Strong and weak hydrogen bonds in protein-ligand complexes of kinases: a comparative study

Strong and weak hydrogen bonds between protein and ligand are analyzed in a group of 233 X-ray crystal structures of the kinase family. These kinases are from both eukaryotic and prokaryotic organisms. The dataset comprises of 44 sub-families, out of which 35 are of human origin and the rest belong to other organisms. Interaction analysis was carried out in the active sites, defined here as a sphere of 10 A radius around the ligand. A majority of the interactions are observed between the main chain of the protein and the ligand atoms. As a donor, the ligand frequently interacts with amino acid residues like Leu, Glu and His. As an acceptor, the ligand interacts often with Gly, and Leu. Strong hydrogen bonds N-H...O, O-H...O, N-H...N and weak bonds C-H...O, C-H...N are common between the protein and ligand. The hydrogen bond donor capacity of Gly in N-H...O and C-H...O interactions is noteworthy. Similarly, the acceptor capacity of main chain Glu is ubiquitous in several kinase sub-families. Hydrogen bonds between protein and ligand form characteristic hydrogen bond patterns (supramolecular synthons). These synthon patterns are unique to each sub-family. The synthon locations are conserved across sub-families due to a higher percentage of conserved sequences in the active sites. The nature of active site water molecules was studied through a novel classification scheme, based on the extent of exposure of water molecules. Water which is least exposed usually participates in hydrogen bond formation with the ligand. These findings will help structural biologists, crystallographers and medicinal chemists to design better kinase inhibitors.     

Substitution reaction mechanisms of dihydrido-ruthenium(II) phosphine complexes: hydribe basicity and molecular hydrogen intermediates

Kinetic and activation parameter data for the reactions of cct-Ru(H)₂(CO)₂(PPh₃)₂ (1) (cct = cis, cis, trans) in THF with thiols, CO and PPh₃ to give cct-RuH(SR)(CO)₂(PPh₃)₂, Ru(CO)₃(PPh₃)₂ and Ru(CO)₂(PPh₃)₂, respectively, reveal a common, rate-determining step, the initial dissociation of H₂ from 1; the activated complex probably resembles the corresponding Ru(η²-H₂) species. Reaction of Ru(H)₂(dppm)₂ (2) (as a cis/trans mixture, DPPM = bis(diphenylphosphino)methane) with thiols initially generated cis- and trans- RuH(SR) (dppm)₂ with a rate that depends on both the type and concentration of thiol. The higher basicity of the hydride ligands in 2 (versus 1), which is demonstrated by deuterium exchange with CD₃OD, gives rise in the thiol reaction to an initial protonation step prior to loss of H₂. A species detected in the thiol reaction is possibly [RuH(η²-H₂ (dppm)₂]², the anticipated intermediate for this reaction and for the hydrogen exchange with alcohol. A longer reaction of 2 with PhCH₂SH gives solely cis-Ru(SCH₂Ph)₂(dppm)₂.     

Similarities between intra- and intermolecular hydrogen bonds in RNA kissing complexes found by means of cross-correlated relaxation

The bond lengths and dynamics of intra- and intermolecular hydrogen bonds in an RNA kissing complex have been characterized by determining the NMR relaxation rates of various double- and triple-quantum coherences that involve an imino proton and two neighboring nitrogen-15 nuclei belonging to opposite bases. New experiments allow one to determine the chemical shift anisotropy of the imino protons. The bond lengths derived from dipolar relaxation and the lack of modulations of the nitrogen chemical shifts indicate that the intermolecular hydrogen bonds which hold the kissing complex together are very similar to the intramolecular hydrogen bonds in the double-stranded stem of the RNA.     

Strong and weak coupling in mixed-valence complexes bridged by 4,4′-azo-di(phenylcyanamido)

The complexes [{Ru(tpy^∗)(bpy)}₂(μ-adpc)][PF₆]₂ where tpy^∗ is 4,4′,4″-tri-(tert-butyl)-2,2′:6′,2″-terpyridine, bpy is 2,2′-bipyridine, and adpc²⁻ is 4,4′-azo-diphenylcyanamide dianion and trans,trans-[{Ru(tpy^∗)(pc)}₂(μ-adpc)] where pc⁻ is 2-pyrazine-carboxylato were prepared and characterized by cyclic voltammetry and spectroelectrochemical methods. Intervalence band properties and IR spectroelectrochemistry of the mixed-valence complexes [{Ru(tpy^∗)(bpy)}₂(μ-adpc)]³⁺ and trans,trans-[{Ru(tpy^∗)(pc)}₂(μ-adpc)]⁺ are consistent with delocalized and valence-trapped mixed-valence properties respectively. The reduction in mixed-valence coupling upon substituting a bipyridine ligand with 2-pyrazine carboxylato strongly suggests that hole-transfer superexchange is the dominant mechanism for metal-metal coupling in these complexes.     

