COPS--cis/trans peptide bond conformation prediction of amino acids on the basis of secondary structure information

SUMMARY: COPS predicts for all 20 naturally occurring amino acids whether the peptide bond in a protein is in cis or trans conformation. The algorithm is based only on secondary structure information of amino acid triplets without considering the amino acid sequence information. Conformation parameters are derived from solved 3D structures deposited in the PDB and led to propensities based on modified Chou-Fasman parameters. COPS analyses amino acid triplets taking only their respective secondary structure into consideration and upon application of a set of rules utilizing the conformation parameters, the N-terminal peptide bond conformation of the middle residue is predicted. COPS was tested on a random selection of protein datasets. AVAILABILITY: The COPS program and further information are freely available from the FMP website at http://www.fmp-berlin.de/nmr/cops CONTACT: labudde@fmp-berlin.de.     

Statistically significant dependence of the Xaa-Pro peptide bond conformation on secondary structure and amino acid sequence

Background  

A reliable prediction of the Xaa-Pro peptide bond conformation would be a useful tool for many protein structure calculation methods. We have analyzed the Protein Data Bank and show that the combined use of sequential and structural information has a predictive value for the assessment of the cis versus trans peptide bond conformation of Xaa-Pro within proteins. For the analysis of the data sets different statistical methods such as the calculation of the Chou-Fasman parameters and occurrence matrices were used. Furthermore we analyzed the relationship between the relative solvent accessibility and the relative occurrence of prolines in the cis and in the trans conformation.     

Splicing of unnatural amino acids into proteins: a peptide model study

S-Ethyl 2-azidohexanethioate (N3-Hex-SEt), an unnatural amino acid analog of leucine, is coupled with L-cysteine ethyl ester (NH2-Cys-OEt) to obtain N3-Hex-Cys-OEt by native chemical ligation. Coupling of this dipeptide with N-t-butoxycarbonyl-2-diphenylphosphinoethanethioglycinate produces the tripeptide, t-Boc-Gly-Hex-Cys-OEt, in high yield. These reactions suggest an approach for the incorporation of unnatural amino acids into proteins by successive native chemical ligation and Staudinger ligation.     

An atoms-in-molecules study of the genetically-encoded amino acids: I. Effects of conformation and of tautomerization on geometric, atomic, and bond properties

The theory of Atoms-In-Molecules (AIM) is a partitioning of the real space of a molecule into disjoint atomic constituents as determined by the topology of the electron density, rho(r). This theory identifies an atom in a molecule with a quantum mechanical open system and, consequently, all of the atom's properties are unambiguously defined. AIM recovers the basic empirical cornerstone of chemistry: that atoms and functional groups possess characteristic and additive properties that in many cases exhibit a remarkable transferability between different molecules. As a result, the theory enables the theoretical synthesis of a large molecule and the prediction of its properties by joining fragments that are predetermined as open systems. The present article is the first of a series (in preparation) that explore this possibility for polypeptides by determining the transferability of the building blocks: the amino acid residues. Transferability of group properties requires transferability of the electron density rho(r), which in turn requires the transferability of the geometric parameters. This article demonstrates that these parameters are conformation-insensitive for a representative amino acid, leucine, and that the atomic and bond properties exhibit a corresponding transferability. The effects of hydrogen bonding are determined and a set of geometrical conditions for the occurrence of such bonding is identified. The effects of transforming neutral leucine into its zwitter-ionic form on its atomic and bond properties are shown to be localized primarily to the sites of ionization.     

The effect of conformation on the CD of interacting helices: a theoretical study of tropomyosin

A recent report [M. E. Holtzer, et al. (1988) Biophysics Journal, 53, 96a] of the anomalous CD spectrum of the tropomyosin (TM) fragment 11TM127 motivated us to model the system as two 21-residue alpha-helices distorted to a coiled-coil conformation. We used strong-coupling exciton theory to model the optical properties of the system. Two backbone amide excited states (n pi* and pi pi*) were considered, as well as four excited states (Lb, La, Bb, Ba) for the phenolic side chain. We calculated the effect of superhelix formation on the backbone CD spectrum. The decrease in molar ellipticity of the alpha-helix parallel-polarized transition at 208 nm was found to be a simple function of superhelix tilt angle. We then modeled a coiled coil (radius = 5.5 A, pitch = -140 A) with one aromatic ring per superhelix. Steric interactions between aromatic side chains in a coiled coil were calculated as a function of side-chain conformation and heptet position. Steric interactions between phenolic rings will be significant for heptet positions a and d, but not for positions b, c, e, f, or g. We calculated the phenolic Lb transition rotational strength as a function of position within the heptet repeats, and of all possible side-chain dihedral angles, chi 1 and chi 2. When tyrosines were placed at heptet positions b, c, e, f, or g, the rotational-strength surface was nearly identical to that of a single tyrosine in an undistorted helix. In contrast, the rotational-strength surface for tyrosines in heptet positions a or d showed substantial intertyrosine coupling components. The rotational-strength surfaces for the three types of heptet positions (position a, position d, and the others) allowed an interpretation of the aromatic CD spectra of TM and its fragments. It was predicted that the three types of heptet positions will be spectroscopically distinguishable.     

