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6403_chap01 - B-598 ch01 FA Chapter 1 Introduction Proteins...

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Chapter 1 Introduction Proteins are an important class of biomolecules. They are encoded in genes and expressed in cells via genetic translation. Proteins are life-supporting (or sometimes, destructive) ingredients and are indis- pensable for almost all biological processes. In order to understand the diverse biological functions of proteins, knowledge of the three- dimensional (3D) structures of proteins and their dynamic behav- iors is essential. Unfortunately, these properties are difficult to be determined either experimentally or theoretically. The goal of com- putational structural biology is to provide an alternative, or some- times, complementary, approach to protein structures and dynamics by using computer modeling and simulation. 1.1. Protein Structure A protein consists of a sequence of amino acids, typically several hun- dreds in length. There are 20 different amino acids. Therefore, mil- lions of different proteins can be formed with different amino acid sequences and often different functions. In the human body alone, there are at least several hundreds of thousands of different proteins, with functions ranging from transporting chemicals to passing elec- trical signals, from activating cellular processes to preventing foreign 1
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2 Computational Structural Biology intrusion, and from forming all kinds of molecular complexes to sup- porting various physical structures of life. 1.1.1. DNA, RNA, and protein Not all sequences of amino acids are biologically meaningful. Those used in proteins are selected or decided by the biological systems. They are encoded as genes in the DNA sequences and expressed in the cells at certain times and places. A typical gene expression process occurs as follows: a gene, as a DNA sequence, that encodes a protein is first transcribed into a corresponding RNA sequence; the RNA sequence is then translated into an amino acid sequence required by the protein (Fig. 1.1). A DNA sequence is made of two complementary chains of four different deoxyribonucleic acids — known as adenine (A), cytosine (C), guanine (G), and thymine (T) — with A in one of the chains pairing with T in another, and C pairing with G. The two chains wrap around each other and form a so-called double helix. During the transcription process, the double helix unwinds, and one of the strands is used as a template to make a single chain of RNA, which consists of four ribonucleic acids — A, C, G, and U (uracil) — that correspond to the deoxyribonucleic acids — A, C, G, and T, respectively — in the DNA templates. In this sense, the RNA sequence is equivalent to the DNA sequence; it is only transcribed in a different form. The RNA DNA RNA Protein GAA GTT GAA AAT CAG GCG AAC CCA CGA CTG GAA GUU GAA AAU CAG GCG AAC CCA CGA CUG GLU GAL GLU ASN GLN ALA ASN PRO ARG LEU Fig. 1.1. Central dogma of molecular biology. A DNA sequence is transcribed into an RNA sequence, and an RNA sequence is translated into an amino acid sequence, which forms a polypeptide chain and folds into a protein.
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Introduction 3 Gly Gly Gly Gly Asp Asp Glu Glu Ala
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