One and two dimensional 1H and 13C high resolution NMR investigation of lariat ethers and their alkali metal ionic complexes: a more tangible evidence for the presence of less common C-H***O hydrogen bonds

The possible existence of less common hydrogen bonds in three lariat ethers and their alkali-metal ionic complexes have been investigated with one- and two-dimensional (1D and 2D) proton and carbon-13 high resolution liquid state NMR spectroscopy. The occurrence of hydrogen-bonding induced by the addition of metal ions has been identified with the observation of indirect dipolar coupling between the coupling partners involved in the hydrogen-bonding. The addition of metal ions, moreover, causes appreciable change of chemical shift of several protons and carbons. The chemical shift change depends on the ion radius, larger ions causing smaller change. Moreover, the change of chemical shift is in coincidence with the occurrence of hydrogen-bonding. The values of the coupling constants have been obtained for each of these hydrogen bonds and were used for evaluating the hydrogen-bond strength. An intriguing and surprising observation is that a C-H***O hydrogen bond identified in solution by this work was not found in the previous study with X-ray diffraction or other methods.     

A computational analysis of some diaryl ureas in relation to their observed crystalline hydrogen bonding patterns

We have carried out anab initio self-consistent-field molecular orbital analysis of the structures, atomic charges and electrostatic potentials of 1,3-bisphenylurea, 1,3-bis(m-nitrophenyl)urea and 1,3-bis(p-nitrophenyl)urea. Our results provide insight into the contrasting hydrogen bond patterns and preferences of these molecules in crystalline environments. The tendency for 1,3-bisphenylurea to form homomeric rather than heteromeric (i.e. host-guest) crystals is attributed to a relatively strong and extended homomeric attractive electrostatic interaction between two like molecules. Our calculated internuclear distances and atomic charges indicate that these molecules have some degree of H...O intramolecular hydrogen bonding between the carbonyl oxygen and the nearest aromatic hydrogens when the aromatic and the urea portions of the molecules are coplanar. This interaction is strongest for the meta nitro derivative, consistent with the latter remaining very nearly planar in its cocrystal structures. Our surface electrostatic potentials for the three diaryl ureas are used to interpret their differing crystallization properties and tendencies to form cocrystals with guest molecules.     

Synthesis and characterization of transition metal fluoride complexes with imidazole: X-ray crystal structure reveals short hydrogen bonds between lattice water and lattice fluoride

A new series of complexes of cobalt(II) fluoride, nickel(II) fluoride, copper(II) fluoride and zinc(II) fluoride with imidazole were synthesized and characterized by elemental analysis, molar conductance, magnetic moments, IR and electronic absorption measurements. Based on elemental and spectral data, the complexes were found to be of [M(im)₆]F₂ · XH₂O type, where M is Co(II), Ni(II), Cu(II) and Zn(II) and X 4-5. The magnetic moments and spectral data suggested that all the complexes possessed an octahedral geometry. The crystal structure of the nickel complex, [Ni(im)₆]F₂ · 5H₂O, is also reported in which nickel atom is surrounded by six nitrogen atoms of imidazole. Strong intra- and inter-molecular hydrogen bonding exists between fluoride ions (uncoordinated), nitrogen of imidazole and the -OH of water molecules.     

