Universal geometrical factor of protein conformations as a consequence of energy minimization

Abstract

The biological activity and functional specificity of proteins depend on their native three-dimensional structures determined by inter-and intra-molecular interactions. In this paper, we investigate the geometrical factor of protein conformation as a consequence of energy minimization in protein folding. Folding simulations of 10 polypeptides with chain length ranging from 183 to 548 residues manifest that the dimensionless ratio (V /A r ) of the van der Waals volume V to the surface area A and average atomic radius r of the folded structures, calculated with atomic radii setting used in SMMP [Eisenmenger F., et. al., Comput. Phys. Commun., 138 (2001) 192], approach 0.49 quickly during the course of energy minimization. A large scale analysis of protein structures show that the ratio for real and well-designed proteins is universal and equal to 0.491 ± 0.005. The fractional composition of hydrophobic and hydrophilic residues does not affect the ratio substantially. The ratio also holds for intrinsically disordered proteins, while it ceases to be universal for polypeptides with bad folding properties.

Physical mechanism for biopolymers to aggregate and maintain in non-equilibrium states

“…The geometric packing, with the assistance of hydrogen-bonding, therefore, plays an important role in the process. Since the efficient stacking of individual protein molecule is essentially guided by the backbone-connectivity 36 , 37 , the focus on the latter property and on the combined effects with external confinement may provide the most relevant factors for the processes shared by a wide range of different peptides. Such issues can always be addressed efficiently by studying simplified models 38 – 40 .…”

Universality and scaling in human and social systems

“…It is of interest to know whether the concepts and methods from critical physical systems can be useful for understanding complicated biological and human-social systems. In previous papers [35][36][37][38][39][40][41][42][43], we had pointed out that the ideas and methods of statistical physics can be useful for understanding some interesting biological problems. In this paper, I would like to point out that such methods and concepts can also be useful for understanding some interesting human and social systems.…”

Eigen Model with Correlated Multiple Mutations and Solution of Error Catastrophe Paradox in the Origin of Life

“…In recent decades, ideas and methods of physics have been widely used to study biological problems at the molecular level, e.g., the structure and folding of proteins, [1][2][3][4] structure and thermal properties of DNA and RNA, [5][6][7][8] molecular models of biological evolution and the origin of life, [9][10][11][12][13][14][15][16][17][18][19][20][21] etc. In this paper, we will address an interesting problem related to the origin of life.…”