Molecular orbital calculations on the conformation of amino acid residues of proteins

Structural Significance of Conformational Preferences and Ribose-Ring-Puckering of Hyper Modified Nucleotide 5'-Monophosphate 2-Methylthio Cyclic N6-Threonylcarbamoyladenosine (p-ms2ct6A) Present at 37th Position in Anticodon Loop of tRNALys

Structural significance of conformational preferences and ribose ring puckering of newly discovered hyper modified nucleotide, 5'-monophosphate 2-methylthio cyclic N⁶-threonylcarbamoyladenosine (p-ms²ct⁶A) have been investigated using quantum chemical semi-empirical RM1 and molecular dynamics simulation techniques. Automated geometry optimization of most stable structure of p-ms²ct⁶A has also been carried out with the help of abinitio (HF SCF, DFT) as well as semi empirical quantum chemical (RM1, AM1, PM3, and PM6) methods. Most stable structure of p-ms²ct⁶A is stabilized by intramolecular interactions between N(3)…HC(2'), N(1)…HC(16), O(13)…HC(15), and O(13)…HO(14). The torsion angles alpha (α) and beta (β) show the significant characteristic patterns with the involvement of intramolecular hydrogen bonding to provide stability to the p-ms²ct⁶A. Further, molecular dynamics simulations of p-ms²ct⁶A revealed the role of ribose sugar ring puckering i.e. C2'-endo and C3'-endo on the structural dynamics of ms²ct⁶A side chain. The modified nucleotide p-ms²ct⁶A periodically prefers both the C2'-endo and C3'-endo sugar with 'anti' and 'syn' conformations. This property of p-ms²ct⁶A could be useful to recognize the starting ANN codons. All atom explicit MD simulation of anticodon loop (ACL) of tRNA^Lys of Bacillus subtilis containing ms²ct⁶A at 37th position showed the U-turn feature, base stacking ability with other adjacent bases and hydrogen bonding interactions similar to the isolated base p-ms²ct⁶A. The ribose sugar puckering contributes to the orientation of the side chain conformation of p-ms²ct⁶A. Thus, the present study could be helpful to understand the structure-function relationship of the hypermodified nucleoside, ms²ct⁶A in recognition of the proper codons AAA/AAG during protein biosynthesis.

A comprehensive conformational space analysis of N-formyl-l-tryptophanamide system by using a genetic algorithm for multi-modal search

The conformational space of protected amino acid HCO-Tryptophane-NH₂ was explored by using a new optimization procedure, in order to localize the stable minima on its potential energy surface (PES). The genetic algorithm based on the Multi-Niche Crowding (MNC) technique was used initially to generate a set of optimized structures for title compound. Resulting structures from the genetic algorithm technique will be used hereafter as input conformers at a hierarchy of increasingly more accurate electronic structure calculations (RHF/6-31G+(d) and DFT/B3LYP/6-31G+(d) geometry optimizations). The lowest energy conformer γ_L(g+g+) presents a folded Backbone that is stabilized by strong hydrogen bond noted C₇. This links the carbonyl oxygen of the formyl group and the hydrogen of the amine group. There are further interactions from one hand between the carbonyl oxygen of the formyl group and the neighboring CH group on the pyrrole ring and from other hand between the N-terminus hydrogen and the indole ring in accordance with the experimental results. This work includes also a comparison between the theoretical calculations and the experimental results of X-ray crystallography extracted from protein data bank (PDB).

Single and multiple peptide γ-turns: literature survey and recent progress

Published data on peptide isolated and repetitive γ-turns are reviewed. Advancements in our laboratories on these 3D-structures are also presented.

