Computer Assisted Modeling Contributions of Computational Approaches to Elucidating Macromolecular Structure and Function (1987) / Chapter Skim
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3 Primary Structure of Proteins and Nucleic Acids
3 Primary Structure of Proteins and Nucleic Acids
Pages 23-31
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From page 23... ...
Foremost among these is that the number of different types of protein is finite. It is becoming increasingly clear that most of the proteins determined thus far belong to identifiable families that are easily recognized by amino acid sequences alone.
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From page 24... ...
~ ~. Thus, the recently determined sequences V~ ~1~; L~-aurenerglC receptor, which binds adrenaline and its derivatives, were found to be similar to that of rhodopsin, the eye pigment protein that responds to stimulation by light.
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From page 25... ...
In this regard, a detailed crystallographic study of a series of serine proteases led to the conclusion that recognizably similar three-dimensional structures may endure as much as 10 times longer than do distinguishably similar amino acid sequences, a natural consequence of the diverse ways in which amino acids may be arranged to yield equivalent structures (James et al., 1978~. As a result, it is reasonable to assume that similar amino acid sequences give rise to similar three-dimensional structures.
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From page 26... ...
Existing Data Bases ~ _, -At The major data bases for sequences are the Protein Identification Resource (PIR) at the National Biomedical Research Foundation, Washington, D.C.; GenBank, operated by Bolt, Beranek, and Newman in Cambridge, Massachusetts; and EMBI' Data Bank in Heidelberg, Germany (Table ~2~.
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From page 27... ...
and EMBE exchange data frequently as a way to enhance the data sets. Currently, these two data bases together contain more than 15 million bases of nucleic acid sequences.
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From page 28... ...
The logistic and policy problems associated with such data bases are enormous and many committees and societies are trying to establish an acceptable policy that will speed things up. At the same time, all indications are that the generation of sequence data will increase exponentially in the next few years.
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From page 29... ...
This view of primary amino acid sequences derives from our belief in a hierarchy of structural descriptions of proteins (see Figure 2-1~. If the only structural information we have about a protein is its sequence or primary structure, we seek patterns in its sequence that will guide us to a better understanding of the protein.
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From page 30... ...
Labelings can be assigned to individual amino acid residues or to groups of residues based on calculations over a partial sequence. Typical properties included are: charges: plus, minus or neutral pK: acidic, basic, neutral; or specific value hydropathicity: a hydrophobicity or hydrophilicity value for one residue or calculated over a set of residues chemical similarity: several possible definitions tendency for replacement over evolutionary time secondary structure calculated over a group of residues (see below)
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From page 31... ...
Third, many of the techniques used to infer higher order structural information in patterns, such as secondary structural analysis and the heuristic techniques described below, are highly empirical. These methods often have a theoretical foundation or justification, but the actual inferences may be based on statistics over data bases of known structures or on judgmental rules based on experience and analysis of patterns in known systems.
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