Disallowed Ramachandran Conformations of Amino Acid Residues in Protein Structures

An analysis of the nature and distribution of disallowed Ramachandran conformations of amino acid residues observed in high resolution protein crystal structures has been carried out. A data set consisting of 110 high resolution, non-homologous, protein crystal structures from the Brookhaven Protein Data Bank was examined. The data set consisted of a total of 18,708 non-Gly residues, which were characterized on the basis of their backbone dihedral angles (φ, ψ). Residues falling outside the defined “broad allowed limits” on the Ramachandran map were chosen and the reportedB-factor value of the α-carbon atom was used to further select well defined disallowed conformations. The conformations of the selected 66 disallowed residues clustered in distinct regions of the Ramachandran map indicating that specific φ, ψ angle distortions are preferred under compulsions imposed by local constraints. The distribution of various amino acid residues in the disallowed residue data set showed a predominance of small polar/charged residues, with bulky hydrophobic residues being infrequent. As a further check, for all the 66 cases non-hydrogen van der Waals short contacts in the protein structures were evaluated and compared with the ideal “Ala-dipeptide” constructed using disallowed dihedral angle (φ, ψ) values. The analysis reveals that short contacts are eliminated in most cases by local distortions of bond angles. An analysis of the conformation of the identified disallowed residues in related protein structures reveals instances of conservation of unusual stereochemistry.

Amino acid sequence of the winged bean (Psophocarpus tetragonolobus) basic lectin. Adenine binding and identification of the active-site tryptophan residue

The complete amino acid sequence of winged bean basic agglutinin (WBA I) was obtained by a combination of manual and gas-phase sequencing methods. Peptide fragments for sequence analyses were obtained by enzymatic cleavages using trypsin and Staphylococcus aureus V8 endoproteinase and by chemical cleavages using iodosobenzoic acid, hydroxylamine, and formic acid. COOH-terminal sequence analysis of WBA I and other peptides was performed using carboxypeptidase Y. The primary structure of WBA I was homologous to those of other legume lectins and more so to Erythrina corallodendron. Interestingly, the sequence shows remarkable identities in the regions involved in the association of the two monomers of E. corallodendron lectin. Other conserved regions are the double metal-binding site and residues contributing to the formation of the hydrophobic cavity and the carbohydrate-binding site. Chemical modification studies both in the presence and absence of N-acetylgalactosamine together with sequence analyses of tryptophan-containing tryptic peptides demonstrate that tryptophan 133 is involved in the binding of carbohydrate ligands by the lectin. The location of tryptophan 133 at the active center of WBA I for the first time subserves to explain a role for one of the most conserved residues in legume lectins.

Protein content and amino acid composition of some varieties of grain sorghum

Determination of the protein content and lysine levels of a number of nonhybrid varieties of grain sorghum indicates large variations in the protein content. Statistical analysis of data on amounts of lysine shows that a negative correlation exists between per cent lysine in the protein and per cent protein in the seed. The proportion of various protein fractions in endosperm of five varieties of grain sorghum of both low- and high-protein type has been determined. Results show that prolamine and glutelin are the principal protein fractions, and increased protein levels in sorghum varieties are correlated with an increase mainly in the prolamine fraction. Nine high- and low-protein varieties of grain sorghum have been analyzed for their amino acid composition by ion exchange procedures. One of the high-protein genetic varieties of sorghum has a high concentration of lysine in the seed. Amino acid composition of the protein fractions of two varieties is also reported. These data permit an evaluation of the nutritional quality of sorghum protein and factors that influence the quality of the protein.

Biochemical Characterization Of Β-N-Oxalyl-L-Α,Β-Diaminopropionic Acid, The Lathyrus Sativus Neurotoxin As An Excitant Amino Acid

Abstract—β-N-Oxalyl-l-α,β-diaminopropionic acid (ODAP), the toxin isolated from the seeds of Luthyrus sativus produces head retraction, tremors and convulsions when injected into a variety of experimental animals. In 12-day-old rats, it has been found that the convulsive behaviour is accompanied by profound biochemical changes in the brain. The brain homogenates prepared from ODAP injected animals show a higher rate of respiration. There is a decrease in the brain glucose, glycogen, ATP, phosphocreatine and acetylcholine levels of the convulsing animals. The inorganic phosphate, lactic acid and acetylcholineesterase levels increase. These results establish that ODAP is a typical convulsant.