Structural significance of hypermodified nucleic acid base hydroxywybutine (OHyW) which occur at 37th position in the anticodon loop of yeast tRNA(Phe)

Conformational preferences of hypermodified nucleic acid base hydroxywybutine (OHyW) have been studied using quantum chemical single point semi-empirical PM3 method. Automated geometry optimization using semi-empirical RM1, molecular mechanics force field (MMFF) along with ab-initio HF-SCF (6-31G** basis set) and DFT (B3LYP/6-31G** basis set) calculations have also been made to compare the salient features. Molecular electrostatic potentials (MEPs) depict the polarities of hydroxywybutine (OHyW) side chain. Another conformational study showed that hydroxywybutosine side chain interacts with adjacent bases within the anticodon loop of tRNA(Phe). The solvent accessible surface area (SASA) calculations revealed the structural role of hydroxywybutine in anticodon loop. Explicit molecular dynamics (MD) simulation has been done over the PM3 most stable structure of OHyW. The hydroxywybutine side chain prefers 'distal' conformation i.e. spreads away from the cyclic five membered imidazole moiety of modified tricyclic guanine base. The predicted preferred conformation of hydroxywybutine may prevent extended Watson-Crick base pairing during protein biosynthesis process. This conformation of OHyW stabilized by intramolecular interactions between O(6)⋯HO(16), O(6)⋯HC(15) and O(20)⋯HC(17). Further stabilization is also expected from interactions between O(22)⋯HC(16) and O(23)⋯HC(15). Explicit molecular dynamics (MD) simulation over the PM3 most stable structure of OHyW support the preferred geometry by preserving the 'distal' orientation of hydroxywybutine side chain and intramolecular hydrogen bonding interactions. MD simulation study revealed the role of hydroxyl group of OHyW to avoid fluctuations and prevent multiple iso-energetic conformations of hydroxywybutine side chain as compared to wybutine (yW).

Conformational preferences of modified nucleoside N(2)-methylguanosine (m(2)G) and its derivative N(2), N(2)-dimethylguanosine (m(2)(2)G) occur at 26th position (hinge region) in tRNA

Conformational preferences of the modified nucleosides N(2)-methylguanosine (m(2)G) and N(2), N(2)-dimethylguanosine (m(2)(2)G) have been studied theoretically by using quantum chemical perturbative configuration interaction with localized orbitals (PCILO) method. Automated complete geometry optimization using semiempirical quantum chemical RM1, along with ab initio molecular orbital Hartree-Fock (HF-SCF), and density functional theory (DFT) calculations has also been made to compare the salient features. Single-point energy calculation studies have been made on various models of m(2)G26:C/A/U44 and m(2)(2)G26:C/A/U44. The glycosyl torsion angle prefers "syn" (χ = 286°) conformation for m(2)G and m(2)(2)G molecules. These conformations are stabilized by N(3)-HC2' and N(3)-HC3' by replacing weak interaction between O5'-HC(8). The N(2)-methyl substituent of (m(2)G26) prefers "proximal" or s-trans conformation. It may also prefer "distal" or s-cis conformation that allows base pairing with A/U44 instead of C at the hinge region. Thus, N(2)-methyl group of m(2)G may have energetically two stable s-trans m(2)G:C/A/U or s-cis m(2)G:A/U rotamers. This could be because of free rotations around C-N bond. Similarly, N(2), N(2)-dimethyl substituent of (m(2)(2)G) prefers "distal" conformation that may allow base pairing with A/U instead of C at 44th position. Such orientations of m(2)G and m(2)(2)G could play an important role in base-stacking interactions at the hinge region of tRNA during protein biosynthesis process.

Iso-energetic multiple conformations of hypermodified nucleic acid base wybutine (yW) which occur at 37(th) position in anticodon loop of tRNA(Phe)

Conformational preferences of wybutine (yW) have been studied by quantum chemical semi-empirical Perturbative Configuration Interaction with Localized Orbitals (PCILO) and PM3 methods. Automated full geometry optimization by using RM1 along with ab-initio Hartree-Fock (HF-SCF) and Density Functional Theory (B3LYP/6-31G**) calculations have also been made to compare the salient features. Molecular dynamics (MD) simulation has been performed to see the solvation effect on wybutine side chain. The preferred conformations of wybutine side chain spreads away 'distal' from five membered imidazole moiety of tricyclic base. The intramolecular interactions provide stability to the preferred wybutine structure. The most stable and alternative stable structures obtained by PCILO and PM3 methods reveal that wybutine side chain may have multiple iso-energetic conformations. Molecular dynamics (MD) simulation study also confirms multiple conformations of wybutine side chain by showing regular periodical fluctuations over the 2 ns time period. These fluctuations occur when torsion angle α takes value ±90° and ±120° as observed in the most stable and alternative stable structures resulted by PCILO and PM3 methods. Such conformational behavior of wybutine may have certain implications on frameshifting to prevent extended Watson-Crick base pairing by maintaining proper codon-anticodon interactions during protein biosynthesis process.

