamic equilibrium between distinctconformers of the protein and as we have proposed eigenvalues of Hessian matrixcorrelate well both with the timescales of these motions and thermodynamics of thesemotions.