Conformational investigation of alpha,beta-dehydropeptides. N-acetyl-(E)-dehydrophenylalanine N'-methylamide: conformational properties from infrared and theoretical studies, part XIV.

N-Acetyl-(E)-dehydrophenylalanine N'-methylamide [Ac-(E)-DeltaPhe-NHMe], one of a few representative (E)-alpha,beta-dehydroamino acids, was studied by FTIR in dichloromethane and acetonitrile. To support spectroscopic interpretations and to gain some deeper insight into the Ac-(E)-DeltaPhe-NHMe molecule, the Ramachandran potential energy surface was calculated by the B3LYP/6-31G*//HF/3-21G method and the conformers localized were fully optimized at the B3LYP/6-31 + G** level. The spectra and calculations were compared with those of the related molecules Ac-DeltaAla-NHMe and Ac-(Z)-DeltaPhe-NHMe. The title compound assumes two conformational states in equilibrium in dichloromethane solution with a predominance of the extended conformer E. The Ac-(E)-DeltaPhe-NHMe spectrum is like that of Ac-DeltaAla-NHMe, particularly in the region of bands AI and AII, and unlike that of Ac-(Z)-DeltaPhe-NHMe. The positions of bands AI and II together with the nu(s)(N1--H1) band proves that the conformers E of both DeltaAla and (E)-DeltaPhe compounds are stabilized by the quite strong C5 hydrogen bonds N1--H1...O2. The same conclusion is drawn from the Ramachandran diagrams. The conformers E of both compounds are placed in the global minima and the gaps in energy order between them and the second conformer are large. The conformers E of DeltaAla and (E)-DeltaPhe, apart from the N1--H1...O2 hydrogen bond, show the Cbeta--H...O1 interaction, and Ac-(E)-DeltaPhe-NHMe displays the NH/pi interaction with the N2--H2 projecting in the first carbon atom of the phenyl ring. The C5 hydrogen bond is stronger in (E)-DeltaPhe than that in the DeltaAla compound. This is in agreement with interactions found in the calculated structures and can be explained by the influence of the phenyl ring in position (E). In acetonitrile, the molecule of Ac-(E)-DeltaPhe-NHMe loses its C5 hydrogen bond and becomes unfolded, whereas that of Ac-DeltaAla-NHMe does not vary practically. Adopting conformation E in a non-polar solvent seems to be a general feature of the (E)-DeltaXaa residues.     

High‐resolution crystal structures reveal a mixture of conformers of the Gly61‐Asp62 peptide bond in an oxidized flavodoxin from Bacillus cereus

Flavodoxins (Flds) are small proteins that shuttle electrons in a range of reactions in microorganisms. Flds contain a redox‐active cofactor, a flavin mononucleotide (FMN), and it is well established that when Flds are reduced by one electron, a peptide bond close to the FMN isoalloxazine ring flips to form a new hydrogen bond with the FMN N5H, stabilizing the one‐electron reduced state. Here, we present high‐resolution crystal structures of Flavodoxin 1 from Bacillus cereus in both the oxidized (ox) and one‐electron reduced (semiquinone, sq) state. We observe a mixture of conformers in the oxidized state; a 50:50 distribution between the established oxidized conformation where the peptide bond is pointing away from the flavin, and a conformation where the peptide bond is pointing toward the flavin, approximating the conformation in the semiquinone state. We use single‐crystal spectroscopy to demonstrate that the mixture of conformers is not caused by radiation damage to the crystal. This is the first time that such a mixture of conformers is reported in a wild‐type Fld. We therefore carried out a survey of published Fld structures, which show that several proteins have a pronounced conformational flexibility of this peptide bond. The degree of flexibility seems to be modulated by the presence, or absence, of stabilizing interactions between the peptide bond carbonyl and its surrounding amino acids. We hypothesize that the degree of conformational flexibility will affect the Fld ox/sq redox potential.     

Relationships between apparent binding energies measured in site-directed mutagenesis experiments and energetics of binding and catalysis

The use of binding energy in molecular recognition and enzyme catalysis is currently being probed by experiments on engineered proteins. The interaction energy of an individual side chain with a substrate may be quantified by comparing the binding and rate constants for wild-type enzyme with those for a mutant in which the side chain has been truncated. An apparent binding energy delta Gapp is obtained. The physical significance of delta Gapp is analyzed with particular reference to hydrogen bonding where one partner in the bond is deleted by mutagenesis. The following conclusions have been drawn for situations where mutagenesis does not unduly perturb the structure of the protein. delta Gapp is always a measurement of specificity of binding and catalysis. But, it does not generally measure the incremental binding energy of the hydrogen bond delta Gbind. The discrepancy between delta Gapp and delta Gbind is especially large when mutation leaves a charged donor or acceptor unpaired. Here, delta Gapp overestimates delta Gbind by possibly several kilocalories per mole. On the other hand, changes in delta Gapp (delta delta Gapp) as a reaction proceeds through its intermediates and transition states are particularly amenable to simple analysis. It is shown that delta delta Gapp can measure changes in delta Gbind (delta delta Gbind). For example, if there is a change in the energy of an individual bond on going from one state to the next, then delta delta Gapp = delta delta Gbind.(ABSTRACT TRUNCATED AT 250 WORDS)     

Can the stereochemical outcome of glycosylation reactions be controlled by the conformational preferences of the glycosyl donor?