Interhelical hydrogen bonds in transmembrane region are important for function and stability of Ca2+-transporting ATPase

Ca²⁺-transporting adenosine triphosphatase (ATPase) of sarcoplasmic reticulum couples ATP hydrolysis with ion transport. Phosphorylation of the cytosolic region of the calcium-bound conformation (E1) of the protein leads to drastic conformational rearrangements of the transmembrane helices and the release of Ca²⁺. The resulting calcium-free conformation (E2) is less stable than the E1 form. The changes in van der Waals interactions and interhelical hydrogen bonding in the E1 and E2 conformations were compared. Conformational changes in the transmembrane region concomitant with the release of Ca²⁺ mainly affect the number of interhelical hydrogen bonds, which is reduced to half of that in E1 form, whereas the number of interhelical atomic pairwise contacts reflecting van der Waals interactions experience little change. The interhelical hydrogen bonds in Ca²⁺-transporting ATPase can be divided into two groups according to their roles: those that play a structural stabilizing role and those that are important for the correct geometry of the Ca²⁺ binding site. Interhelical hydrogen bonds in the transmembrane regions play important roles for the stability and specificity of helix-helix interactions in proteins where change of conformation is required for transport of ions or small molecules.     

Structural and Thermodynamic Characterization of Pre- and Postpolymerization States in the F4 Fimbrial Subunit FaeG

Enterotoxigenic Escherichia coli expressing F4 fimbriae are the major cause of porcine colibacillosis and are responsible for significant death and morbidity in neonatal and postweaned piglets. Via the chaperone-usher pathway, F4 fimbriae are assembled into thin, flexible polymers mainly composed of the single-domain adhesin FaeG. The F4 fimbrial system has been labeled eccentric because the F4 pilins show some features distinct from the features of pilins of other chaperone-usher-assembled structures. In particular, FaeG is much larger than other pilins (27  versus ∼ 17 kDa), grafting an additional carbohydrate binding domain on the common immunoglobulin-like core. Structural data of FaeG during different stages of the F4 fimbrial biogenesis process, combined with differential scanning calorimetry measurements, confirm the general principles of the donor strand complementation/exchange mechanisms taking place during pilus biogenesis via the chaperone-usher pathway.     

Sequence and temperature effect on hydrogen bond disruption in DNA determined by a statistical analysis

We use the modified self-consistent phonon approximation theory to calculate temperature dependent interbase hydrogen bond disruption profiles for a number of six base pair repeating sequence infinite B-DNA polymers with various guanine-cytosine/adenine-thymine ratios. For comparison we also include results we have obtained in our earlier work on several B-DNA homopolymers, copolymers and a four-base-pair repeating sequence polymer. Our theory gives a statistical estimate of thermal fluctuational disruption probability of individual hydrogen bonds in individual base pairs in DNA as a function of temperature. The calculated probabilities show no sequence dependence at premelting temperatures, in agreement with proton exchange measurements. These probabilities however become very sensitive to base sequence at temperatures close to the observed melting temperatures. Multi-phasic critical transitions are found in which a portion of base pairs are disrupted at temperatures below the final disruption temperature. These transitions include localized as well as non-localized base pair opening. The localized transitions involve disruption of a few base-pairs at every other location without large scale base unstacking, and they may not appear in the observed UV curves with current resolution. On the other hand the overall disruption behavior is consistent with observations. The midpoint transition temperatures are close to the observed melting temperatures and these temperatures show the observed linear dependence on guanine-cytosine content. Our calculations indicate that our theory can be used effectively to calculate H-bond disruption behavior of different DNA sequences. Received: 20 February 1996 / Accepted: 2 May 1996     

Stability and fluctuations of amide hydrogen bonds in a bacterial cytochrome c: a molecular dynamics study

Molecular dynamics (MD) simulations on a bacterial cytochrome c were performed to investigate the lifetime and fluctuations of backbone hydrogen bonds and to correlate these data with protection factors for hydrogen exchange measured by NMR spectroscopy (Bartalesi et al. in Biochemistry, 42:10923–10930, 2003). The MD simulations provide a consistent pattern in that long lifetimes of hydrogen bonds go along with small amplitude fluctuations. In agreement with experiments, differences in stability were found with a rather flexible N-terminal segment as compared with a more rigid C-terminal part. Protection factors of backbone hydrogen exchange correlate strongly with the number of contacts but also with hydrogen-bond occupancy, hydrogen-bond survival times, as well as the inverse of fluctuations of backbone atoms and hydrogen-bond lengths derived from MD simulation data. We observed a conformational transition in the C-terminal loop, and significant motion in the N-terminal loop, which can be interpreted as being the structural units involved in the onset of the protein unfolding process in agreement with experimental evidence on mitochondrial cytochrome c. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users. Gernot Kieseritzky and Giulia Morra both contributed equally to this work.     

Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank

1. Download : Download high-res image (176KB)
2. Download : Download full-size image

     

Asymmetry in membrane protein sequence and structure: glycine outside rule

The growth in the number of known membrane protein structures enables us to conduct new statistical analyses that were not possible before. Using the recently developed Orientation of Protein in Membrane database that has explicit orientation information, here we address the asymmetry in sequence and structure of transmembrane helical proteins. We found that the Gly is markedly more populated at the outer side, the noncytoplasmic side, rather than the inner side, and that Lys, Arg, Leu, and Ile are biased toward the inner side. The asymmetry in Gly distribution is partly attributed to the fact that the coil is more populated in the outer side. Moreover, the frequency of Gly in the coil, but not in the helix, is weakly biased toward the outer side. The asymmetry in Gly distribution is confirmed by a genome-wide sequence-based analysis of membrane proteins accompanied by transmembrane helix prediction.     

Synthesis and structural characterization of Pd(II) complexes containing 2,6-bis[(dimethylamino)methyl]-4-methylphenolate ligand

Treatment of 2,6-bis[(dimethylamino)methyl]-4-methylphenol (1) with [Pd(PhCN)₂Cl₂] in a 1:1 molar ratio gives the mononuclear Pd(II) complex [PdCl₂(OC₆H₂(CH₂NMe₂)-2-Me-4-(CH₂NHMe₂)-6)] (2) containing one ligand with an ammonium hydrogen atom, which forms a bifurcated hydrogen bonding to the phenoxy oxygen and the chlorine atoms, as shown by the single crystal X-ray diffraction study. The reaction between the lithium salt of 1 and [Pd(COD)Cl₂] gives the mononuclear Pd(II) complex [Pd(OC₆H₂(CH₂NMe₂)₂-2,6-Me-4)₂] (3). The X-ray structure of 3 showed the presence of two ligands coordinated to one palladium metal center in a trans fashion with two dangling dimethylamine groups. The yield of the complex 3 was improved by carrying out the reaction between [Pd(OAc)₂] and 1 in acetone. The solid state structures of the complexes 2 and 3 were confirmed by ¹H, ¹³C, HETCOR NMR, IR and elemental analysis methods. The ¹H NMR spectra of 2 and 3 showed two different chemical shifts corresponding to the coordinated and uncoordinated amine groups of the ligand. No decoalescence of signals for the chelate ring puckering process was observed in variable-temperature NMR spectra.     

The self-diffusion and hydrogen bond interaction in neat liquid alkanols: a molecular dynamic simulation study

Self-diffusion of methanol, ethanol, 1-propanol and 2-propanol has been studied by molecular dynamics simulation in the temperature range between the melting pressure curve and 478 K at pressures up to 300 MPa. The simulation results on self-diffusion of methanol, ethanol and 2-propanol (for 2-propanol, at high temperatures) agree well with experiment, which suggests that the simulation method is a powerful tool to obtain self-diffusion coefficients over wide range of temperature and pressure, under which it is rather difficult for experiments. The local structures of methanol, ethanol and 2-propanol are investigated by calculating the radial distribution functions, H-bond numbers, coordination numbers and the ratios of H-bond number divided by coordination number. The correlation between self-diffusion and structural properties, and the influence of temperature and pressure on them are discussed. The degree of forming H-bond space network in methanol, ethanol and water is higher than that in 2-propanol, and they are all higher than those in ammonia and methylamine. The simulation results demonstrate that the effect of hydrogen bonding on the translational dynamics in methanol and ethanol is more pronounced than that in 2-propanol.     

Purification, stabilization, and concentration of very weak protein-protein complexes: Shifting the association equilibrium via complex selective adsorption on lowly activated supports

Very weak protein-protein interactions are very difficult to detect because these complexes could be under the detection limit or they tend to dissociate. Here, using as a model the antibody-antigen interaction weaken by the presence of dioxane, we have shown a strategy for the protein complexes purification by selective adsorption of the associated proteins. This strategy is based on the use of poorly activated anionic exchanger supports to selectively adsorb large complexes. This selective adsorption of the associated proteins shifted the association equilibrium of the soluble proteins toward the associated form. Thus, in the presence of 15% v/v dioxane, a concentration that is able to almost fully break the immunocomplex (less that 3% of the immunocomplex appeared associated when soluble antigen-antibody mixture was cross-linked with aldehyde-dextran), we can obtain more than 90% of the fully pure immunocomplex from the non-associated protein, adsorbed on anionic exchanger supports having a very low activation. This simple strategy may be a very useful tool to solve one of the most relevant challenges in the modern proteomics, the detection of very weak protein-protein interactions.     