Studies in the polarographic behaviour of zinc-amino acid complexes

1. The polarographic behaviour of amino-acid complexes of zinc has been studied using seven amino acids as complexing agents. 2. The effect of varying the pH of the base solution and the concentration of amino-acid anion on the polarographic behaviour of zinc in these solutions have indi cated the formation of twelve amino-acid complexes. The stability constants could not be calculated due to the irreversible nature of the waves. 3. The effect of sodium hydroxide, sodium carbonate, and ammonia on the polarographic behaviour of zinc has been investigated. The results can be interpreted as due to the formation of mixed complexes in many systems. 4. Amino-acid base solutions have been found to be suitable for the polarographic estimation of zinc.

Studies in the polarography of metal-amino acid complexes - Part I. Cadmium

1. A detailed polarographic study of cadmium has been made employing glycine, α-alanine, β-alanine, valine, aspartic acid, glutamic acid and asparagine as complexing agents at various pH values. The effect of incorporating sodium hydroxide, sodium carbonate and ammonium nitrate + ammonium hydroxide, on the polarographic behaviour of amino acid complexes of cadmium has also been investigated. 2. The reduction process has been found to be reversible in all systems. 3. The small shifts in the half-wave potentials noticed due to increase in the concentration of sodium hydroxide and sodium carbonate in presence of amino acids have been explained on the basis of formation of mixtures of pure and mixed amino acid complexes of cadmium. Mixed complexes have also been noticed in presence of ammonium hydroxide and ammonium nitrate and amino acids. 4. Polarographic evidence has been obtained for the formation of over 30 pure and mixed complexes. The dissociation constant Kd, the Δ F° value for the dissociation, and standard potential value for the formation, of each complex have been computed. 5. It has been found that cadmium can be polarographically estimated in amino acid solutions.

Studies in the polarography of metal-amino acid complexes -Part II. Lead

1. The polarographic behaviour of glycine, α-alanine, β-alanine, valine, aspartic acid, glutamic acid and asparagine complexes of lead has been studied at various pH values and in presence of (1) NaOH, (2) Na2CO3 and (3) NH4 NO3+NH4OH. All the polarographic waves have been found to be reversible. 2. Experiments conducted on the effect of variation of pH, i.e., 7amino-acid have indicated the formation of Pb A and Pb A2. The data have been analysed employing the equations developed by DeFord and Hume as modified by McKenzie and Mellor. 3. Only pure complexes are produced below pH 11·2 in the case of aspartic acid, glutamic acid and glycine, while mono hydroxy complexes are produced in α-alanine, valine and asparagine systems. 4. It has been found that no mixed hydroxy and mixed ammonia complexes are produced in presence of sodium hydroxide and ammonia-ammonium nitrate, respectively. However evidence is obtained for the formation of mixed carbonate complexes in glycine and aspartic acid systems in presence of sodium carbonate. 5. Thermodynamic data have been calculated from polarographic measurements for 18 complexes. 6. The suitability of incorporating amino acids in base solutions for the polarographic estimation of lead has been tested.

Protein sequence design on the basis of topology optimization techniques -Using continuous modeling of discrete amino acid types

The notion of optimization is inherent in protein design. A long linear chain of twenty types of amino acid residues are known to fold to a 3-D conformation that minimizes the combined inter-residue energy interactions. There are two distinct protein design problems, viz. predicting the folded structure from a given sequence of amino acid monomers (folding problem) and determining a sequence for a given folded structure (inverse folding problem). These two problems have much similarity to engineering structural analysis and structural optimization problems respectively. In the folding problem, a protein chain with a given sequence folds to a conformation, called a native state, which has a unique global minimum energy value when compared to all other unfolded conformations. This involves a search in the conformation space. This is somewhat akin to the principle of minimum potential energy that determines the deformed static equilibrium configuration of an elastic structure of given topology, shape, and size that is subjected to certain boundary conditions. In the inverse-folding problem, one has to design a sequence with some objectives (having a specific feature of the folded structure, docking with another protein, etc.) and constraints (sequence being fixed in some portion, a particular composition of amino acid types, etc.) while obtaining a sequence that would fold to the desired conformation satisfying the criteria of folding. This requires a search in the sequence space. This is similar to structural optimization in the design-variable space wherein a certain feature of structural response is optimized subject to some constraints while satisfying the governing static or dynamic equilibrium equations. Based on this similarity, in this work we apply the topology optimization methods to protein design, discuss modeling issues and present some initial results.

