The occurrence of CH…O hydrogen bonds in α-helices and helix termini in globular proteins

Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases

The prevention of blood coagulation is important in treating thromboembolic disorders, and several serine proteases involved in the coagulation cascade have been classified as pharmaceutically relevant. Whereas structure-based drug design has contributed to the development of some serine protease inhibitors, traditional computational methods have not been able to fully describe structure-activity relationships (SAR). Here, we study the SAR for a number of serine proteases by using a method that calculates the thermodynamic properties (enthalpy and entropy) of the water that solvates the active site. We show that the displacement of water from specific subpockets (such as S1-4 and the ester binding pocket) of the active site by the ligand can govern potency, especially for cases in which small chemical changes (i.e., a methyl group or halogen) result in a substantial increase in potency. Furthermore, we describe how relative binding free energies can be estimated by combining the water displacement energy with complementary terms from an implicit solvent molecular mechanics description binding.

Hyperfine-shifted 13C resonance assignments in an iron-sulfur protein with quantum chemical verification: aliphatic C-H···S 3-center-4-electron interactions

Although the majority of noncovalent interactions associated with hydrogen and heavy atoms in proteins and other biomolecules are classical hydrogen bonds between polar N−H or O−H moieties and O atoms or aromatic π electrons, high-resolution X-ray crystallographic models deposited in the Protein Data Bank show evidence for weaker C−H···O hydrogen bonds, including ones involving sp³-hybridized carbon atoms. Little evidence is available in proteins for the (even) weaker C−H···S interactions described in the crystallographic literature on small molecules. Here, we report experimental evidence and theoretical verification for the existence of nine aliphatic (sp³-hybridized) C−H···S 3-center−4-electron interactions in the protein Clostridium pasteurianum rubredoxin. Our evidence comes from the analysis of carbon-13 NMR chemical shifts assigned to atoms near the iron at the active site of this protein. We detected anomalous chemical shifts for these carbon-13 nuclei and explained their origin in terms of unpaired spin density from the iron atom being delocalized through interactions of the type: C−H···S−Fe, where S is the sulfur of one of the four cysteine side chains covalently bonded to the iron. These results suggest that polarized sulfur atoms in proteins can engage in multiple weak interactions with surrounding aliphatic groups. We analyze the strength and angular dependence of these interactions and conclude that they may contribute small, but significant, stabilization to the molecule.

Investigation on the individual contributions of N-H...O=C and C-H...O=C interactions to the binding energies of beta-sheet models

In this article, the binding energies of 16 antiparallel and parallel beta-sheet models are estimated using the analytic potential energy function we proposed recently and the results are compared with those obtained from MP2, AMBER99, OPLSAA/L, and CHARMM27 calculations. The comparisons indicate that the analytic potential energy function can produce reasonable binding energies for beta-sheet models. Further comparisons suggest that the binding energy of the beta-sheet models might come mainly from dipole-dipole attractive and repulsive interactions and VDW interactions between the two strands. The dipole-dipole attractive and repulsive interactions are further obtained in this article. The total of N-H...H-N and C=O...O=C dipole-dipole repulsive interaction (the secondary electrostatic repulsive interaction) in the small ring of the antiparallel beta-sheet models is estimated to be about 6.0 kcal/mol. The individual N-H...O=C dipole-dipole attractive interaction is predicted to be -6.2 +/- 0.2 kcal/mol in the antiparallel beta-sheet models and -5.2 +/- 0.6 kcal/mol in the parallel beta-sheet models. The individual C(alpha)-H...O=C attractive interaction is -1.2 +/- 0.2 kcal/mol in the antiparallel beta-sheet models and -1.5 +/- 0.2 kcal/mol in the parallel beta-sheet models. These values are important in understanding the interactions at protein-protein interfaces and developing a more accurate force field for peptides and proteins.

