Amino acid pairs

Abstract. A smooth empirical potential is constructed for use in off-lattice protein folding studies. Our potential is a function of the amino acid labels and of the distances between the Ca atoms of a protein. The potential is a sum of smooth surface potential terms that model solvent interactions and of pair potentials that are functions of a distance, with a smooth cutoff at 12 Angstrom. Techniques include the use of a fully automatic and reliable estimator for smooth densities, of cluster analysis to group together amino acid pairs with similar distance distributions, and of quadratic progrmnming to find appropriate weights with which the various terms enter the total potential. For nine small test proteins, the new potential has local minima within 1.3-4.7A of the PDB geometry, with one exception that has an error of S.SA. 

We therefore use smooth density estimation techniques that are more reliable than the histogram estimates. To improve the reliability for rare amino acid pairs, we use clustering techniques that identify similar pairs that can be modeled by the same density. 

Fig. 1. Cumulative distribution function of half squared distances of amino acid pairs at residue distance d (d = 1,..., 20), truncated at Cmax = 72 (12Acutoff)...

Fig. 3. Some representative pair potentials Uy(r), sealed to move their interesting range to [0,5]. The numbers above each potential denote the class label 7 and the iiinnber of data points available for the fit. (For example, elass 63 gives distanee 3 potentials for the amino acid pairs Lys-Asp, Arg-Lys and Glu-Tyr.) The spectrum below each potential consists of 50 lines pieked uniformly from the data.

Turner, J.M., S.E. Swalley, E.E. Baird, and P. B. Dervan. Aliphatic/aromatic amino acid pairings for polyamide recog-... 

The paired box is another sequence motif that is very well conserved during evolution and is found in a number of genes known to be of developmental significance in lower organisms. The paired box encodes the 128-amino acid paired domain, which binds DNA(Chalapakis et al., 1991), and shows similarity, with a helix-tum-helix motif, to the homeodomain. 

D. C. Pimenta, M. A. Juliano, L. Juliano, Hydrolysis of Somatostatin by Human Tissue Kallikrein after the Amino Acid Pair Phe-Phe , Biochem. J. 1997, 327, 27-30. 

Fooks HM, Martin ACR, Woolfson DN, Sessions RB, Hutchinson EG. Amino acid pairing preferences in parallel /3-sheets in proteins. J Mol Biol 2006 356 32-44. 

Since the frequencies of rare amino acid pairs can be relatively small, procedures to treat sparse data are employed [6]. 

Weigelt, J., et al., Site-selective screening by NMR spectroscopy with labeled amino acid pairs. JAm Chem Soc, 2002, 124, 2446-2447. 

P. Jurecka, J. Sponer, J. Cerny, P. Hobza, Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs. Phys. Chem. Chem. Phys. 8, 1985-1993 (2006)... 

Chen J, Liu H, Yang J, Chou KC (2007) Prediction of linear B-cell epitopes using amino acid pair antigenicity scale. Amino Acids 33 423-428... 

Another frequently used global information that covers protein context is the residue frequencies. The composition is often calibrated with that from the database as in Gamier et al. (1996), where only observed frequencies of amino acids and amino acid pairs are used for protein secondary structure prediction. 

Studies aimed at clarifying the mechanism of enantioselection associated with 41, making use of a combination of molecular dynamics calculations and NMR techniques <2001J(P2)1685>, as well as X-ray diffraction data <20040BC3470>, have led to a better comprehension of the subtle interactions that characterize and differentiate the diastereomeric complexes of tetra-acid 41 with the D,L-amino acid pairs. 

Relations between Amino Acid Pairs When Comparing the Complete Structure of the a- and 0-Chain of Hemoglobin... 

Park, K.J. and Kanehisa, M. (2003) Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs. Bioinformatics 19, 1656-1663. 

Figure 4 The dependence of the elements of the BLOSUM62 substitution matrix on the interaction energies between amino acid residues (approximated by the Miyazawa-Jernigan parameter). Top chart. Only nonsynonymous substitutions are presented. The curved line represents the parabolic fit to highlight the nonmonotonic nature of the plot. Bottom chart. Blowup of the right upper corner of the top chart. Amino acid pairs are labeled, and pairs of amino acids that can contribute to positive and negative components of design are shown.

Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs ... 

Fig 3 presents the capillary LC separation and direct collection onto PVDF membrane of the peptide fragments generated from carbonic anhydrase. Peaks 2,3,4 and 5 from the cLC possessed sequences from carbonic anhydrase either fiom Met- cleavage (peaks 2,3 and 4) or fixjm formic acid induced cleavages between Asp-Pro amino acid pairs at elevated temperature (peaks 4 and 5). AlAough there was no difficulty in identifying the major sequences, some of... 

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