Critical amino acids in the active site of meprin metalloproteinases for substrate and peptide bond specificity

The protease domains of the evolutionarily related alpha and beta subunits of meprin metalloproteases are approximately 55% identical at the amino acid level; however, their substrate and peptide bond specificities differ markedly. The meprin beta subunit favors acidic residues proximal to the scissile bond, while the alpha subunit prefers small or aromatic amino acids flanking the scissile bond. Thus gastrin, a peptide that contains a string of five Glu residues, is an excellent substrate for meprin beta, while it is not hydrolyzed by meprin alpha. Work herein aimed to identify critical amino acids in the meprin active sites that determine the substrate specificity differences. Sequence alignments and homology models, based on the crystal structure of the crayfish astacin, showed electrostatic differences within the meprin active sites. Site-directed mutagenesis of active site residues demonstrated that replacement of a hydrophobic residue by a basic amino acid enabled the meprin alpha protease to cleave gastrin. The meprin alphaY199K mutant was most effective; the corresponding mutation of meprin betaK185Y resulted in decreased activity toward gastrin. Peptide cleavage site determinations and kinetic analyses using a variety of peptides extended evidence that meprin alphaTyr-199/betaLys-185 are substrate specificity determinants in meprin active sites. These studies shed light on the molecular basis for the substrate specificity differences of astacin metalloproteinases.     

Differential geometry and protein conformation. V. Medium-range conformational influence of the individual amino acids

A previous differential geometric analysis of the conformational properties of the various amino acids has been extended to study their influence on folding over a larger backbone interval. In addition, statistical effects associated with variation in the number of the individual amino acids in the database have been treated in greater detail, using a simulation method. It is found that the amino acids can be divided into three groups on the basis of their conformational influence over four-C^α units in the interval i ? 6 ? j ? i + 6. Group Ia is composed of seven amino acids (His, Leu, Ala, Met, Lys, Gln, Ile) that encourage the formation of A_R-helical structure. Group Ib (Glu, Phe, Trp, Val, Asp) is composed of amino acids with some helix-forming tendency but that also show positive extended-strand formation tendency. They therefore act as a bridge between group Ia and group II (Cys, Gly, Asn, Pro, Arg, Ser, Thr, Tyr) that contains amino acids that encourage the formation of extended structure and bends. The detailed four-C^α conformational properties of each of the amino acids are shown, and the ability of amino acids to exert conformational influence in both directions along the backbone is examined. It is shown that, in general, such influence extends farther in the N-terminal direction than in the C-terminal direction. A framework is briefly sketched for using the present data to investigate actual folding mechanisms.     

Influence of amino acid and peptide counterions on the conformation of DNA

We describe fibre diffraction studies on the interaction of DNA with different amino acids and peptides. The B form of DNA, with ten base-pairs per turn, is always found at high levels of humidity. We suggest that this pitch is observed because the DNA molecules are maintained in a straight position. In solution, the DNA molecules are bent and may have a larger pitch. The A form of DNA is never found upon dehydration. Instead, the B form may be either stabilized by the counterions or altered so that the number of base-pairs per helical turn decreases upon dehydration. Alteration is favoured either by small counterions that have a single charge or by large basic polypeptides and proteins. Stabilization is favoured by small counterions that have several charged groups. A third type of behaviour is found with some amino acids that contain hydrophobic groups, which destabilize the secondary structure of DNA, probably due to a modification of its intramolecular interactions. We have not detected any specific effect of amino acid side-chains, although the amino acid sequence has a clear influence on the interaction. We think that these observations are of interest in the pursuit of more detailed crystallographic studies on protein-DNA interactions.     

