Proteins alignments

S Henikoff, JG Henikoff, S Pietrokovski. BLOCKS+ A non-redundant database of protein alignment blocks derived from multiple compilations. Biomformatics 15 471-479, 1999. 

Wohnert, J., Franz, K.J., Nitz, M., Imperiali, B., and Schwalbe, H. (2003) Protein alignment by a coexpressed lanthanide-binding tag for the measurement of residual dipolar couplings. J. Am. Chem. Soc. 125,13338-13339. 

Orienting systems of quasi-ternary mixtures composed of cetylpyridinium chloride/hexa-nol/NaCl [26] and cetylpyridinium bromide/hexanol/NaBr [27] have been reported to form lamellar liquid crystalline phases that allow a large temperature range over which dipolar couplings can be measured. The optimum condition for protein alignment consists of a 1 1.33 (w/w) ratio of cetylpyridinium bromide/hexanol. The residual 2H quad-rupolar splitting of the HOD resonance increases from 5 Hz to 20 Hz as the concentration of the mixture is varied from 30 to 65 mg/mL. These quasi-ternary mixtures are positively charged. 

When predicting consensus structures, be aware that the quality of the prediction is limited by the quality of the input alignment. Nucleic acid alignments are generally more error-prone than protein alignments. For coding sequences it is sometimes preferable to back-translate a protein alignment. 

TOPITS, Predict Protein alignment of secondary structure motifs... 

Neuwald, A. F., et al., Extracting protein alignment models from the sequence database. Nucleic Acids Res, 1997. 25(9) p. 1665-77. 

Sadreyev, R., and N. Grishin. 2003. COMPASS A tool for comparison of multiple protein alignments with assessment of statistical significance. J Mol Biol 326 317-26. 

Gille, C S. Lorenzen, E. Michalsky, and C. Frommel. 2003. KISS for STRAP User extensions for a protein alignment editor. Bioinformatics 12 2489-90. 

Shatsky, M., H. J. Wolfson, and R. Nussinov. 2002. Flexible protein alignment and hinge detection. Proteins 48 242-56. 

All commonly used substitution matrices are derived from a large collection of protein alignments, containing both enzymes and non-enzymes. Thus, favorable residue groupings tend to refled a structural compatibility rather than a functional equivalence. It would be expected that a substitution matrix derived from particular sets of enzymes would have quite different values for residues that are frequently found in active sites. 

Yu, C.-N., Joachims, T., Elber, R., PiUardy, J. Support vector training of protein alignment models. In Research in Computational Molecular Biology. Lecture Notes in Computer Science, vol. 4453. Berlin Springer/Heidelberg 2007, pp. 253-67. 

Yao LS, Bax A (2007) Modulating protein alignment in a liquid-crystalline medium through conservative mutagenesis. J Am Chem Soc 129(37) 11326... 

Koenig BW et al (1999) NMR measurement of dipolar couplings in proteins aligned by transient binding to purple membrane fragments. J Am Chem Soc 121(6) 1385-1386... 

An introduction of a coexpressed lanthanide-binding tag (LBT) as a method for protein alignment facilitating the measurement of RDCs has been proposed by Wohnert et The LBT chosen by them had the sequence YID-TNNDGWYEGDELLA, and was appended to the terminus of human ubiquitin by standard cloning techniques. 

Fig. 5. Amino acid sequence comparison of E3/19K proteins. Alignment was carried out as explained in Fig. 2. The putative signal sequences as predicted by the Signal software (Nielsen et al. 1997) are omitted. The consensus is shaded black, and strictly conserved aa are marked by arrowheads above the sequences. References to the sequences are either given in the legend to Figs. 2 and 3 or are as follows Ad 1. Y16037 Ad6. G2828254 Ad7 (Hermiston et al. 1993)...

It should also be noticed that in proteins, aligned in a membrane, the excitation energy may be transferred from a particular excited protein to its neighbor, thus providing transport of energy that is nearly loss free. 

Randic (2012) introduced a novel approach to the problem of protein alignments. It is based on superposition of amino acid adjacent matrices of a pair of proteins, which have been modified to record the sequential order of amino acids. 

M. Randic, The connectivity index 25 years after, J. Mol. Graphics Modell. 20 (2001b) 19-35. M. Randic, Very efficient search for protein alignment— VESPA, J. Comput. Chem. 33 (2012) 702-707. 

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