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IPRS, Inc.
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Protein Structures and Functions Introduction to Protein Structures and Function Proteins are organic compounds comprised of an assortment of amino acids linked together by the interaction of a carboxyl group and an amine group. The sequence of the amino acids determines the properties of the protein. The functions of proteins a very broad ranging from providing transport vehicles across barriers and through systems and across cell membranes (as channel proteins forming pores in lipophilic membranes, serving structural components (as the endoplasmic reticulum where RNA is read as proteins are synthesized), providing mechanical forces (as in muscle proteins) and providing highly specific catalysis of most biochemical reactions (as all the enzymes). It has been shown that the functionality of a protein is determined in part by its primary sequence (the number of type of amino acids) and in part by the secondary structure such as in a filament or global form (specifically alpha or beta helixes, sheet forms, loops, etc.) and in part by tertiary (3-dimensional form) and quaternary structures (solvent and other interactions). Examples of different levels of structures are provided below.
Primary & Secondary Structure/characterization of a Calcium-associated protein Chain 1CFD: Calmodulin Molecular Weight 16690 Number of Residues 148 Sequence and secondary structure 1 ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD HHHHH HHHHHHHTTT TTSSSEEEHH HHTHHHHHTT HHHHHH 51 MINEVDADGN GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI HHHHHTTSSS EEEHHHHHH HHHHHSSTT SHHHHHHHHH HHTTTSSSEE 101 SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK EHHHHHHHHH HTT HHH HHHHHHHTT STTSEEESHH HHHHHH Proteins - The DSSP Code http://www.wordiq.com/definition/Secondary_structure The DSSP code is frequently used to describe the protein secondary structures with a single letter code. DSSP is an acronym for "Dictionary of Protein Secondary Structure", which was the title of the original article actually listing the secondary structure of the proteins with known 3D structure (Kabsch and Sander 1983). The secondary structure is assigned based on hydrogen bonding patterns as those initially proposed by Pauling et al. in 1951 (before any protein structure had ever been experimentally determined).
In DSSP residues which are not in any of the above conformations is designated as ' ' (space), which sometimes gets designated with C (coil) or L (loop). The helices (G,H and I) and sheet conformations are all required to have a reasonable length. This means that 2 adjacent residues in the primary structure must form the same hydrogen bonding pattern. If the helix or sheet hydrogen bonding pattern is too short they are designated as T or B, respectively. Other protein secondary structure assignment categories exist (sharp turns, Omega loops etc.), but they are less frequently used. Tertiary Structure:
Functions
Enzymatic Roles
Transcription, Synthesis, A-A, Regulation thereof - RNA, tRNA, iRNA, miRNA etc. Many of the proteins and enzymes indicated are involved in or require the presence of Magnesium, Calcium or other electrolytes. -------------------------------------------------
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Basic Research
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