Conformation dependence of the C(alpha)D(alpha) stretch mode in peptides. II. explicitly hydrated alanine peptide structures

Our previous studies of the potential utility of the C(alpha)D(alpha) stretch frequency, nu(CD), as a tool for determining conformation in peptide systems (Mirkin and Krimm, J Phys Chem A 2004, 108, 10923-10924; 2007, 111, 5300-5303) dealt with the spectroscopic characteristics of isolated alanine peptides with alpha(R), beta, and polyproline II structures. We have now extended these ab initio calculations to include various explicit-water environments interacting with such conformers. We find that the structure-discriminating feature of this technique is in fact enhanced as a result of the conformation-specific interactions of the bonding waters, in part due to our finding (Mirkin and Krimm, J Phys Chem B 2008, 112, 15268) that C(alpha)--D(alpha)...O(water) hydrogen bonds can be present in addition to those expected between water and the CO and NH of the peptide groups. In fact, nu(CD) is hardly affected by the latter bonding but can be shifted by up to 70 cm(-1) by the former hydrogen bonds. We also discuss the factors that will have to be considered in developing the molecular dynamics (MD) treatment needed to satisfactorily take account of the influence of outer water layers on the structure of the first-layer water molecules that hydrogen bond to the peptide backbone.

Inter-helical interactions in membrane proteins: analysis based on the local backbone geometry and the side chain interactions

The availability of a significant number of the structures of helical membrane proteins has prompted us to investigate the mode of helix-helix packing. In the present study, we have considered a dataset of alpha-helical membrane proteins representing structures solved from all the known superfamilies. We have described the geometry of all the helical residues in terms of local coordinate axis at the backbone level. Significant inter-helical interactions have been considered as contacts by weighing the number of atom-atom contacts, including all the side-chain atoms. Such a definition of local axis and the contact criterion has allowed us to investigate the inter-helical interaction in a systematic and quantitative manner. We show that a single parameter (designated as alpha), which is derived from the parameters representing the mutual orientation of local axes, is able to accurately capture the details of helix-helix interaction. The analysis has been carried out by dividing the dataset into parallel, anti-parallel, and perpendicular orientation of helices. The study indicates that a specific range of alpha value is preferred for interactions among the anti-parallel helices. Such a preference is also seen among interacting residues of parallel helices, however to a lesser extent. No such preference is seen in the case of perpendicular helices, the contacts that arise mainly due to the interaction of surface helices with the end of the trans-membrane helices. The study supports the prevailing view that the anti-parallel helices are well packed. However, the interactions between helices of parallel orientation are non-trivial. The packing in alpha-helical membrane proteins, which is systematically and rigorously investigated in this study, may prove to be useful in modeling of helical membrane proteins.

Peptide C(alpha)D(alpha) stretch frequencies in a hydrated conformation are perturbed mainly by C(alpha)-D(alpha)...O hydrogen bonding

We have shown (J. Phys. Chem. A 2004, 108, 10923; 2007, 111, 5300) that the C(alpha)D(alpha) stretch frequency, nu(CD), can discriminate between uniform alpha(R), beta, and polyproline II conformations of isolated peptides. Similar results for such peptides to which explicit waters are hydrogen bonded exhibit shifts in nu(CD) from those of the isolated structures. We demonstrate that the main source of these frequency shifts is the formation of C(alpha)-D(alpha)...O hydrogen bonds to water. Taking into account C-H...O(water) hydrogen bonding, together with the traditional bonding of peptide groups to water, can be expected to increase our understanding of the interaction of proteins with their aqueous environment.

Molecular interactions between pyrazine and n-propanol, chloroform, or tetrahydrofuran

The molecular interactions of pyrazine (PZ) with n-propanol, chloroform, and tetrahydrofuran (THF) have been investigated by employing ultraviolet spectroscopy and quantum chemical calculation methods. A new quantity, excess absorption coefficient, was introduced to represent the strength of the interaction. It was found that the interaction decreased in the order: PZ-propanol>PZ-chloroform>PZ-THF. The Benesi-Hildebrand method indicated that the interaction stoichiometries of the PZ-chloroform and PZ-THF systems were both 1:1 and the equilibrium constants were determined to be 2.07 and 0.64M(-1), respectively. Using a nonlinear fitting method, we demonstrated that the PZ-propanol was a two-step 1:2 interaction pair and the equilibrium constants were determined to be 8.8 and 0.19M(-1). Quantum chemical calculations showed the existence of hydrogen-bonding interactions in all the three system: normal Ncdots, three dots, centeredH-O hydrogen bond in the PZ-propanol system, unconventional Ncdots, three dots, centeredH-C hydrogen bond in the PZ-chloroform, and weak N-C-Hcdots, three dots, centeredO hydrogen bond in the PZ-THF system. Methodologically, we pointed out that special care must be taken when the Benesi-Hildebrand method is used to evaluate 1:2 interactions.