Previous static and dynamical density functional theory studies of the 2,6-di-O-acetyl-3,4-O-isopropylidene-D-galactopyranosyl cations and their methanol adducts has led to an hypothesis that these cations exist in two families of conformers characterized as (2)S(O) and B(2,5), respectively. These families differ by ring inversion, each with its own reactivity. New calculations on the 2,6-di-O-acetyl-3,4-di-O-methyl-D-galactopyranosyl cation confirmed these trends. Removing the isopropylidene group allows more flexibility, but two families of conformers can be discerned with the monocyclic oxocarbenium ions in the E(3) conformation and the bicyclic dioxolenium ions in the (4)H(5) conformation. Attack on the beta-face of these monocyclic cations is favored by hydrogen bonding and the anomeric effect. The experimentally observed high beta-stereoselectivity of mannopyranosyl donors and high alpha-stereoselectivity of glucopyranosyl donors with the 4,6-O-benzylidene protecting groups can be rationalized assuming that the trans-fused 1,3-dioxane ring allows population of only one family of conformers. The combination of hydrogen bonding and conformational changes of the pyranose ring in response to the C-5[bond]O-5[bond]C-1[bond]C-2 torsion angle changes are identified as key factors in stereoselectivity. Based on these observations a strategy to design face discriminated glycosyl donors that exist predominantly in only one family of conformers is proposed.     

Structural studies on the two forms of 8-bromo-2'',3''-O-isopropylideneadenosine.

The crystal and molecular structures of two forms of 8-bromo-2',3'-O-isopropylideneadenosine have been determined by X-ray methods. In one form, the molecular structure has planar conformation in the sugar moiety and no intramolecular hydrogen bond. On the other hand, the molecular structure of the second form has C(2')-endo conformation and an intramolecular hydrogen bond. No stacking interaction between adjacent bases is found in either form, but two modes of the base-pairing hydrogen bond exist in the second form.     

Conformer-specific and two-fold adiabatic photoisomerization of ZZ-1,4-di-(2-quinolylethenyl)benzene.

Irradiation of the ZZ stereoisomer of 1,4-di-(2'-quinolylethenyl)-benzene was found to cause direct adiabatic (one photon-two bond) isomerization to a product having the same lifetime as the EE isomer but a rather different spectrum with respect to that obtained by direct excitation of the EE one. To clarify this unexpected behaviour, the conformational equilibria of the EE stereoisomer have been studied in non-polar solvent by fluorimetry. The most abundant conformers, formed by the hindered rotation of the condensed-ring groups around the quasi-single bond with the ethenic carbons, have been characterized by the selective effect of the excitation energy on the fluorescence spectrum. The combined application of the principal component analysis allowed the separation of the spectral properties of three conformers to be achieved. Information on their structures was obtained by theoretical calculations. The results of the present conformational study clearly indicated that the fluorescence spectrum of the photoproduct of ZZ belongs to a specific component of the conformer mixture of the EE isomer.     

A theoretical investigation on the conformation and the interaction of CHF2OCF2CHF2 (desflurane II) with one water molecule

The conformation and the interaction of CHF₂OCF₂CHF₂ (desflurane II) with one water molecule is investigated theoretically using the ab initio MP2/aug-cc-pvdz and DFT-based M062X/6-311++G(d,p) methods. The calculations include the optimized geometries, the harmonic frequencies of relevant vibrational modes along with a natural bond orbital (NBO) analysis including the NBO charges, the hybridization of the C atom and the intra- and intermolecular hyperconjugation energies. In the two most stable conformers, the CH bond of the F₂HCO- group occupies the gauche position. The hyperconjugation energies are about the same for both conformers and the conformational preference depends on the interaction between the non-bonded F and H atoms. The deprotonation enthalpies of the CH bonds are about the same for both conformers, the proton affinity of the less stable conformer being 3 kcal mol^?1 higher. Both conformers of desflurane II interact with water forming cyclic complexes characterized by CH…O and OH…F hydrogen bonds. The binding energies are moderate, ranging from ?2.4 to ?3.2 kcal mol^?1 at the MP2 level. The origin of the blue shifts of the ν(CH) vibrations is analyzed. In three of the complexes, the water molecule acts as an electron donor. Interestingly, in these cases a charge transfer is also directed to the non bonded OH group of the water molecule. This effect seems to be a property of polyfluorinated ethers.     

