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Folding of proteins in presculpted free energy landscape

In this study, we investigate the role of amino a id sequen es in the folding of proteins. We onsider two models that are di ered by sequen espe i ity: the tube HP model with hydrophobi (H) and polar (P) sequen es, and the tube Go model with native- entri onta t potentials | Communi ations in Physi s, Vol. 23, No. 4 (2013), pp. 313-319 FOLDING OF PROTEINS IN PRESCULPTED FREE ENERGY LANDSCAPE NGUYEN BA HUNG Vietnam Military Medi al University, 104 Phung Hung, Ha Dong, Hanoi, Vietnam TRINH XUAN HOANG Center for Computational Physi s, Institute of Physi s, Vietnam A ademy of S ien e and Te hnology, 10 Dao Tan, Ba Dinh, Hanoi, Vietnam E-mail: hoang iop.vast.a .vn Re eived 30 June 2013 A epted for publi ation 30 August 2013 Re ent studies of the tube model of protein have indi ated that the free energy lands ape of proteins is pres ulpted by symmetry of the protein ba kbone and geometri al onstraints played by the hydrogen bonds. In this study, we investigate the role of amino a id sequen es in the folding of proteins. We onsider two models that are di ered by sequen e spe i ity: the tube HP model with hydrophobi (H) and polar (P) sequen es, and the tube Go model with native- entri onta t potentials. Monte Carlo simulations are arried out for two sequen es of length of 48 amino a ids, whose ground states are a three-helix bundle and a GB1-like stru ture. The results show that folding in the Go model is more ooperative than in the HP model. In the HP model the ollapse transition and the folding transition are separated, whereas in the Go model the two transitions oin ide. Abstra t. I. INTRODUCTION Proteins are biomole ules omposed by one or more hains of amino a ids. There are nearly 100,000 di erent types of proteins in the human body. Proteins are engaged in every pro ess on whi h our lives depend. They perform a vast array of fun tions in luding atalyzing metaboli rea tions, repli ating DNA, transporting mole ules from one lo ation to another, and parti ipation in our immune system. Proteins intera t with many types of mole ules, in luding other proteins, to arry out their biologi al fun tions. Ex ept for a lass of intrinsi ally disordered proteins, biologi al a tivity is found only when protein is found in a folded