Conformational study of methylphosphocholine: a prototype for phospholipid headgroups in membranes

Phospholipid bilayers constitute the largest structural component of cell membranes, in which choline phospholipids are abundant. In this study, through a theoretical sampling on a methylphosphocholine (MePC) potential energy surface, a set of conformers was selected as a prototype for the membrane phospholipid head. We performed a detailed conformational study of such a prototype, both as an isolated moiety and in a solvated system. We used the polarizable continuum model (PCM) to account for solvation effects. We used a quantum-mechanical methodology based on density functional theory (DFT) and the 6-31G(d,p) basis set for the calculations. Through this methodology we were able to obtain a set of conformations that presented a mirror-image pattern, in good agreement with the experimental geometric values for the different phosphocholine derivatives. Potential curves for the main parameters of the dihedral space of MePC were obtained and are provided to guide future force-field parameterizations.

Conformation of peptides constructed from achiral amino acid residues Aib and ?ZPhe: Computational study of the effect ofL/D- Leu at terminal positions

Conformational studies of the peptides constructed from achiral amino acid residues Aib and Delta(Z)Phe (I) Ac-Aib-Delta(Z)Phe-NHMe (II), and Ac-(Aib-Delta(Z)Phe)(3)-NHMe; peptides III-VI having L-Leu or D-Leu at either the N- or the C-terminal position and of peptides VII-X having Leu residues in different enantiomeric combinations at both the N- and the C-terminal positions in peptide II have been studied to design the peptide with the required helical sense. Peptide II, as expected, adopts degenerate left- and right-handed helical structures. It has been shown that the peptides IV and VI having D-Leu at either the N or the C terminus can be realized in the right-handed helical structure with the phi,psi values of -20 degrees and -60 degrees for the Aib/Delta(Z)Phe residues. L-Leu and D- Leu at both the terminals in peptides VII and VIII, respectively, have hardly any effect as both the left- and the right-handed structures are found to be degenerate. Peptides III and IX can be realized in right- and left-handed helical structures, respectively, in solvents of low polarity whereas peptides V and X are predicted to be in the right-handed helical structures stabilized by carbonyl-carbonyl interactions without the formation of hydrogen bonds. The conformational states with the phi,psi values of 0 degrees and -85 degrees in peptide V are characterized by rise per residue of 2.03 A, rotation per residue of 117.5 degrees , and 3.06 residues per turn. In all peptides having Leu residue at the N terminus, the methyl moiety of the acetyl group is involved in the CH/pi interactions with the Cepsilon--Cdelta edge of the aromatic ring of Delta(Z)Phe (3) and the amino group NH of Delta(Z)Phe is involved in the NH/pi interactions with its own aromatic ring. The CH(3) groups of the Aib residues are also involved in CH/pi interactions with the i + 1th and i + 3th Delta(Z)Phe's aromatic side chains.

Conformational preferences of the base substituent in hypermodified nucleotide queuosine 5'-monophosphate 'pQ' and protonated variant 'pQH+'