Are aromatic carbon donor hydrogen bonds linear in proteins?

Proteins fold and maintain structure through the collective contributions of a large number of weak, noncovalent interactions. The hydrogen bond is one important category of forces that acts on very short distances. As our knowledge of protein structure continues to expand, we are beginning to appreciate the role that weak carbon-donor hydrogen bonds play in structure and function. One property that differentiates hydrogen bonds from other packing forces is propensity for forming a linear donor-hydrogen-acceptor orientation. To ascertain if carbon-donor hydrogen bonds are able to direct acceptor linearity, we surveyed the geometry of interactions specifically involving aromatic sidechain ring carbons in a data set of high resolution protein structures. We found that while donor-acceptor distances for most carbon donor hydrogen bonds were tighter than expected for van der Waals packing, only the carbons of histidine showed a significant bias for linear geometry. By categorizing histidines in the data set into charged and neutral sidechains, we found only the charged subset of histidines participated in linear interactions. B3LYP/6-31G**++ level optimizations of imidazole and indole-water interactions at various fixed angles demonstrates a clear orientation dependence of hydrogen bonding capacity for both charged and neutral sidechains. We suggest that while all aromatic carbons can participate in hydrogen bonding, only charged histidines are able to overcome protein packing forces and enforce linear interactions. The implications for protein modeling and design are discussed.

Stabilization of the human beta2-adrenergic receptor TM4-TM3-TM5 helix interface by mutagenesis of Glu122(3.41), a critical residue in GPCR structure

G protein-coupled receptor (GPCR) instability represents one of the most profound obstacles in the structural study of GPCRs that bind diffusible ligands. The introduction of targeted mutations at nonconserved residues that lie proximal to helix interfaces has the potential to enhance the fold stability of the receptor helix bundle while maintaining wild-type receptor function. To test this hypothesis, we studied the effect of amino acid substitutions at Glu122(3.41) in the well-studied beta(2)-adrenergic receptor (beta(2)AR), which was predicted from sequence conservation to lie at a position equivalent to a tryptophan residue in rhodopsin at the 3,4,5 helix interface among transmembrane (TM) domains 3, 4, and 5. Replacement of Glu122(3.41) with bulky hydrophobic residues, such as tryptophan, tyrosine, and phenylalanine, increases the yield of functionally folded beta(2)AR by as much as 5-fold. Receptor stability in detergent solution was studied by isothermal denaturation, and it was found that the E122W and E122Y mutations enhanced the beta(2)AR thermal half-life by 9.3- and 6.7-fold, respectively, at 37 degrees C. The beta(1)AR was also stabilized by the introduction of tryptophan at Glu147(3.41), and the effect on protein behavior was similar to the rescue of the unstable wild-type receptor by the antagonist propranolol. Molecular modeling of the E122W and E122Y mutants revealed that the tryptophan ring edge and tyrosine hydroxyl are positioned proximal to the helical break in TM5 introduced by the conserved Pro211(5.50) and may stabilize the helix by interacting favorably with the unpaired carbonyl oxygen of Val206(5.45). Conformational flexibility of TM5 is likely to be a general property of class A GPCRs; therefore, engineering of the TM4-TM3-TM5 interface at the 3.41 position may provide a general strategy for the stabilization of other receptors.

