Abstract
A macroscopic description of a protein structure allows an understanding of the protein conformations in a more simplistic manner. Here, a new macroscopic approach that utilizes the joints of the protein secondary structures as a basic descriptor for the protein structure is proposed and applied to study the arrangement of secondary structures in helical membrane proteins. Two types of dihedral angle, Ω and λ, were defined based on the joint points of the transmembrane (TM) helices and loops, and employed to analyze 103 non-homologous membrane proteins with 3 to 14 TM helices. The Ω-λ plot, which is a distribution plot of the dihedral angles of the joint points, identified the allowed and disallowed regions of helical arrangement. Analyses of consecutive dihedral angle patterns indicated that there are preferred patterns in the helical alignment and extension of TM proteins, and helical extension pattern in TM proteins is varied as the size of TM proteins increases. Finally, we could identify some symmetric protein pairs in TM proteins under the joint-based coordinate and 3-dimensional coordinates. The joint-based approach is expected to help better understand and model the overall conformational features of complicated large-scale proteins, such as membrane proteins.
Highlights
Protein structures are strongly related to their physical properties, such as folding, stability, and function
The conformation of TM helices of the membrane proteins can be represented by a set of two types of dihedral angles (Ω1, λ1, Ω2, λ2, Ω3 ...) composed of a set of joints (P1, P2, P3, P4 ...) at the macroscopic level
The primary feature of the approach is to use a joint of secondary structures as the basic element for a description of the protein structure, whereas most developed protein structure description methods utilize physical entities, such as atoms, amino acids, and secondary structures
Summary
Protein structures are strongly related to their physical properties, such as folding, stability, and function. Many studies have examined protein structures with an all atom-based description[1, 2]. The Ramachandran’s plot[1] with the backbone dihedral angle φ (N-Cα) and ψ (Cα-C) is a representative way of microscopic descriptions of the protein structure. Our new strategy is to use the joints of secondary structures as the basic constituents for a description of the protein structure and to study the protein conformational features by examining the 3-dimensional arrangement of the joints with their dihedral angles (Fig. 1b). The macroscopic description method is applied to study the conformational features of the membrane proteins. The conformation of the TM helices was investigated by the new description method using the structural joints at the macroscopic level. Some common and interesting features of membrane proteins reflecting the conformational heterogeneity and specificity are suggested based on an analysis of the conformations of non-homologous membrane proteins with the dihedral angles of the joints
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