Conformational preferences of the base substituent in hypermodified nucleotide queuosine 5'-monophosphate 'pQ' and its protonated form 'pQH+' have been studied using quantum chemical Perturbative Configuration Interaction with Localized Orbitals PCILO method. The salient points have also been examined using molecular mechanics force field MMFF, parameterized modified neglect of differential overlap PM3 and Hartree Fock-Density Functional Theory HF DFT (pBP/DN*) approaches. Aqueous solvation of pQ and pQH+ has also been studied using molecular dynamics simulations. Consistent with the observed crystal structure, in isolated protonated form pQH+, the quaternary amine HN(13)(+)H, of the sidechain having 7-aminomethyl linkage, hydrogen bonds with the carbonyl oxygen O(10) of the base. However, N(13)H-O(10) hydrogen bonding is not preferred for unprotonated pQ, whether isolated or hydrated. Interaction between the 5'-phosphate and the 7-aminomethyl group is more likely for isolated pQ. The cyclopentenediol hydroxyl group O4"H may hydrogen bond with the O(10) in isolated pQ as well as in pQH+. The O4"H may hydrogen bond with the 5'-phosphate as well. The presence of -CH2-NH- and O"H groups in pQ and pQH+ allows interesting possibilities for intranucleotide hydrogen bonds and interactions across the anticodon loop. Simultaneous hydrogen bonds O2P-HN(13)+H-O(10) are indicated for hydrated pQH+. Unlike weak involvement of O4"H, these interactions also persist in hydrated pQH+ and may much reduce backbone flexibility. Resulting sub-optimal Q:C base pairing leads to unbiased reading of U or C as the third codon letter. Cyclopentenediol hydroxyl groups may interact with other biomolecules, allowing specific recognition. Prospective pQ(34) and pQ(34)H+ sites for codon-anticodon base pairing remain unhindered, but non canonical Q:G base pairing (amber-suppression) is ruled out.

Conformational preferences of anticodon 3'-adjacent hypermodified nucleic acid base cis-or trans-zeatin and its 2-methylthio derivative, cis-or trans- ms(2)zeatin

Conformational preferences of the hypermodified nucleic acid bases N6-(Delta(2)-cis-hydroxyisopentenyl)adenine, cis-io(6)Ade also known as cis-zeatin, and N(6)-(Delta(2)-trans-hydroxyisopentenyl)adenine, trans-io(6)ade or trans-zeatin, and 2-methylthio derivatives of these cis-ms(2)io(6)Ade or cis-ms(2)zeatin, and trans-ms(2)io6Ade or trans-ms(2)zeatin have been investigated theoretically by the quantum chemical Perturbative Configuration Interaction with Localized Orbitals (PCILO) method. Automated geometry optimization using quantum chemical MNDO, AM1 and PM3 methods has also been made to compare the salient features. The predicted most stable conformation of cis-io(6)Ade, trans-io(6)Ade, cis-ms(2)io(6)Ade and trans-ms(2)io(6)Ade are such that in each of these molecules the isopentenyl substituent spreads away (has "dista" conformation) from the five membered ring imidazole moiety of the adenine. The atoms N(6), C(10) and C(11) remain coplanar with the adenine ring in the predicted preferred conformation for each of these molecules. In cis-io(6)Ade as well as cis-ms(2)io(6)Ade the hydroxyl oxygen may participate in intramolecular hydrogen bonding with the H-C(10)-H group. In trans-io(6)Ade the hydroxyl group is oriented towards the H-C(2) instead. This orientation is retained in trans-ms(2)io(6)Ade, possible O-H...S hydrogen bonding may be a stabilizing factor. In all these four modified adenines C(11)-H is favourably placed to participate in intramolecular hydrogen bonding with N(1). In cis-ms(2)io(6)Ade as well as trans-ms(2)io(6)Ade the 2-methylthio group preferentially orients on the same side as C(2)-N(3) bond, due to this non-obstrusive placing, orientation of the hydroxyisopentenyl substituent remains unaffected by 2-methylthiolation. Thus the N(1) site remains shielded irrespective of the 2-methylthiolation status in these various cis-and trans-zeatin analogs alike. Firmly held orientation of hydroxyisopentenyl substituent in zeatin isomers and derivatives, in contrast to adaptable orientation of isopentenyl substituent in i(6)Ade and ms(2)i(6)Ade, may account for the increased efficiency of suppressor tRNA and reduced codon context sensitivity accompanied with the occurrence of ms(2)-zeatin (ms(2)io(6)Ade) modification.