Strength of Calpha-H...O=C hydrogen bonds in transmembrane proteins

A large number of Calpha-H...O contacts are present in transmembrane protein structures, but contribution of such interactions to protein stability is still not well understood. According to previous ab initio quantum calculations, the stabilization energy of a Calpha-H...O contact is about 2-3 kcal/mol. However, experimental studies on two different Calpha-H...O hydrogen bonds present in transmembrane proteins lead to conclusions that one contact is only weakly stabilizing and the other is not even stabilizing. We note that most previous computational studies were on optimized geometries of isolated molecules, but the experimental measurements were on those in the structural context of transmembrane proteins. In the present study, 263 Calpha-H...O=C contacts in alpha-helical transmembrane proteins were extracted from X-ray crystal structures, and interaction energies were calculated with quantum mechanical methods. The average stabilization energy of a Calpha-H...O=C interaction was computed to be 1.4 kcal/mol. About 13% of contacts were stabilizing by more than 3 kcal/mol, and about 11% were destabilizing. Analysis of the relationships between energy and structure revealed four interaction patterns: three types of attractive cases in which additional Calpha-H...O or N-H...O contact is present and a type of repulsive case in which repulsion between two carbonyl oxygen atoms occur. Contribution of Calpha-H...O=C contacts to protein stability is roughly estimated to be greater than 5 kcal/mol per helix pair for about 16% of transmembrane helices but for only 3% of soluble protein helices. The contribution would be larger if Calpha-H...O contacts involving side chain oxygen were also considered.

Structural properties of liquid N-methylacetamide via ab initio, path integral, and classical molecular dynamics

In order to better understand the physical interactions that stabilize protein secondary structure, the neat liquid state of a peptidic fragment, N-methylacetamide (NMA), was studied using computer simulation. Three different descriptions of the molecular liquid were examined: an empirical force field treatment with classical nuclei, an empirical force field treatment with quantum mechanical nuclei, and an ab initio density functional theory (DFT) treatment. The DFT electronic structure was evaluated using the BLYP approximate functional and a plane wave basis set. The different physical effects probed by the three models, such as quantum dispersion, many-body polarization, and nontrivial charge distributions on the liquid properties, were compared. Much of the structural ordering in the liquid is characterized by hydrogen bonded chains of NMA molecules. Modest structural differences are present among the three models of liquid NMA. The average molecular dipole in the liquid under the ab initio treatment, however, is enhanced by 60% over the gas phase value.

Contributions of NH...O and CH...O hydrogen bonds to the stability of beta-sheets in proteins

Ab initio quantum calculations are applied to both the parallel and the antiparallel arrangements of the beta-sheets of proteins. The energies of the NH...O and CH...O hydrogen bonds present in the beta-sheet are evaluated separately from one another by appropriate modifications of the model systems. The bond energies of these two sorts of hydrogen bonds are found to be very nearly equal in the parallel beta-sheet. The NH...O bonds are stronger than CH...O in the antiparallel geometry but only by a relatively small margin. Moreover, the former NH...O bonds are weakened when placed next to one another, as occurs in the antiparallel beta-sheet. As a result, there is little energetic distinction between the NH...O and CH...O bonds in the full antiparallel beta-sheet, just as in the parallel structure.

Structure and hydrogen bonding in neat N-methylacetamide: classical molecular dynamics and Raman spectroscopy studies of a liquid of peptidic fragments

The results of classical molecular dynamics (MD) simulations and Raman spectroscopy studies of neat liquid N-methylacetamide (NMA), the simplest model system relevant to the peptides, are reported as a function of temperature and pressure. The MD simulations predict that near ambient conditions, the molecules form a hydrogen bond network consisting primarily of linear chains. Both the links between molecules within the hydrogen-bonded chains and the associations between chains are stabilized by weak methyl-donated "improper" hydrogen bonds. The three-dimensional structural motifs observed in the liquid show some similarity to protein beta-sheets. The temperature and pressure dependence of the hydrogen bond network, as probed by the mode frequency of the experimentally determined amide-I Raman band, blue shifts on heating and red shifts under compression, respectively, suggesting weakened and enhanced hydrogen bonding in response to temperature and pressure increases. Disruption of the hydrogen-bonding network is clearly observed in the simulation data as temperature is increased, whereas the improper hydrogen bonding is enhanced under compression to reduce the energetic cost of increasing the packing fraction. Because of the neglect of polarizability in the molecular model, the computed dielectric constant is underestimated compared to the experimental value, indicating that the simulation may underestimate dipolar coupling in the liquid.