A theoretical study on the stability of CNT encased cyclic peptide beyond hydrogen bond cut-off

The Carbon nanotubes (CNT) are potential candidate for many biomedical applications especially in targeted drug delivery for cancer diseases. However, the use of CNT has limitations due to its insolubility in aqueous media. The self-assembly of cyclic peptide encased on the CNT has enhanced its dispersion in aqueous medium which extend their applications as antibacterial and drug delivery agents. To understand this process, an attempt has been made to investigate the dynamics and stability of trimer cyclic peptide encasing with CNT using classical molecular dynamics. The model cyclic peptide monomer constitutes 14 series of amino acids viz.; (cyclo-[(D-ARG-L-VAL-D-ARG-L-THR-D-AGR-L-LYS-D-GLY-L-ARG-D-ARG-L-ILE-D-ARG-L-ILE-D-PRO-L-PRO)]). Each cyclic peptide in the assembly stacking far apart at approximately 15 Å each other beyond hydrogen bond cut-off distance. The trimer was observed to be stable only over 10 ns of entire MD trajectory. But when there is electrostatic interaction between cyclic peptides at 6.5 Å distance then assembly is stable for entire 50 ns. Our result reveals that for a stable assembly, beyond the hydrogen bond cut-off distance, the electrostatic interaction plays significant role.     

Optical properties of cyclic dimers of amino acids: An experimental and theoretical study

CD spectra have been measured in the vacuum-uv region to about 135 nm for cyclo(L alanyl-glycine), cyclo(L alanyl-L -alanine), and cyclo(L -prolyl-L -proline). In addition to the amide CD bands usually observed at wavelengths longer than 180 nm, a Independent systems calculations show that these intense short-wavelenght bands can be attributed to σσ* transitions of the backbone. Transitions of the amide chromophore expected at wavelenghts shorter than 180 nm cannot account for the observed CD.     

An FT-IR study of the beta-amyloid conformation: standardization of aggregation grade

The aggregation of beta-amyloid peptides is very important for their neurotoxic effect; standardization of the aggregation grade is necessary for biological experiments. Measurement of aggregation with physicochemical methods is a difficult task. The present work revealed that FT-IR can be used for studying the aggregation properties of beta-amyloid peptides and the effects of environmental variables (solvent, pH, ions, and temperature) on aggregation. In dimethyl sulfoxide or hexafluoroisopropanol, amyloid peptides are in a monomeric state; on dilution with phosphate buffer just before measurement is made, aggregation begins. A detailed two-dimensional FT-IR correlation spectroscopic study was made of the conformational transitions that occur during the aggregation of beta-amyloid peptides. Two processes (random/helix-to-beta-sheet and aggregation of beta-sheets) and multiple conformational states were observed before the most stable form was attained. beta-Amyloid peptides undergo decomposition in basic buffers containing Ca(2+); this process should be avoided during aging experiments.     

The circular dichroism of synthetic ribonucleic acids and the influence of uracil on conformation

We present CD spectra of four trinucleoside diphosphates, UpUpG, GpUpG, ApUpA, and ApUpG, of four single-stranded polymers, poly AC, poly GU, poly AU, and poly AdU, and of five double-stranded polymers, poly A:U, poly G:C, poly AU:AU, poly AdU:AdU, and poly GC:GC. The measured spectra are compared with empirical firstneighbor calculations. Our results, taken together with data from the literature, suggest that UpA and UpG sequences are relatively unstacked in a single-stranded RNA compared with these isolated dimers in solution. These sequences may influence the structure and function of natural RNAs. Our results on double-stranded RNAs indicate that the spectral changes which occur upon formation of a double helix are unique to the type of base pair involved and are relatively independent of sequence.     

The influence of extrusion on loss and racemization of amino acids

Summary. The influence of the operation conditions (temperature and residence time) of a thermic treatment on the total amount (free and protein-bound) of amino acid enantiomers of dry fullfat soya was investigated. Total amino acid content was determined using conventional ion-exchange amino acid analysis of total hydrolysates and chiral amino acid analysis was performed by HPLC after precolumn derivatization with o-phthaldialdehyde and 1-thio-β-D-glucose tetraacetate. Contrary to corn that was investigated previously, notable racemization was detected even at lower temperatures. At 140 °C the ratio of the D-enantiomer was 0.87% for glutamic acid, 2.81% for serine, and 1.92% for phenylalanine; at 220 °C the ratios of the D-enantiomer of the above amino acids were 1.43, 4.61, and 4.68%, respectively. The concentration of several L-amino acids decreased. At 220 °C there was 10% less L-glutamic acid, 17% less L-serine, 5% less L-phenylalanine, 6.6% less L-aspartic, acid and 21% less L-lysine than in the control; their loss can be assigned to different degrees of L – D conversion. While nearly complete transformation of L-phenylalanine can be attributed to racemization, the main cause of the loss of L-lysine is not racemization. The treatments in the same order of magnitude resulted in the formation of more D-amino acids and greater extent of racemization of amino acids in fullfat soya than that of maize. Authors’ address: J. Csapó, Faculty of Animal Science, Institute of Chemistry, University of Kaposvár, Guba S. u. 40., H-7400 Kaposvár, Hungary     