Synthesis and NMR solution structure of an alpha-helical hairpin stapled with two disulfide bridges

Helical coiled-coils and bundles are some of the most common structural motifs found in proteins. Design and synthesis of alpha-helical motifs may provide interesting scaffolds that can be useful as host structures to display functional sites, thus allowing the engineering of novel functional miniproteins. We have synthesized a 38-amino acid peptide, alpha2p8, encompassing the alpha-helical hairpin present in the structure of p8MTCP1, as an alpha-helical scaffold particularly promising for its stability and permissiveness of sequence mutations. The three-dimensional structure of this peptide has been solved using homonuclear two-dimensional NMR techniques at 600 MHz. After sequence specific assignment, a total of 285 distance and 29 dihedral restraints were collected. The solution structure of alpha2p8 is presented as a set of 30 DIANA structures, further refined by restrained molecular dynamics, using simulated annealing protocol with the AMBER force field. The RMSD values for the backbone and all heavy atoms are 0.65+/-0.25 and 1.51+/-0.21 A, respectively. Excised from its protein context, the alpha-hairpin keeps its native structure: an alpha-helical coiled-coil, similar to that found in superhelical structures, with two helices spanning residues 4-16 and 25-36, and linked by a short loop. This motif is stabilized by two interhelical disulfide bridges and several hydrophobic interactions at the helix interface, leaving most of its solvent-exposed surface available for mutation. This alpha-helical hairpin, easily amenable to synthetic chemistry and biological expression system, may represent a stable and versatile scaffold to display new functional sites and peptide libraries.

Article

The ab initio conformational energy minima of the model tripeptide N-formyl-L-alanyl-L-alanine amide (ALA-ALA) were determined by ab initio RHF/4-21G and RHF/6-31G* gradient geometry refinement. For the current investigation, 11 664 RHF/4-21G structures were optimized, representing grid points in the four-dimensional (phi1, psi1, phi2, psi2) conformational space, which were constructed in 40° increments along the outer torsions phi1 and psi2 and in 30° increments along the inner torsions psi1 and phi2 of ALA-ALA. Two new energy minima, previously not reported, are described. The positions of the RHF/6-31G* energy minima in phi,psi-space can differ significantly from the corresponding RHF/4-21G locations, and both sets are not clustered in the centers but on the fringes of the most populated regions of phi, psi-space in protein crystal structures. Thus, the torsion angles of the ab initio energy minima are not those of the typical substructures of proteins: the most stable helices are not alphaR, and the torsion angles of the most stable bend forms are not those most frequently encountered in protein bends. Limitations of the dipeptide approximation are explored, illustrating how the conformational energies of an amino acid residue depend on the state of its neighbor.Key words: alanyl alanine amide, dipeptide approximation, model tripeptide, peptide models, structure of peptides.

Solution structure of human p8MTCP1, a cysteine-rich protein encoded by the MTCP1 oncogene, reveals a new alpha-helical assembly motif

MTCP1 (for Mature-T-Cell Proliferation) is the first gene unequivocally identified in the group of uncommon leukemias with a mature phenotype. The three-dimensional solution structure of the human p8(MTCP1) protein encoded by the MTCP1 oncogene was determined by homonuclear proton two-dimensional NMR methods at 600 MHz. After sequence specific assignments, a total of 931 distance restraints and 57 dihedral restraints were collected. The location of the three previously unassigned disulfide bridges was determined from preliminary DIANA structures, using a statistical analysis of intercystinyl distances. The solution structure of p8(MTCP1) is presented as a set of 30 DIANA structures, further refined by restrained molecular dynamics using a simulated annealing protocol with the AMBER force field. The r.m.s.d. values with respect to the mean structure for the backbone and all heavy atoms for a family of 30 structures are 0.73(+/-0.28) and 1.17(+/-0.23) A, when the structured core of the protein (residues 5 to 63) is considered. The solution structure of p8(MTCP1) reveals an original scaffold consisting of three alpha helices, associated with a new cysteine motif. Two of the helices are covalently paired by two disulfide bridges, forming an alpha-hairpin which resembles an antiparallel coiled-coil. The third helix is oriented roughly parallel to the plane defined by the alpha-antiparallel motif and its axis forms an angle of approximately 60 degrees with respect to the main axis of this motif.

