Amino add sequences

Besides such textual databases that provide bibhographic information, sequence databases have attained an even more important role in biochemistry. Sequence databases are composed of amino add sequences of peptides or proteins as well as nudeotide sequences of nudeic acids. The 20 amino adds are mostly represented by a three-letter code or by one letter according to the biochemical conventions) the four nudeic adds are defined by a one-letter code. Thus the composition of a biochemical compound is searchable by text retrieval methods. 

How can we apply molecular dynamics simulations practically. This section gives a brief outline of a typical MD scenario. Imagine that you are interested in the response of a protein to changes in the amino add sequence, i.e., to point mutations. In this case, it is appropriate to divide the analysis into a static and a dynamic part. What we need first is a reference system, because it is advisable to base the interpretation of the calculated data on changes compared with other simulations. By taking this relative point of view, one hopes that possible errors introduced due to the assumptions and simplifications within the potential energy function may cancel out. All kinds of simulations, analyses, etc., should always be carried out for the reference and the model systems, applying the same simulation protocols. 

Polyclonal antibodies Antibodies derived from a mixture of cells, hence containing various populations of antibodies with different amino add sequences. They are of limited use in that they will not all bind to the same epitopes following immunization with a haptenlcarrier protein conjugate. They are also difficult to purify and characterize, but have been used with success in the catELISA system. 

SCHLESINGER, D. H., GOLDSTEIN, G., and Niall, H. D. The complete amino add sequence of ubiquitin, an adenylate cydase stimulating polypeptide probably universal in living cells, Biochemistry, 1975, 14, 2214-8. 

Gene expression and DNA replication are compared in Table I-l-l. Transcription, the first stage in gene expression, involves transfer of information found in a double-stranded DNA molecule to the base sequence of a single-stranded RNA molecule. If the RNA molecule is a messenger RNA, then the process known as translation converts the information in the RNA base sequence to the amino add sequence of a protein. 

For Trichoderma reesei the cellulases most thoroughly investigated with respect to their structural properties are CBH I and CBH II and to a lesser extent the two en-doglucanases (EG I and EG III) 11 (Table I). For most other cellulases structural characterizations are confined to the amino add sequence as deduced from the base sequence of the respective genes and to sequence related investigations such as hydro-phobic cluster analysis 10 or computer aided molecular modelling and homology... 

Such a polypeptide chain folding into two distinct domains could be correlated with the amino add sequence. The N-terminus of the polypeptide chain is located at an as yet unknown site of the head part and starts with the sequence Pyr.Glu-Ser-Ala-Cys-Thr-, the C-terminal region is located at the end of the tail and has the sequence -Pro-Tyr-TVr-Ser-Gln-Cys-Leu. From the total of 497 amino acids about 430 are located in the head part, where the chain is partially ordered in jS-structures. Ten disulfide bridges give stability and rigidity to this part of the molecule 24. The bridges interconnect the cysteine residues 4-50, 19-25, 61-71(7), 67-72(7), 138-397, 172-209(7), 176-210(7), 230-256, 238-243, and 261-331. The exact position of some... 

Figure 3. Amino add sequence of Peptococcus aerogenes ferredoxin.

Fig. 4. Amino add sequence of human serum high-density lipoprotein apoprotein (apo HDL), fraction IV (dimer). Data from Brewer et al. (B5).

The choice of protecting groups and of the type of resin-anchor required for synthesis of cyclic peptides on solid supports not only depends upon the particular amino add sequence of the target molecule, but decisively upon the mode of cyclization, particularly whether the C-terminal carboxy group should act as bridgehead or not. Correspondingly, the synthetic routes can be subdivided into two main classes either based on the attachment of the C-terminus to the solid support by suitable anchors or where side-chain functionalities are exploited for this purpose. 

As a specific example the mechanism of action of bovine pancreatic ribonudease A is now considered. Ribonudease A is a relatively small enzyme consisting of a single polypeptide chain of molecular weight 13,680. It has been extensively studied by many methods The amino add sequence and three-dimensional structure are known and extensive equilibrium and kinetic studies have been carried out as well as other... 

The enzyme has been well characterized, the complete amino acid sequence is known, and there have been many crystal structure determinations. The complete amino add sequence for the liver enzyme was determined by Jornvall in 1970 1335 it contained 374 residues, consistent in... 

By examining the amino add sequence of tropomyosin, the smallest and simplest proteins postulated at the time 1819 to contain the coiled-coil motif, we identified the hydrophobic repeat responsible for the formation and stabilization of the coiled-coil structure. 18 A coiled coil can be considered as a repeating heptad of seven amino acid residues a-b-c-d-e-f-g, where positions a and d are occupied by hydrophobic residues. This 3-4 (or 4-3) hydro-... 

The three-dimensional structure of a protein does not depend on environmental factors within the cell but is determined solely by the amino add sequence information (Epstein, 1963) this is called the Anfinsen dogma. Model systems of enzymes converted into linear polypeptide chains devoid of disulfide bonds and of secondary and tertiary structures support the theory that the folding process is essentially a thermodynamic one and that no genetic information other than that present in the amino acid sequence of the protein is required. 

It is a long sought-after goal of biocatalysis research to find a general correlation between the stability of an enzyme and its structure, especially its primary structure (amino add sequence). 

This is far more than the number of atoms that make up the Earth. It is also the reason why directing the evolution of an existing enzyme is much likelier to succeed than searching for catalytically active amino add sequences in random peptide libraries. 

Fischli, W., Goldstein, A., Hunkapiller, M. W., and Hood, L. E. (1982). Isolation and amino add sequence analysis of a 4,000-dalton dynorphin from porcine pituitary. Proc. Natl. Acad. Sci. USA 79, 5435-5437. 

G. M. Crippcn. Prediction of protein folding ftom amino add sequence over discrete... 

M. J. Sippl andS. Wtitdas. Detection of native like models for amino add sequences of unloiown three-dimensional structure in a database of known protein conformations. Proteins 75 258-271 (1992). 

P. Argos, A sensitive pmedne to compare amino add sequences. J, MoL BioL /9Ji385-396 (1987),... 

The amino add sequence of glycyl endopeptidase was published by Ritonja et al. [45] (Fig. 1). The enzyme exists as a single unglycosylated polypeptide of 216 amino add residues (Mr 23.313). Glycyl endopeptidase is clearly a member of the papain family of cysteine proteinases [46], The three-dimensional structure... 

Ritonja et al. [45] revealed the complete amino add sequence of stem bromelain. Their results show that stem bromelain exists as a single polypeptide chain with... 

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