Relative strengths of NH..O and CH..O hydrogen bonds between polypeptide chain segments

Correlated ab initio calculations are used to compare the energetics when the CH and NH groups of the model dipeptide CHONHCH2CONH2 are each allowed to form a H-bond with the proton acceptor O of a peptide group. When the dipeptide is in its C7 conformation, the NH..O H-bond energy is found to be 7.4 kcal/mol, as compared to only 2.8 kcal/mol for the CH..O interaction. On the other hand, the situation reverses, and the CH..O H-bond becomes stronger than NH..O, when the dipeptide adopts a C5 structure. This reversal is important as C5 is nearly equal in stability to C7 for the dipeptide, and is representative of the commonly observed beta-sheet structure in a protein. Immersing the dipeptide-peptide pair in a model solvent weakens both sorts of H-bonds, and in a fairly uniform manner. Consequently, the trends observed in the in vacuo situation retain their validity in either aqueous solution or the protein interior. Likewise, the desolvation penalty, suffered by removing a H-bonded complex from water and placing it in the less polar interior of a protein, is quite similar for the NH..O and CH..O bonds.

Effect of solvent upon CH...O hydrogen bonds with implications for protein folding

The series of CH...O bonds formed between CF(n)H(4-n) (n = 0-3) and water are studied by quantum calculations under vacuum and in various solvents, including aqueous environment. The results are compared with the OH...O bond of the water dimer in the same solvents. Increasing polarity of the solvent leads in all cases to a lessening of the H-bond interaction energy, in a uniform fashion such that the CH...O bonds all remain weaker than OH...O in any solvent. These H-bond weakenings are coupled to a shortening of the inter-subunit separation. The contraction of the covalent CH bond to the bridging proton is reduced as the solvent becomes more polar, and the blue shift of its stretching vibration is likewise diminished. A process is considered that simulates protein folding by starting from a pair of noninteracting subunits in aqueous solvent and then goes to a H-bonded pair within the confines of a protein environment. This process is found to be energetically more favorable for some of the CH...O H-bonds than for the nominally stronger conventional OH...O H-bond. This finding suggests that CH...O bonds can make important energetic contributions to protein folding, on par with those made by traditional H-bonds.

Geometry of nonbonded interactions involving planar groups in proteins

Although hydrophobic interaction is the main contributing factor to the stability of the protein fold, the specificity of the folding process depends on many directional interactions. An analysis has been carried out on the geometry of interaction between planar moieties of ten side chains (Phe, Tyr, Trp, His, Arg, Pro, Asp, Glu, Asn and Gln), the aromatic residues and the sulfide planes (of Met and cystine), and the aromatic residues and the peptide planes within the protein tertiary structures available in the Protein Data Bank. The occurrence of hydrogen bonds and other nonconventional interactions such as C-H...pi, C-H...O, electrophile-nucleophile interactions involving the planar moieties has been elucidated. The specific nature of the interactions constraints many of the residue pairs to occur with a fixed sequence difference, maintaining a sequential order, when located in secondary structural elements, such as alpha-helices and beta-turns. The importance of many of these interactions (for example, aromatic residues interacting with Pro or cystine sulfur atom) is revealed by the higher degree of conservation observed for them in protein structures and binding regions. The planar residues are well represented in the active sites, and the geometry of their interactions does not deviate from the general distribution. The geometrical relationship between interacting residues provides valuable insights into the process of protein folding and would be useful for the design of protein molecules and modulation of their binding properties.

Propensities of polar and aromatic amino acids in noncanonical interactions: nonbonded contacts analysis of protein-ligand complexes in crystal structures

The nonbonded contacts analysis of 14 polar and aromatic amino acid side chains was carried out for protein-ligand complexes derived from the crystal structures in the Protein Data Bank. Through the exhaustive analysis, several unusual contacts were observed as well as the well-known interactions. CH-S interactions were frequently found in Met-related contacts, which have not yet been the subject of systematic investigations. We have also described the propensity of each amino acid for nonbonded interactions. All amino acids studied in this work showed high frequencies for the canonical hydrogen-bonding NH-O, OH-N, and OH-O interactions, while the preferences in noncanonical interactions such as CH- pi interactions were not always consistent among the side chains with similar characteristics. Understanding such amino acid side chain propensities is important for improving the accuracy of structure-based drug design, and this study will open new possibilities for developing unique compounds with high binding affinity.