Bayesian statistical analysis of protein side-chain rotamer preferences

We present a Bayesian statistical analysis of the conformations of side chains in proteins from the Protein Data Bank. This is an extension of the backbone-dependent rotamer library, and includes rotamer populations and average chi angles for a full range of phi, psi values. The Bayesian analysis used here provides a rigorous statistical method for taking account of varying amounts of data. Bayesian statistics requires the assumption of a prior distribution for parameters over their range of possible values. This prior distribution can be derived from previous data or from pooling some of the present data. The prior distribution is combined with the data to form the posterior distribution, which is a compromise between the prior distribution and the data. For the chi 2, chi 3, and chi 4 rotamer prior distributions, we assume that the probability of each rotamer type is dependent only on the previous chi rotamer in the chain. For the backbone-dependence of the chi 1 rotamers, we derive prior distributions from the product of the phi-dependent and psi-dependent probabilities. Molecular mechanics calculations with the CHARMM22 potential show a strong similarity with the experimental distributions, indicating that proteins attain their lowest energy rotamers with respect to local backbone-side-chain interactions. The new library is suitable for use in homology modeling, protein folding simulations, and the refinement of X-ray and NMR structures.

A pentapeptide model for an early folding step in the refolding of staphylococcal nuclease: the role of its turn propensity

Recently the folding of a staphylococcal nuclease (P117G) variant was examined with the hydrogen-deuterium (H-D) exchange technique. Many of the residues that showed significant protection are located in beta-sheet regions. About half the residues protected belong to an antiparallel beta-hairpin structure (residues 21-35) in the native structure. The beta-hairpin structure is formed by strands 2 and 3 of sheet 2 connected by the sequence 27Y KGQP31 in a type 1' reverse turn conformation with a 4-->1 hydrogen bonding between Q30 NH and Y27 C = O. We have targeted the conformational characterization of the peptide model Ac-YKGQP-NH2 with 1H two-dimensional nmr techniques in aqueous solution with a view to assessing its propensity to sample turn conformational forms and thus initiate the formation of beta-hairpin structure. Based upon the observed d alpha n (i, i + 1), d alpha n (i, i + 3), and dnn (i, i + 1) nuclear Overhauser effect connectivities, temperature coefficients for amide protons and conformational analysis with quantum mechanical perturbative configuration interaction over localized orbitals method, we conclude that the model peptide samples turn conformational forms with reduced conformational entropy. We suggest that the turn can nucleate the formation of the beta-hairpin structure in the refolding of nuclease. Observation of turn propensity for this sequence is consistent with the folding mechanism of the Greek key motif (present in Staphylococcal nuclease) proposed in the literature.

Deviations from planarity of the peptide bond in peptides and proteins

The work described here is the result of a survey of the peptide omega angles in the Cambridge Structural Database of small molecules, which was carried out to establish "ideal" or "target" values for their distribution. We have shown that substantial deviations from planarity can be tolerated with a standard deviation in the angle of up to 6 degrees about a mean value for the trans peptide that is less than 180 degrees . The distortion can arise from pyramidalization at the amino nitrogen atom as well as simple twist about the peptide bond. We include an analysis of omega angles in the existing database of protein structure (PDB) and show that their distributions can depend on the refinement method used, but no correlation with resolution is evident. A surprising finding was a systematic variation of omega in phi,psi space in proteins as well as in the linear and cyclic peptides. This is particularly manifest as a consistent difference between the mean omega values in chains of left and right-hand chirality. This dichotomy is observed for all the standard amino acids and is especially striking in the absence of secondary structure. The phenomenon is discussed in the context of theoretical work on peptide analogues, and the implications for protein conformation and structure are briefly considered.

