2. Background[The elasticity of alpha-helix, pi-helix]

2.1. Biophysics

It is an attempt to understand the essence of life phenomena from the point of view of physical laws or matter by expanding and applying various methods of advanced physics to living things. For example, it is important to interpret how the action of an organism is made in view of the properties of the molecules or atoms that make up it. In order to understand this, the methods of physiology, biochemistry, and biology must be used comprehensively. Some important research achievements in biophysics include physical research on the structure and properties of molecules constituting living organisms, especially high molecular substances such as proteins and nucleic acids. This study was intended to study elasticity among the physical properties according to the structure of proteins.

 

2.2. 분자동력학과 접근 방법(Molecular Dynamics)

Molecular dynamics is a method to investigate the microscopic motion of individual molecules in solid, liquid, or gaseous states in detail. It is a technique to study the dynamic structure or physical properties of molecules by simulating molecular motion using a computer. In this study, the bending-modulus of proteins was studied based on molecular dynamics.

 

2.3. Proteins and physical models

2.3.1. Composition of proteins

It is a polymer organic substance that composes the body of all living things and is a linkage of numerous amino acids. It is important as a constituent of the body of an organism and as a catalyst for various chemical reactions in cells. Proteins are complex molecules made up of relatively simple molecules called amino acids, and generally have a very large molecular weight. There are about 20 kinds of amino acids that make up proteins, and these amino acids are linked to each other through chemical bonds to make a polypeptide. In this case, the combination of amino acids is called a peptide bond, and it is called a polypeptide in the sense that there are several (poly-) of these peptide bonds. In a broad sense, a protein can also be called a polypeptide, and in general, when the molecular weight is relatively small, it is called a polypeptide, and when the molecular weight is very large, it is called a protein.

Amino acids are the basic building blocks of proteins that make up the body of living things. When a protein is completely hydrolyzed, ammonia and amino acids are produced. Amino acids refer to all molecules including an amino group and a carboxyl group. The table constituting the types of amino acids is as follows.

2.3.2. Structure of proteins

alpha-helix

• It has a spiral shape winding upwards counterclockwise.
• Every 3.6 amino acids makes one cycle.
• It maintains its shape by hydrogen bonds formed between each fourth amino acid.
• The phi and psi angles are -57 and -47 degrees, respectively.

 

pi-helix

• It has a spiral shape winding upwards counterclockwise.
• Every 4.1 amino acids makes one cycle.
• There is a hydrogen bond between each fifth amino acid
• The phi and psi angles are -57 degrees and -70 degrees, respectively.

 

3_10 - helix

• It has a spiral shape winding upwards counterclockwise.
• Every three amino acids makes one cycle.
• There is a hydrogen bond between each third amino acid.
• The phi and psi angles are -49 degrees and -26 degrees, respectively.

 

2.4. Program

2.4.1. MD(Molecular Dynamics simulation)

단백질의 구성을 알 수 있는 프로그램으로, 위치에너지(Potential energy)→힘→질량→가속도→위치를 알 수 있다.

 

VMD(Visual Molecular Dynamics)

VMD can be used to identify more general molecules because it can read VMD standard protein data bank (PDB) files and displays designed for the modeling, visualization and analysis of isoprotein, nucleic acid, lipid bilayer assemblies, and biological systems. Contained structure. VMD rendering provides a variety of methods: simple dots and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings and more. VMD can be used to analyze the trajectories of animation and molecular dynamics (MD) simulations. Specifically, the VMD serves as a graphical front-end to external MD programs, displaying and animating molecules running simulations on a remote computer. In this study, after creating a helix using VMD, put it in a water box (Water box) to create a pdb file.

 

NAMD

NAMD has won the Gordon Bell Award in 2002 and the Sydney FERNBACH Award in 2012, and is a design parallel molecular dynamics code for high-performance simulation of large biomolecular systems. Based on parallel objects, NAMD can scale hundreds of cores, with more than 50 cores for typical and largest simulations. It uses the molecular graphics program VMD for NAMD simulation setup and trajectory analysis - and also uses the file compatible AMBER, CHARMm and X-PLOR. In this study, the shape change over time of the helix pdb file created using VMD is obtained using NAMD.

 

2.4.2. Data analysis

MATLAB

As a technical computing language, millions of engineers and scientists around the world use MATLAB to analyze and design systems and products. MATLAB is used in automotive active safety systems, interplanetary spacecraft, health monitoring devices, smart power grids, LTE cellular networks, etc. being used in the field. mainly math. graph. It is in the programming area. The MATLAB platform is optimized for solving engineering and scientific problems. The matrix-based MATLAB language is a way of expressing computational mathematics. Built-in graphics make it easy to visualize data and gain insights. A variety of pre-built toolbox libraries are provided so we can get started right away with the algorithms our domain needs. The desktop environment makes it easy to experiment, explore, and discover. In this study, it is used to obtain the rotation matrix, probability distribution for torsion, and bending-modulus of alpha-helix according to physical modeling.

 

VideoMach

Use to convert video, audio and image files between media formats. VideoMach feature has the following features: Suports video and image formats (MPEG, AVI, DivX, FLC, JPEG, PNG, TIF, GIF, BMP, etc.), Audio format support (MP3, MP2, OGG, WAV, AC3), fast image sequence detection, support more than 50,000 images per second). In this study, it is used to convert the result into an image after executing NAMD.

 

2.4.3. CSCW(컴퓨터 지원 공동 작업, computer support cooperative work)

WinSCP

WinSCP is a graphical SFTP and FTP client program for Windows and is an open source freeware. It also supports the legacy SCP protocol and can be used to copy files between a local computer and a remote computer. In this study, it was used for connection between computers (work station and laptop).

 

PuTTY

PuTTY helps we establish a secure connection to the Internet, and is a Secure Shell (SSH) and telnet client. For programmers and network administrators, it features a simple and easy interface.