Phylogenetic trees constructed from hydrophobicity values of protein sequences

The Cipher of the Genetic Code

A new approach to understanding of the genetic code is developed. In order to overcome the key paradox (and Darwinian selection problem) that the highly complex amino acid Phe is encoded by the simplest codons (UUY), and the simplest Gly encoded by the most complex codons (GGN); as well as the paradox of the duplication of some amino acids in the encoding process (Leu, Ser, Arg), we proposed an extension of the notion (and concept) of genetic code. For a better (and lighter) understanding of genetic coding, we proposed a hypothesis after that (under the conditions of allowed metaphoricity and modeling in biology) genetic code has to be understood, analogously in cryptology, as the unity of three entities: the code, the cipher of the code and the key of the cipher. In this hierarchy the term (and notion) "genetic code" remains what has been from the beginning: a connection between four-letter alphabet (four Py-Pu nucleotides, in form of codons) and a twenty-letter alphabet (twenty amino acids); the cipher is a specific chemical complementarity in chemical properties of molecules in the form: similarity in dissimilarity versus dissimilarity in similarity ("Sim in Diss vs Diss in Sim") and the key of cipher: the complementarity on the binary tree of the genetic code in the form: 0-15, 1-14, 2-13, …, 6-9, 7-8. These concepts improve understanding that within the two main Genetic Code Tables (of the nucleotide doublets and nucleotide Triplets) exists a sophisticated nuancing and balancing in the properties of the constituents of GC, including the balance of the number of molecules, atoms, and nucleons.

Peptides quantitative structure-function relationships: an automated mutation strategy to design peptides and pseudopeptides from substitution matrices

The process by which analogs in peptide chemistry are currently designed does not include any quantitative basis for amino acid substitutions from pharmacological leads. Here, we show that substitution matrices such as PAM 250 can provide quantitative constraints compatible with biological activity. This article describes its use in a strategy of rational amino acid substitution in peptides and proteins: we have computed a chemically derived matrix equivalent to the well-known PAM 250 matrix, reflecting the natural mutability rates of amino acids in protein evolutions but that can be extended to all the noncoded amino acids. Some of these noncoded amino acids are widely used to mimic secondary structure, to constrain backbone conformation, or to evade protease degradation. An automated sequence mutation (ASM) strategy has been defined to generate mutations within constraints. Application of such a substitution matrix to quantitative structure-function relationship studies will be of use in the design of proteins and peptides destined to become pharmaceutical drugs. In particular, issues such as which functionally conserved substitutions are able to satisfy conformational restrictions, oral bioavailability, or formulation demands can be quantitatively addressed.

Molecular anatomy: phyletic relationships derived from three-dimensional structures of proteins

A distance measure that reflects the dissimilarity among structures has been developed on the basis of the three-dimensional structures of similar proteins, this being totally independent of sequence in the sense that only the relative spatial positions of mainchain alpha-carbon atoms need be known. This procedure leads to phyletic relationships that are in general correlated with the sequence phylogenies based on residue type. Such relationships among known protein three-dimensional structures are also a useful aid to their classification and selection in knowledge-based modeling using homologous structures. We have applied this approach to six homologous sets of proteins: immunoglobulin fragments, globins, cytochromes c, serine proteinases, eye-lens gamma crystallins, and dinucleotide-binding domains.

Antibody recognition of amino acid divergence within an HIV-1 neutralization epitope

Antibodies elicited by HIV-1 strains, and which neutralize such strains in vitro, bind to synthetic peptides of 5-8 amino acids in length. These amino acids, although variable, have a fixed location between two cysteines in the carboxyl terminus of the HIV-1 external envelope. Nine peptides of 9 amino acids corresponding to the gp120 domains of European and American (LAV-1, NY5, CDC4, SF2), Haitian (RF) and African (ELI, MAL, Z3, Z6) HIV-1 strains, were synthesized using LAV-1 and RF neutralization epitopes as models. Serum of chimpanzees infected with LAV-1, HTLV-IIIB or HTLV-IIIRF reacted predominantly with the homologous peptide, although cross-reactivity with heterologous peptides occurred: 8 out of 11 human sera with HTLV-IIIB-neutralizing activity bound the LAV-1/HTLV-IIIB peptide, and 6 out of 7 sera with HTLV-IIIRF-neutralizing activity bound the RF peptide. African sera reacted most frequently with the Z3 peptide (78%) while only 35% (p = 0.0001) of European and 20% (p less than 0.0001) of American sera recognized it. Recognition patterns of children from the USA and Europe were different. Although multiple reactivities were observed, blocking experiments favoured cross-reactivity as the explanation. Based on the antibody profiles of nonapeptide recognition, peptides LAV-1, RF and SF2 were clustered, as were NY5 and CDC4, and so were Z6, MAL and ELI. This antigenic relatedness of HIV-1 strains could not entirely be explained by the physico-chemical characteristics of the nonamers per se. Resemblance was observed with the clustering of HIV-1 strains based on the divergence of the nucleotide sequence of entire HIV-1 envelopes. This implies a role of peripheral envelope residues, in the context of infectious particles or infected cells, in determining the specificity of antibodies reactive to the V3 domain. Therefore, the neutralization domain in this variable region may be considered part of a conformational structure involving several envelope regions which appear distinct from each other in the primary sequence.

A structural comparison of type c lysozymes based on their hydropathic profiles

Hydropathic profiles can be considered as an approach to the three-dimensional structure of a protein and so their use for comparison of homologous proteins is proposed, as they provide information on relative structural conservativeness. A simple approach was developed for comparison of hydropathic profiles and applied to 19 lysozymes c of known primary structure. Trees were constructed in order to discover which method yielded the best estimation of the phenotypic differences between the proteins considered, by means of the goodness-of-fit criterion. Iterative methods, such as the Fitch-and-Margoliash and the unweighted-pair-group methods, gave a better fit than did a non-iterative method. When the hydropathic approach is used for comparison of lysozymes c, the enzyme obtained from chachalaca egg-white is placed closer to those from pheasant-like birds than to those of ducks; this result agrees with the morphological resemblance of the chachalaca to pheasant-like birds. Pigeon egg-white and equine milk lysozymes differ greatly in sequence from other lysozymes c and their hydropathic analysis shows important differences with respect to the other homologous enzymes.

Relationship between hydropathic variability and functional properties of alpha-lactalbumins and type c lysozymes

Hydropathic profiles obtained from the amino acid sequences of 8 alpha-lactalbumins were averaged and compared to the average profile deduced from the primary structure of 21 type c lysozymes. This analysis was performed in order to detect differences between both types of molecules, since it could explain their different functional properties. The application of the method herein described reveals the existence of very significative differences (P less than 0.001) between the amino acid residues located at positions 31-32, 34-35, 37-45, 47-48, 80-85 and 108-113 of alpha-lactalbumins and their homologous in type c lysozymes. These differences are in agreement with the chemical data about the interaction sites of both galactosyltransferase and calcium ions with alpha-lactalbumin, which are not required for the lysozyme function.