Protein amino acid sequences

By deletion of the N-terminal part of the SslA protein sequence (amino acids 1-341), SSIA341.1097 N is created. Similarly, by deletion of the C-terminal part (amino acids 925-1097), SSIA32-925 C was constructed. Finally a construct having both N- and C-terminals truncated (amino acids 1-341 and 925—1097) named SSIA341.925 CN was designed. 

As shown in Figure 45.1, the bases appear in complementary pairs, A with T and G with C in this particular example, the sequence for one strand of DNA is A-T-C-G-T- while the other strand is -T-A-G-C-A-. The sequences of the bases attached to the sugar-phosphate backbone direct the production of proteins from amino acids. Along each strand, groups of three bases, called codons, correspond to individual amino acids. For example, in Figure 45.1, the triplet CGT, acting as a codon, would correspond to the amino acid serine. One codon, TAG, indicates where synthesis should begin in the DNA strand, and other codons, such as ATT, indicate where synthesis should stop. 

Enzymes are excellent catalysts for two reasons great specificity and high turnover rates. With but few exceptions, all reac tions in biological systems are catalyzed by enzymes, and each enzyme usually catalyzes only one reaction. For most of the important enzymes and other proteins, the amino-acid sequences and three-dimensional structures have been determined. When the molecular struc ture of an enzyme is known, a precise molecular weight could be used to state concentration in molar units. However, the amount is usually expressed in terms of catalytic activity because some of the enzyme may be denatured or otherwise inactive. An international unit (lU) of an enzyme is defined as the amount capable of producing one micromole of its reaction product in one minute under its optimal (or some defined) reaction conditions. Specific activity, the activity per unit mass, is an index of enzyme purity. 

Sickle-cell anemia is the classic example of an inherited disease that is caused by a change in a protein s amino acid sequence. Linus Pauling proposed in 1949 that it was caused by a defect in the hemoglobin molecule he thus coined the term molecular disease. Seven years later Vernon Ingram showed that the disease was caused by a single mutation, a change in residue 6 of the P chain of hemoglobin from Glu to Val. 

The World Wide Web has transformed the way in which we obtain and analyze published information on proteins. What only a few years ago would take days or weeks and require the use of expensive computer workstations can now be achieved in a few minutes or hours using personal computers, both PCs and Macintosh, connected to the internet. The Web contains hundreds of sites of Interest to molecular biologists, many of which are listed in Pedro s BioMolecular Research Tools (http // www.fmi.ch/biology/research tools.html). Many sites provide free access to databases that make it very easy to obtain information on structurally related proteins, the amino acid sequences of homologous proteins, relevant literature references, medical information and metabolic pathways. This development has opened up new opportunities for even non-specialists to view and manipulate a structure of interest or to carry out amino-acid sequence comparisons, and one can now rapidly obtain an overview of a particular area of molecular biology. We shall here describe some Web sites that are of interest from a structural point of view. Updated links to these sites can be found in the Introduction to Protein Structure Web site (http // WWW.ProteinStructure.com/). 

Proteins have four levels of structure. Primary structure describes a protein s amino acid sequence secondary structure describes how segments of the protein chain orient into regular patterns—either a-helix or /3-pleated sheet tertiary structure describes how the entire protein molecule coils into an overall three-dimensional shape and quaternary structure describes how individual protein molecules aggregate into larger structures. 

TABLE 2 Survey of S-Layer Proteins Whose Amino Acid Sequences Are Known... 

An alternative approach is to synthesize an artificial gene in the test-tube starting with the appropriate deoxyribonucleotides. This approach, which demands that the entire amino acid sequence be known, has been used to clone genes encoding proteins 200 amino acids long. 

Signal sequence Amino acid sequence in protein, whose function is to direct its final intracellular or exh acellular location. 

Empirical statistical methods, which are based upon data generated from studying proteins of known three-dimensional structure and correlation of such proteins primary amino acid sequences with structural features. 

Silk type Function Proteins (ratio )a Predicted structure from sequence Amino acid (%Y Structure in solution Conformational change in solutione Fiber degree of crystallinity mf Fiber extensibility (%)e... 

Lathrop, R. FI. (1994). The protein threading problem with sequence amino acid interaction preferences is NP-complete. Protein Eng. 7, 1059—1068. 

A protein, of course, is a polypeptide chain made up of amino acid residues linked together in a definite sequence. Amino acids are handed (except for glycine, in which the normally asymmetric o-carbon has two hydrogens), and naturally occurring proteins contain only L-amino acids. That handedness has far-reaching effects on protein structure, as we shall see, and it is very useful to be able to distin-... 

The relationship between the base sequence in DNA and the amino acid sequence in the protein is known as the genetic code. With four bases (A, C, G and T) 64 three-base combinations are possible to provide the code for the amino acids (e.g. GTA, CCG). All but three of these are used to code for the polymerisation of the 20 different amino acids (in fact, 21, see Chapter 8) to form a polypeptide chain that can then form a protein. Most amino acids are, therefore, coded for by more than one three-base combination (Appendix 20.2). The link between the three-base... 

Since the primary structure of a peptide determines the global fold of any protein, the amino acid sequence of a heme protein not only provides the ligands, but also establishes the heme environmental factors such as solvent and ion accessibility and local dielectric. The prevalent secondary structure element found in heme protein architectures is the a-helix however, it should be noted that p-sheet heme proteins are also known, such as the nitrophorin from Rhodnius prolixus (71) and flavocytochrome cellobiose dehydrogenase from Phanerochaete chrys-osporium (72). However, for the purpose of this review, we focus on the structures of cytochromes 6562 (73) and c (74) shown in Fig. 2, which are four-a-helix bundle protein architectures and lend themselves as resource structures for the development of de novo designs. 

Peptide chains have a direction and therefore two different ends. The amino terminus (N terminus) of a peptide has a free ammonium group, while the carboxy terminus (C terminus) is formed by the carboxylate group of the last amino acid. In peptides and proteins, the amino acid components are usually linked in linear fashion. To express the sequence of a peptide, it is therefore suf cient to combine the three-letter or single-letter abbreviations for the amino acid residues (see p. 60). This sequence always starts at the N terminus. For... 

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