Vibrational frequency shifts as a probe of hydrogen bonds: thermal expansion and glass transition of myoglobin in mixed solvents

The contribution of hydrogen bonds to protein-solvent interactions and their impact on structural flexibility and dynamics of myoglobin are discussed. The shift of vibrational peak frequencies with the temperature of myoglobin in sucrose/water and glycerol/water solutions is used to probe the expansion of the hydrogen bond network. We observe a characteristic change in the temperature slope of the O–H stretching frequency at the glass transition which correlates with the discontinuity of the thermal expansion coefficient. The temperature-difference spectra of the amide bands show the same tendency, indicating that stronger hydrogen bonding in the bulk affects the main-chain solvent interactions in parallel. However, the hydrogen bond strength decreases relative to the bulk solvent with increasing cosolvent concentration near the protein surface, which suggests preferential hydration. Weaker and/or fewer hydrogen bonds are observed at low degrees of hydration. The central O–H stretching frequency of protein hydration water is red-shifted by 40 cm^–1 relative to the bulk. The shift increases towards lower temperatures, consistent with contraction and increasing strength of the protein-water bonds. The temperature slope shows a discontinuity near 180 K. The contraction of the network has reached a critical limit which leads to frozen-in structures. This effect may represent the molecular mechanism underlying the dynamic transition observed for the mean square displacements of the protein atoms and the heme iron of myoglobin. Received: 10 July 1996 / Accepted: 10 April 1997     

A survey of hydrogen bond geometries in the crystal structures of amino acids

An analysis of the geometries of the hydrogen bonds observed by neutron diffraction in thirt-two crystal structures of amino acids shows the following results. Of the 168 hydrogen bonds in the data set, 64 involve the zwitterion groups 

and $\text{C}$O₂. Another 18 are from

to sulphate or carbonyl oxygens. The majority, 46, of these

H … O bonds are three-centered (bifurcated). Nine are four-centered (trifurcated). The geometry in which the three-centered hydrogen bond involves both oxygens of the same carboxylate group is not especially favoured. When it does occur, one hydrogen bond is generally shorter and the other longer, than when the bonding involves oxygens on different carboxylate groups. The shortest hydrogen bonds are the OH … O $\text{C}$, from a carboxylic acid hydroxyl to a carboxylate oxygen, and NH … O$\text{C}$ when the nitrogen is the ring atom in histidine or proline. Carboxylate groups, on average, accept six hydrogen bonds, with no examples of less than four bonds. The reason for the large number of three-centered

H … O$\text{C}$ bonds is therefore a proton deficiency arising from the disparity between the tripled donor property of the

groups and the sextuple, on average, acceptor property of the carboxylate groups. There is good geometrical evidence for the existence of H … O and H … Cl^? hydrogen bonds, especially involving the hydrogen atoms on α-atoms.     

Insights into metalloregulation by M-box riboswitch RNAs via structural analysis of manganese-bound complexes

The M-box riboswitch couples intracellular magnesium levels to expression of bacterial metal transport genes. Structural analyses on other riboswitch RNA classes, which typically respond to a small organic metabolite, have revealed that ligand recognition occurs through a combination of base-stacking, electrostatic, and hydrogen-bonding interactions. In contrast, the M-box RNA triggers a change in gene expression upon association with an undefined population of metals, rather than responding to only a single ligand. Prior biophysical experimentation suggested that divalent ions associate with the M-box RNA to promote a compacted tertiary conformation, resulting in sequestration of a short sequence tract otherwise required for downstream gene expression. Electrostatic shielding from loosely associated metals is undoubtedly an important influence during this metal-mediated compaction pathway. However, it is also likely that a subset of divalent ions specifically occupies cation binding sites and promotes proper positioning of functional groups for tertiary structure stabilization. To better elucidate the role of these metal binding sites, we resolved a manganese-chelated M-box RNA complex to 1.86 Å by X-ray crystallography. These data support the presence of at least eight well-ordered cation binding pockets, including several sites that had been predicted by biochemical studies but were not observed in prior structural analysis. Overall, these data support the presence of three metal-binding cores within the M-box RNA that facilitate a network of long-range interactions within the metal-bound, compacted conformation.