Polyproline II helix conformation in a proline-rich environment: a theoretical study

Interest centers here on whether a polyproline II helix can propagate through adjacent non-proline residues, and on shedding light on recent experimental observations suggesting the presence of significant PP(II) structure in a short alanine-based peptide with no proline in the sequence. For this purpose, we explored the formation of polyproline II helices in proline-rich peptides with the sequences Ac-(Pro)(3)-X-(Pro)(3)-Gly-Tyr-NH(2), with X = Pro (PPP), Ala (PAP), Gln (PQP), Gly (PGP), and Val (PVP), and Ac-(Pro)(3)-Ala-Ala-(Pro)(3)-Gly-Tyr-NH(2) (PAAP), by using a theoretical approach that includes a solvent effect as well as cis <--> trans isomerization of the peptide groups and puckering conformations of the pyrrolidine ring of the proline residues. Since (13)C chemical shifts have proven to be useful for identifying secondary-structure preferences in proteins and peptides, and because values of the dihedral angles (phi,psi) are the main determinants of their magnitudes, we have, therefore, computed the Boltzmann-averaged (13)C chemical shifts for the guest residues in the PXP peptide (X = Pro, Ala, Gln, Gly, and Val) with a combination of approaches, involving molecular mechanics, statistical mechanics, and quantum mechanics. In addition, an improved procedure was used to carry out the conformational searches and to compute the solvent polarization effects faster and more accurately than in previous work. The current theoretical work and additional experimental evidence show that, in short proline-rich peptides, alanine decreases the polyproline II helix content. In particular, the theoretical evidence accumulated in this work calls into question the proposal that alanine has a strong preference to adopt conformations in the polyproline II region of the Ramachandran map.     

Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts

We present a program, named Promega, to predict the Xaa-Pro peptide bond conformation on the basis of backbone chemical shifts and the amino acid sequence. Using a chemical shift database of proteins of known structure together with the PDB-extracted amino acid preference of cis Xaa-Pro peptide bonds, a cis/trans probability score is calculated from the backbone and ¹³C^β chemical shifts of the proline and its neighboring residues. For an arbitrary number of input chemical shifts, which may include Pro-¹³C^γ, Promega calculates the statistical probability that a Xaa-Pro peptide bond is cis. Besides its potential as a validation tool, Promega is particularly useful for studies of larger proteins where Pro-¹³C^γ assignments can be challenging, and for on-going efforts to determine protein structures exclusively on the basis of backbone and ¹³C^β chemical shifts.     

The influence of amino acids on the biomineralization of hydroxyapatite in gelatin

The effects of pH on the calcium phosphate phase, of Tris and of amino acids, such as aspartic acid, glutamic acid, and serine on hydroxyapatite formation and morphology, were studied in double diffusion experiments. In this system, hydroxyapatite was only formed when the pH was around 7.4 or higher for the duration of the reaction. A decrease in pH resulted in the transformation of hydroxyapatite to octacalcium phosphate. Amino acids and Tris or the buffering capacity of Tris have an effect on the morphology of the synthetic hydroxyapatite. The presence of the additive results in spheres consisting of needles, blades or plates depending on the reaction system.     

New tools for the control of peptide conformation and supramolecular chemistry: crown-carrier, C(alpha)-methyl L-DOPA amino acids

The preferred conformation of five, terminally protected, model peptide series to the hexamer level, based on three novel crowned, C(alpha)-methyl L-DOPA amino acids combined with either L-Ala/Aib or Gly/Aib, were assessed in structure supporting solvents using FT-IR absorption, (1)H NMR, and CD techniques. The FT-IR absorption spectra strongly suggest that the contribution of the crowned C(alpha)-tetrasubstituted residue to intramolecular H-bonding is equivalent to that of Aib and is much more significant than that of either L-Ala or Gly. In addition, the (1)H NMR titrations and the CD patterns resemble those typically exhibited by (right-handed) 3(10)-helical structures.