Three-dimensional structure of the RGD-containing snake toxin albolabrin in solution, based on 1H NMR spectroscopy and simulated annealing calculations

Albolabrin is a snake toxin that contains a RGD-(Arg-Gly-Asp) sequence motif and competes with fibrinogen to bind to the integrin alpha IIb beta 3 (GpIIb-IIIa) on platelets. It thus inhibits platelet aggregation and cell-cell adhesion. It shows a high sequence similarity to other disintegrins, yet the reported disulfide bonding pattern for this peptide differs from that of others in this family. Recently we reported the assignment of the 1H-NMR spectrum of albolabrin and a preliminary description of its secondary structure [Jaseja, M., Smith, K.J., Lu, X. Williams, J.A., Trayer, H., Trayer, I.P. & Hyde, E.I. (1993) Eur. J. Biochem. 218, 853-860]. Here we present a more detailed description of the secondary and the tertiary structure, based on the 1H NMR results and simulated annealing methods. The structure of albolabrin in solution was calculated using 318 distance and 18 dihedral angle restraints. The average atomic RMS deviation between 12 refined structures and the mean structure was 3.1 A for the backbone. The protein appears to be highly mobile. Its structure is dominated by a series of turns and by three hairpins, each with a short region of distorted antiparallel beta-pleated sheet, held together by six disulfide bridges. The most well defined area is the hydrophobic core, residues 21-47 and 57-67, which is clustered around F40 and has a backbone atomic RMS deviation of only 1.3 A from the mean structure. The RGD adhesion sequence is found at the highly mobile tip of one of the beta-hairpins, protruding from the body of the protein. Many of these structural features are similar to those of other disintegrins, and differences in the disulfide bonding pattern of the disintegrins can be accomodated without significant energy penalty. Comparison of this structure with other proteins of similar function suggests that it is the RGD-loop, rather than the precise technology of the proteins, that is important to antagonist activity.

Hydrogen bonding and stacking of DNA bases: a review of quantum-chemical ab initio studies

Ab initio quantum-chemical calulations with inclusion of electron correlation made since 1994 (such reliable calculations were not feasible before) significantly modified our view on interactions of nucleic acid bases. These calculations allowed to perform the first reliable comparison of the strength of stacked and hydrogen bonded pairs of nucleic acid bases, and to characterize the nature of the base-base interactions. Although hydrogen-bonded complexes of nucleobases are primarily stabilized by the electrostatic interaction, the dispersion attraction is also important. The stacked pairs are stabilized by dispersion attraction, however, the mutual orientation of stacked bases is determined rather by the electrostatic energy. Some popular theories of stacking were ruled out: The theory based on attractive interactions of polar exocyclic groups of bases with delocalized electrons of the aromatic rings (Bugg et al., Biopolymers 10, 175 (1971), and the pi-pi interactions model (C.A. Hunter, J. Mol. Biol. 230, 1025 (1993)). The calculations demonstrated that amino groups of nucleobases are very flexible and intrinsically nonplanar, allowing hydrogen-bond-like interactions which are oriented out of the plane of the nucleobase. Many H-bonded DNA base pairs are intrinsically nonplanar. Higher-level ab initio calculations provide a unique set of reliable and consistent data for parametrization and verification of empirical potentials. In this article, we present a short survey of the recent calculations, and discuss their significance and limitations. This summary is written for readers which are not experts in computational quantum chemistry.

Non-planar structure of nitrous bases and non-coplanarity of Watson-Crick pairs

We discuss the non-planar structural stability of the NH2-group in formamide, cytosine, adenine, guanine and aniline molecules. Based on the microwave data available on small amino derivatives and on the results of PCILO conformation study it is shown that the slope of the amino group HNH plane to the molecular plane in nitrous bases should be close to 40 degrees. One of the main consequences of the non-planar structure of bases is a comparatively large (approximately equal to 15 degrees) propeller twisting of purine and pyrimidine planes in the complementary adenine-thymine and guanine-cytosine pairs. It is concluded that the non-coplanarity of single Watson-Crick base pairs is their intrinsic property. The specificity of hydrogen bonding in pairs along with stacking is believed to be the original cause of their peculiar packing in crystals and in DNA and RNA structures.