Structure of the extended diarrhea-inducing domain of rotavirus enterotoxigenic protein NSP4

Rotavirus nonstructural protein 4 (NSP4) is a multidomainal and multifunctional protein and is recognized as the first virus-encoded enterotoxin. Extensive efforts to crystallize the complete cytoplasmic tail (CT), which exhibits all the known biological functions, have been unsuccessful, and to date, the structure of only a synthetic peptide corresponding to amino acids (aa) 95-137 has been reported. Recent studies indicate that the interspecies-variable domain (ISVD) from aa 135 to 141 as well as the extreme C-terminus are critical determinants of virus virulence and the diarrhea-inducing ability of the protein. Among the five NSP4 genotypes identified, those belonging to genotypes A1, B and C possess either a proline at position 138 or a glycine at 140, while those of A2, D and E lack these residues in the ISVD, suggesting conformational differences in this region among different NSP4s. Here, we examined the crystallization properties of several deletion mutants and report the structure of a recombinant mutant, NSP4:95-146, lacking the N-terminal 94 and C-terminal 29 aa, from SA11 (A1) and I321 (A2) at 1.67 and 2.7 A, respectively. In spite of the high resolution of one of the structures, electron density for the C-terminal 9 residues could not be seen for either of the mutants, and the crystal packing resulted in the creation of a clear empty space for this region. Extension of the unstructured C-terminus beyond aa 146 hindered crystallization under the experimental conditions. The present structure revealed significant differences from that of the synthetic peptide in the conformation of amino acids at the end of the helix as well as the crystal packing owing to the additional space required to accommodate the un structured virulence-determining region. The crystal structure and secondary structure prediction of the NSP4:95-146 mutants from different genotypes suggest that the region C-terminal to aa 137 in all the NSP4 proteins is likely to be unstructured, and this might be of structural and biological functional significance.

Interaction geometry involving planar groups in protein-protein interfaces

The geometry of interactions of planar residues is nonrandom in protein tertiary structures and gives rise to conventional, as well as nonconventional (X--H...pi, X--H...O, where X = C, N, or O) hydrogen bonds. Whether a similar geometry is maintained when the interaction is across the protein-protein interface is addressed here. The relative geometries of interactions involving planar residues, and the percentage of contacts giving rise to different types of hydrogen bonds are quite similar in protein structures and the biological interfaces formed by protein chains in homodimers and protein-protein heterocomplexes--thus pointing to the similarity of chemical interactions that occurs during protein folding and binding. However, the percentage is considerably smaller in the nonspecific and nonphysiological interfaces that are formed in crystal lattices of monomeric proteins. The C--H...O interaction linking the aromatic and the peptide groups is quite common in protein structures as well as the three types of interfaces. However, as the interfaces formed by crystal contacts are depleted in aromatic residues, the weaker hydrogen bond interactions would contribute less toward their stability.

Catalytic roles for carbon-oxygen hydrogen bonding in SET domain lysine methyltransferases

SET domain enzymes represent a distinct family of protein lysine methyltransferases in eukaryotes. Recent studies have yielded significant insights into the structural basis of substrate recognition and the product specificities of these enzymes. However, the mechanism by which SET domain methyltransferases catalyze the transfer of the methyl group from S-adenosyl-L-methionine to the lysine epsilon-amine has remained unresolved. To elucidate this mechanism, we have determined the structures of the plant SET domain enzyme, pea ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit methyltransferase, bound to S-adenosyl-L-methionine, and its non-reactive analogs Aza-adenosyl-L-methionine and Sinefungin, and characterized the binding of these ligands to a homolog of the enzyme. The structural and biochemical data collectively reveal that S-adenosyl-L-methionine is selectively recognized through carbon-oxygen hydrogen bonds between the cofactor's methyl group and an array of structurally conserved oxygens that comprise the methyl transfer pore in the active site. Furthermore, the structure of the enzyme co-crystallized with the product epsilon-N-trimethyllysine reveals a trigonal array of carbon-oxygen interactions between the epsilon-ammonium methyl groups and the oxygens in the pore. Taken together, these results establish a central role for carbon-oxygen hydrogen bonding in aligning the cofactor's methyl group for transfer to the lysine epsilon-amine and in coordinating the methyl groups after transfer to facilitate multiple rounds of lysine methylation.