Empirical torsional potential functions from protein structure data. Phi- and psi-potentials for non-glycyl amino acid residues.

The torsional potential functions Vt(phi) and Vt(psi) around single bonds N--C alpha and C alpha--C, which can be used in conformational studies of oligopeptides, polypeptides and proteins, have been derived, using crystal structure data of 22 globular proteins, fitting the observed distribution in the (phi, psi)-plane with the value of Vtot(phi, psi), using the Boltzmann distribution. The averaged torsional potential functions, obtained from various amino acid residues in L-configuration, are Vt(phi) = 1.0 cos (phi + 60 degrees); Vt(psi) = 0.5 cos (psi + 60 degrees) - 1.0 cos (2 psi + 30 degrees) - 0.5 cos (3 psi + 30 degrees). The dipeptide energy maps Vtot(phi, psi) obtained using these functions, instead of the normally accepted torsional functions, were found to explain various observations, such as the absence of the left-handed alpha helix and the C7 conformation, and the relatively high density of points near the line psi = 0 degrees. These functions derived from observational data on protein structures, will, it is hoped, explain various previously unexplained facts in polypeptide conformation.

Amino acid-lanthanide interactions, Part 2. The X-ray crystal structures of lanthanide and calcium complexes of 1-amino-cyclohexane-1-carboxylic acid (Acc6)

The structures of [Nd-2(Acc(6))(H2O)(6)](ClO4)(6) .(H2O)(6) (1) [Er-2(Acc(6))(4)(H2O)(8)](ClO4)(6) .(H2O)(11) (2) and [Ca-5(Acc(6))(12)(H2O)(6)](ClO4)(10).(H2O)(4) (3) (Acc(6) = 1-aminocyclohexane-1-carboxylic acid) have been determined by X-ray crystallography. The lanthanide complexes 1 and 2 are dimeric in which two lanthanide cations are bridged by four carboxylato groups of Acc(6) molecules. In addition, the neodymium complex (1) features the unidentate coordination of the carboxyl group of an Acc(6) molecule in place of a water molecule in the erbium complex (2). The coordination number in both 1 and 2 is eight. The calcium Acc(6) complex (3) is polymeric; three different calcium environments are observed in the asymmetric unit. Two calcium ions are hexa-coordinated and one is hepta-coordinated. Considerable differences are observed between the solid state structures of Ln(III) and Ca-II complexes of Acc(6

Effect of amino acid substitutions at the subunit interface on the stabiity and aggregation properties of a dimeric protein: role of Arg 178 and Arg 218 at the dimer interface of thymidylate synthase

The significance of two interface arginine residues on the structural integrity of an obligatory dimeric enzyme thymidylate synthase (TS) from Lactobacillus casei was investigated by thermal and chemical denaturation. While the R178F mutant showed apparent stability to thermal denaturation by its decreased tendency to aggregate, the Tm of the R218K mutant was lowered by 5 degrees C. Equilibrium denaturation studies in guanidinium chloride (GdmCl) and urea indicate that in both the mutants, replacement of Arg residues results in more labile quaternary and tertiary interactions. Circular dichroism studies in aqueous buffer suggest that the protein interior in R218K may be less well-packed as compared to the wild type protein. The results emphasize that quaternary interactions may influence the stability of the tertiary fold of TS. The amino acid replacements also lead to notable alteration in the ability of the unfolding intermediate of TS to aggregate. The aggregated state of partially unfolded intermediate in the R178F mutant is stable over a narrower range of denaturant concentrations. In contrast, there is an exaggerated tendency on the part of R218K to aggregate in intermediate concentrations of the denaturant. The 3 A crystal structure of the R178F mutant reveals no major structural change as a consequence of amino acid substitution. The results may be rationalized in terms of mutational effects on both the folded and unfolded state of the protein. Site specific amino acid substitutions are useful in identifying specific regions of TS involved in association of non-native protein structures.

C-H…O hydrogen bond mediated chain reversal in a peptide containing g-amino acid residue, determined directly from powder X-ray diffraction data

The finding that peptides containing -amino acid residues give rise to folding patterns hitherto unobserved in -amino acid peptides[1] has stimulated considerable interest in the conformational properties of peptides built from , and residues,[2] as the introduction of additional methylene (CH2) units into peptide chains provides further degrees of conformational freedom.