Conformational analysis of the tetrapeptide Pro-D-Phe-Pro-Gly in aqueous solution

Conformational investigations of the tetrapeptide Pro-D-Phe-Pro-Gly in water solution were carried out by 1H and 13C NMR spectroscopy. The internal proline residue allows for the possibility of cis/trans isomerization about the D-Phe-Pro peptide bond resulting in two conformational isomers. The major isomer was identified as the trans isomer. The pH-dependence of the cis/trans equilibrium supports an additional stabilisation of the trans isomer by an intramolecular ionic interaction between the amino- and carboxy-terminus in the zwitterionic state. Based on 13C spin-lattice relaxation times (T1), different pyrrolidine ring conformations of Pro1 and Pro3 could be determined. By combination of several NMR data (vicinal coupling constants 3JN alpha, temperature dependence of the NH chemical shifts, differences in the chemical shifts between the beta and gamma carbons of the proline residues) and energy minimization calculations, a type II' beta-turn should contribute considerably to the overall structure of the trans isomer.

Conformational preferences of modified nucleic acid bases N6-methyl-N6-(N-threonylcarbonyl) adenine and 2-methylthio-N6-(N-threonylcarbonyl) adenine by the quantum chemical PCILO calculations

Conformational preferences of the hypermodified nucleic acid bases N6-methyl-N6-(N-threonylcarbonyl) Adenine, m6tc6 Ade, and 2-methylthio-N6-(N-threonylcarbonyl) Adenine, mS2 tc6 Ade, have been studied theoretically using the quantum chemical PCILO (Perturbative Configuration Interaction using Localized Orbitals) method. The multidimensional conformational space has been searched using selected grid points formed by combining the various torsion angles which take the favoured values obtained from energy variation with respect to each torsion angle individually. In m6 tc6 Ade and mS 2tc6 Ade alike the threonylcarbonyl substituent preferably orients away (distal) from the imidazole moiety of the adenine ring. And as in the simpler N6-(N-threonylcarbonyl) Adenine, tc6 Ade, the atoms in the ureido group as well as the amino acid carbon atoms C(12) and C(13) remain coplanar with the purine base. As in tc6 Ade, this conformation is stabilized by the intramolecular hydrogen bond between N(11)H of the amino acid and N(1) of the adenine base. The N6-methyl protons, in m6 tc6 Ade, take trans-staggered orientation with respect to the C(6)-N(6) bond. The preferred orientation of the 2-methylthio group is cis to the C(2)-N(3) bond in mS 2tc6 Ade. This is in marked contrast to the modified nucleic acid base 2-methylthio-N6-(delta 2-isopentenyl) Adenine, mS 2i6 Ade, where the 2-methylthio group orients trans to the C(2)-N(3) bond, causing a change in the preferred orientation of the isopentenyl component on methylthiolation. The present results thus indicate that unlike in the isopentenyl adenine the role of further chemical substitutions in threonylcarbonyl adenine may be indirect and less pronounced.

Crystal structure of a protein-toxin alpha 1-purothionin at 2.5A and a comparison with predicted models

Alpha 1-Purothionin (alpha 1-P), a wheatgerm protein and lytic toxin, has a secondary and tertiary structure similar to that of crambin as revealed by CD and NMR studies. alpha 1-P crystallizes in the tetragonal space group 1422 with unit cell dimensions: a = b = 53.59 and c = 69.79 A. X-ray diffraction data have been measured to 2.5 A Bragg spacing. The crystal structure has been determined by molecular replacement methods, using an energy-minimized alpha 1-P model structure derived from crambin (Whitlow and Teeter: Journal of Biomolecular Structure and Dynamics 2:831-848, 1985, Journal of the American Chemical Society 108:7163-7172, 1986). The energy-minimized model gives a slightly cleaner rotation solution and better refinement against the x-ray data than do the crambin or unminimized alpha 1-P structures. The final crystallographic residual with the data in the 10-2.5 A resolution range is 0.216. The refined alpha 1-P structure has a backbone rms difference of 0.74 A from crambin and 0.55 A from the energy-minimized alpha 1-P model. A low resolution NMR model of alpha 1-P calculated from metric matrix distance geometry and restrained molecular dynamics differs from crambin's backbone by 2.3 A rms deviation (Clore et al.: EMBO Journal 5:2729-2735, 1986). Backbone dihedral angles for our predicted model differ from the refined alpha 1-P structure in only one region (at a turn where there is a deletion relative to crambin). The NMR model had differences in four regions.