Probing the nature of hydrogen bonds in DNA base pairs

Energy decomposition analyses based on the block-localized wave-function (BLW-ED) method are conducted to explore the nature of the hydrogen bonds in DNA base pairs in terms of deformation, Heitler-London, polarization, electron-transfer and dispersion-energy terms, where the Heitler-London energy term is composed of electrostatic and Pauli-exchange interactions. A modest electron-transfer effect is found in the Watson-Crick adenine-thymine (AT), guanine-cytosine (GC) and Hoogsteen adenine-thymine (H-AT) pairs, confirming the weak covalence in the hydrogen bonds. The electrostatic attraction and polarization effects account for most of the binding energies, particularly in the GC pair. Both theoretical and experimental data show that the GC pair has a binding energy (-25.4 kcal mol(-1) at the MP2/6-31G** level) twice that of the AT (-12.4 kcal mol(-1)) and H-AT (-12.8 kcal mol(-1)) pairs, compared with three conventional N-H...O(N) hydrogen bonds in the GC pair and two in the AT or H-AT pair. Although the remarkably strong binding between the guanine and cytosine bases benefits from the opposite orientations of the dipole moments in these two bases assisted by the pi-electron delocalization from the amine groups to the carbonyl groups, model calculations demonstrate that pi-resonance has very limited influence on the covalence of the hydrogen bonds. Thus, the often adopted terminology "resonance-assisted hydrogen bonding (RHAB)" may be replaced with "resonance-assisted binding" which highlights the electrostatic rather than electron-transfer nature of the enhanced stabilization, as hydrogen bonds are usually regarded as weak covalent bonds.

Characterization of β-turn and Asx-turns mimicry in a model peptide: Stabilization via CH · · · O interaction

The chemical synthesis and single-crystal X-ray diffraction analysis of a model peptide, Boc-Thr-Thr-NH2 (1) comprised of proteinogenic residues bearing an amphiphilic Cbeta -stereogenic center, has been described. Interestingly, the analysis of its molecular structure revealed the existence of a distinct conformation that mimics a typical beta-turn and Asx-turns, i.e., the two Thr residues occupy the left- and right-corner positions. The main-chain torsion angles of the N- and C-terminal residues i.e., semiextended: phi = -68.9 degrees , psi = 128.6 degrees ; semifolded: phi = -138.1 degrees , psi = 2.5 degrees conformations, respectively, in conjunction with a gauche- disposition of the obligatory C-terminus Thr CgammaH3 group, characterize the occurrence of the newly described beta-turn- and Asx-turns-like topology. The preferred molecular structure is suggested to be stabilized by an effective nonconventional main-chain to side-chain Ci=O . . . H--Cgamma(i+2)-type intraturn hydrogen bond. Noteworthy, the observed topology of the resulting 10-membered hydrogen-bonded ring is essentially similar to the one perceived for a classical beta-turn and the Asx-turns, stabilized by a conventional intraturn hydrogen bond. Considering the signs as well as magnitudes of the backbone torsion angles and the orientation of the central peptide bond, the overall mimicked topology resembles the type II beta-turn or type II Asx-turns. An analysis of Xaa-Thr sequences in high-resolution X-ray elucidated protein structures revealed the novel topology prevalence in functional proteins (unpublished). In view of indubitable structural as well as functional importance of nonconventional interactions in bioorganic and biomacromolecules, we intend to highlight the participation of Thr CgammaH in the creation of a short-range C=O . . . H--Cgamma -type interaction in peptides and proteins.

The environment of amide groups in protein–ligand complexes: H-bonds and beyond

A comprehensive structural analysis of interactions involving amide NH and C=O groups in protein-ligand complexes has been performed based on 3,275 published crystal structures (resolution < or =2.5 A). Most of the amide C=O and NH groups at the protein-ligand interface are highly buried within the binding site and involved in H-bonds with corresponding counter-groups. Small percentages of C=O and NH groups are solvated or embedded in hydrophobic environments. In particular, C=O groups show a higher propensity to be solvated or embedded in a hydrophobic environment than NH groups do. A small percentage of carbonyl groups is involved in weak hydrogen bonds with CH. Cases of dipolar interactions, involving carbonyl oxygen and electrophilic carbon atoms, such as amide, amidinium, guanidium groups, are also identified. A higher percentage of NH are in contact with aromatic carbons, interacting either through hydrogen bonds (preferably with the NH group pointing towards a ring carbon atom) or through stacking between amide plane and ring plane. Comprehensive studies such as the present one are thought to be important for future improvements in the molecular design area, in particular for the development of new scoring functions. [Figure: see text].

