Critical amino acids responsible for converting specificities of proteins and for enhancing enzyme evolution are located around beta-turn potentials: data-based prediction

Amino acid propensities for secondary structures are influenced by the protein structural class

Amino acid propensities for secondary structures were used since the 1970s, when Chou and Fasman evaluated them within datasets of few tens of proteins and developed a method to predict secondary structure of proteins, still in use despite prediction methods having evolved to very different approaches and higher reliability. Propensity for secondary structures represents an intrinsic property of amino acid, and it is used for generating new algorithms and prediction methods, therefore our work has been aimed to investigate what is the best protein dataset to evaluate the amino acid propensities, either larger but not homogeneous or smaller but homogeneous sets, i.e., all-alpha, all-beta, alpha-beta proteins. As a first analysis, we evaluated amino acid propensities for helix, beta-strand, and coil in more than 2000 proteins from the PDBselect dataset. With these propensities, secondary structure predictions performed with a method very similar to that of Chou and Fasman gave us results better than the original one, based on propensities derived from the few tens of X-ray protein structures available in the 1970s. In a refined analysis, we subdivided the PDBselect dataset of proteins in three secondary structural classes, i.e., all-alpha, all-beta, and alpha-beta proteins. For each class, the amino acid propensities for helix, beta-strand, and coil have been calculated and used to predict secondary structure elements for proteins belonging to the same class by using resubstitution and jackknife tests. This second round of predictions further improved the results of the first round. Therefore, amino acid propensities for secondary structures became more reliable depending on the degree of homogeneity of the protein dataset used to evaluate them. Indeed, our results indicate also that all algorithms using propensities for secondary structure can be still improved to obtain better predictive results.

Predicting amino acid residues responsible for enzyme specificity solely from protein sequences

We describe a general, modular method for developing protocols to identify the amino acid residues that most likely define the division of a protein superfamily into two subsets. As one possibility, we use PROBE to gather superfamily members and perform an ungapped alignment. We then use a modified BLOSUM62 substitution matrix to determine the discriminating power of each column of aligned residues. The overall method is particularly useful for predicting amino acids responsible for substrate or binding specificity when no structures are available. We apply our method to three pairs of protein classes in three different superfamilies, and present our results, some of which have been experimentally verified. This approach may accelerate the elucidation of enzymic substrate specificity, which is critical for both mechanistic insights into biocatalysis and ultimate application.

Design and solution structure of functional peptide mimetics of nerve growth factor

The C-D loop in nerve growth factor (NGF) is involved in binding to the NGF receptor, TrkA. It is flexible and adopts several different types conformations in different NGF crystal forms. We have previously shown that a small cyclic peptide derived from the C-D loop of NGF binds to the TrkA receptor by mimicking the structure of this loop. To understand structure-function relationships in NGF C-D loop mimetics, we have produced a series of peptides predicted to form different types of beta-turns. The peptides were tested for their ability to promote cell survival in serum-free medium and to induce TrkA tyrosine phosphorylation. NMR structural studies were used to determined the backbone conformation and the spatial orientation of side chains involved in binding to the TrkA receptor. Peptides that form type I or type gammaL-alphaR beta-turns were the most active. The variety of active loop conformations suggests that the mimetics (and NGF) accommodate the binding site on TrkA by an 'induced fit' mechanism. In agreement with this hypothesis, NMR relaxation measurements detected both fast and slow motion in the peptides. We also characterized a retro-inverso peptide derived from the NGF C-D loop. This D-amino acid cyclic peptide did not adopt a conformation homologous to the NGF C-D loop and was inactive. This may be representative of difficulties in producing structural and functional mimetics by retro-inverso schemes.

Deciphering cryptic similarities in protein binding sites

Rapid expansion in the number of plausible drug targets arising from genomics research has created new pressures for increased efficiency in discovery of high specificity candidate drug compounds. Improved understanding of conserved features among protein structures provides a promising route to achieving this goal. Indirect evidence implies that important similarities are now ripe for elucidation by emerging experimental approaches.

Structural features that make oligopeptides susceptible substrates for hydrolysis by recombinant thimet oligopeptidase

A systematic analysis of the peptide sequences and lengths of several homologues of bioactive peptides and of a number of quenched-fluorescence (qf) opioid- and bradykinin-related peptides was performed to determine the main features leading the oligopeptides to hydrolysis by the recombinant rat testis thimet oligopeptidase (EC 3.4.24.15). The results indicate that a minimum substrate length of six amino acids is required and that among the oligopeptides six to thirteen amino acid residues long, their susceptibility as substrates is highly variable. Thimet oligopeptidase was able to hydrolyse, with similar catalytic efficiency, peptide bonds having hydrophobic or hydrophilic amino acids as well as proline in the P1 position of peptides, ranging from a minimum of six to a maximum of approximately thirteen amino acid residues. An intriguing observation was the shift of the cleavage site, at a Leu-Arg bond in qf dynorphin-(2-8) [qf-Dyn2-8; Abz-GGFLRRV-EDDnp, where Abz stands for o-aminobenzoyl and EDDnp for N-(2,4-dinitrophenyl)ethylenediamine], to Arg-Arg in qf-Dyn2-8Q, in which Gln was substituted for Val at its C-terminus. Similarly, a cleavage site displacement was also observed with the hydrolysis of the internally quenched-fluorescence bradykinin analogues containing Gln at the C-terminal position, namely Abz-RPPGFSPFR-EDDnp and Abz-GFSPFR-EDDnp are cleaved at the Phe-Ser bond, but Abz-RPPGFSPFRQ-EDDnp and Abz-GFSPFRQ-EDDnp are cleaved at the Pro-Phe bond.

Critical amino acids responsible for conferring calcium channel characteristics are located on the surface and around beta-turn potentials of channel proteins

Calcium ion is thought to be one of the initial signals in the process of synaptic modification. Various reports have described that the critical amino acids responsible for determining calcium permeability of ion channels are glutamic acid, glutamine, arginine, and asparagine. By using a computational method (MacPROT) distinguishing transmembrane, globular, and surface sequences of proteins, the present work predicts that the critical amino acids exist within surface regions of the proteins. Furthermore, occurrence of beta-turn probabilities can be predicted around these critical residues by the protein conformational prediction method of Chou and Fasman. The results suggest that the critical amino acids exist at hydrophilic spaces or canals of membranous channel proteins and that the redirection potential of the protein chain induced by the turn structures provides the conformational change requisite for the ion selectivity and gating (opening/closing) of the channels.

Amino acid preferences at protein binding sites

An analysis of the amino acid distribution at protein binding sites was carried out using 50 diverse macromolecules for which crystallographic data with a bound ligand are available. The purpose of this study is to determine whether differential trends in amino acid distributions exist at binding sites compared to other regions in the proteins. The results indicate that some residues, particularly Arg, His, Trp and Tyr are substantially more frequent at the binding sites, compared to the number of times these residues are present in proteins generally. These effects go beyond the differences seen comparing surface exposed residues to bulk protein. The resemblance in the residue utilization at the binding sites of unrelated proteins restricts the possible types of interactions with ligands, possibly accounting for the repetition of substructural motifs in chemicals with diverse pharmacological action. Further, the use of these diagnostic features may permit identification of ligand binding pockets in a protein structure deduced from sequence information or from data in the absence of a ligand. Some of these findings complement and extend previously described trends for antibody binding sites.