3(10)-Helix adjoining alpha-helix and beta-strand: sequence and structural features and their conservation

Does the amino acid use at the terminal positions of an alpha-helix become altered depending on the context-more specifically, when there is an adjoining 3(10)-helix, and can a single helical cylinder encompass the resultant composite helix? An analysis of 138 and 107 cases of 3(10)-alpha and alpha-3(10) composite helices, respectively, found in known protein structures indicate that the secondary structural element occurring first imposes its characteristics on the sequence of the structural element coming next. Thus, when preceded by a 3(10)-helix, the preference of proline to occur at the N1 position of an alpha-helix is shifted to the N2 position, a typical characteristic of the C-terminal capping of the 3(10)-helix. When an alpha- or a 3(10)-helix leads into a helix of the other type, there is a bend at the junction, especially for the 3(10)-alpha composite, with the two junction residues facing inward and buried within the structure. Thus a single helical cylinder may not properly represent a composite helix, the bend providing a means for the tertiary structure to assume a globular shape, very much akin to what a proline-induced kink does to an alpha-helix. The tertiary structural context in which beta-3(10) and 3(10)-beta composites occurs can be different, causing the angle between the secondary structural elements in the two cases to be different. Composites of 3(10)-helices and beta-strands are much more conserved among members in families of homologous structures than those between two types of helices; in many of the former instances, the 3(10)-helix constitutes the loops in beta-hairpin or beta-beta-corner motifs. The overall fold of the chain may be more conserved than the actual identify of the secondary structure elements in a composite.

Short hydrogen bonds in proteins

Short hydrogen bonds are present in many chemical and biological systems. It is well known that these short hydrogen bonds are found in the active site of enzymes and aid enzyme catalysis. This study aims to systematically characterize all short hydrogen bonds from a nonredundant dataset of protein structures. The study has revealed that short hydrogen bonds are commonly found in proteins and are widely present in different regions of the protein chain, such as the backbone or side chain, and in different secondary structural regions such as helices, strands and turns. The frequency of occurrence of donors and acceptors from the charged side chains as well as from the neutral backbone atoms is equally high. This suggests that short hydrogen bonds in proteins occur either due to increased strength or due to geometrical constraints and this has been illustrated from several examples.

Helix packing motif common to the crystal structures of two undecapeptides containing dehydrophenylalanine residues: Implications for the de novo design of helical bundle super secondary structural modules

De novo designed peptide based super secondary structures are expected to provide scaffolds for the incorporation of functional sites as in proteins. Self-association of peptide helices of similar screw sense, mediated by weak interactions, has been probed by the crystal structure determination of two closely related peptides: Ac-Gly1-Ala2-Delta Phe3-Leu4-Val5-DeltaPhe6-Leu7-Val8-DeltaPhe9-Ala10-Gly11-NH2 (I) and Ac-Gly1-Ala2-DeltaPhe3-Leu4-Ala5-DeltaPhe6-Leu7-Ala8-DeltaPhe9-Ala10-Gly11-NH2 (II). The crystal structures determined to atomic resolution and refined to R factors 8.12 and 4.01%, respectively, reveal right-handed 3(10)-helical conformations for both peptides. CD has also revealed the preferential formation of right-handed 3(10)-helical conformations for both molecules. Our aim was to critically analyze the packing of the helices in the solid state with a view to elicit clues for the design of super secondary structural motifs such as two, three, and four helical bundles based on helix-helix interactions. An important finding is that a packing motif could be identified common to both the structures, in which a given peptide helix is surrounded by six other helices reminiscent of transmembrane seven helical bundles. The outer helices are oriented either parallel or antiparallel to the central helix. The helices interact laterally through a combination of N--H...O, C--H...O, and C--H...pi hydrogen bonds. Layers of interacting leucine residues are seen in both peptide crystal structures. The packing of the peptide helices in the solid state appears to provide valuable leads for the design of super secondary structural modules such as two, three, or four helix bundles by connecting adjacent antiparallel helices through suitable linkers such as tetraglycine segments.