Linear free energy relationship for the anomeric effect: MP2, DFT and ab initio study of 2-substituted-1,4-dioxanes

The anomeric effect of 2-substituted 1,4-dioxane derivatives was calculated and compared with the values for substituted cyclohexane. The bond lengths, bond angles, torsion angles, and relative energies of axial and equatorial conformers of 2-substituted 1,4-dioxanes were calculated by the second-order Møller–Plesset (MP2), density functional theory (DFT/B3LYP), and Hartree–Fock (HF) methods using 6-31G^∗ basis set. The energy differences between the axial and equatorial conformers, endo and exo-anomeric effects, repulsive non-bond and H-bonding interactions were investigated. A linear free energy relationship (LFER) between calculated (MP2/6-31G^∗) anomeric effect and inductive substituent constants (σ_I) was obtained for 2-substituted-1,4-dioxanes (slope = 6.19 and r² = 0.967). The calculated energy differences indicate lower equatorial orientation for 2-substituted-1,4-dioxanes compared to the 2-substituted-tetrahydropyrans. The contribution of resonance, hyperconjugation, inductive, steric, hydrogen bonding, electrostatic interaction, and level of theory influences the anomeric effect.     

Combined use of molecular dynamics simulations and NMR to explore peptide bond isomerization and multiple intramolecular hydrogen-bonding possibilities in a cyclic pentapeptide, cyclo(Gly-Pro-D-Phe-Gly-Val).

The conformational behavior of a model cyclic pentapeptide--cyclo(Gly-L-Pro-D-Phe-Gly-L-Val)--has been explored through the combined use of in vacuo molecular dynamics simulations and a range of nmr experiments (preceding paper). The molecular dynamics analysis suggests that, despite the conformational constraints imposed by formation of the pentapeptide cycle, this pentapeptide undergoes conformational transitions between various hydrogen-bonded conformations, characterized by low energy barriers. An inverse gamma turn with Pro in position i + 1 and a gamma turn with D-Phe in position i + 1 are two alternatives occurring frequently. Like other DLDDL cyclic pentapeptides, cyclo(Gly-Pro-D-Phe-Gly-Val) is also stabilized by an inverse gamma-turn structure with the beta-branched Val residue in position i + 1, and this hydrogen bond is retained in the different conformational families. The gamma-turn around D-Phe3 and the inverse gamma turn around Val5 are consistent with the nmr observations. 3JNH-CH alpha coupling constants of the all-trans forms were calculated from one of the molecular dynamics trajectories and are comparable to nmr experimental data, suggesting that the conformational states visited during the simulation are representative of the conformational distribution in solution. In addition to the equilibrium among various hydrogen-bonded all-trans conformers, the observation in nmr spectra of two sets of resonances for all peptide protons indicated a slow conformational interconversion of the Gly-Pro peptide bond between trans and cis isomers. The activation energy between these two conformers was determined experimentally by magnetization transfer and was calculated by high temperature constrained molecular dynamics simulation. Both methods yield a free energy of activation of ca. 20 kcal/mol. Furthermore, the free energy of activation is dependent on the direction of rotation of the Gly-Pro peptide bond.     

The anomeric effect revisited. A possible role of the CH/n hydrogen bond

Ab initio MO calculations were carried out at the MP2/6-311++G(d,p) level to investigate the conformational energy of 2-substituted oxanes and 1,3-dioxanes. It has been found that the Gibbs free energies of the axial conformers are smaller than those of the corresponding equatorial conformers in every case when the 2-substituent Z is electron withdrawing (OCH(3), F, Cl, Br). The difference in Gibbs energy between the equatorial and axial conformers DeltaG(eq-ax) increases from Z=OCH(3) to F, Cl, and then to Br. In the axial conformers, the interatomic distance between Z and the axial C-H, separated by four covalent bonds, has been found to be appreciably shorter than the van der Waals distance, suggesting the importance of the five-membered CH/n (CH/O or CH/halogen) hydrogen bond in stabilizing these conformations. Natural bonding orbital (NBO) charges of the relevant atoms have been shown to be different between the two conformers: more positive for H and more negative for C in the axial conformers than in the corresponding equatorial conformers. In view of the above findings, we suggest that the CH/n hydrogen bond plays an important role in stabilizing the axial conformation in 2-substituted oxanes and 1,3-dioxanes, and by implication, in the anomeric effect in carbohydrate chemistry.     

Differential stability of the triple helix of (Pro-Pro-Gly)10 in H2O and D2O: thermodynamic and structural explanations

(Pro-Pro-Gly)10 [(PPG10)], a collagen-like polypeptide, forms a triple-helical, polyproline-II structure in aqueous solution at temperatures somewhat lower than physiological, with a melting temperature of 24.5 degrees C. In this article, we present circular dichroism spectra that demonstrate an increase of the melting temperature with the addition of increasing amounts of D2O to an H2O solution of (PPG)10, with the melting temperature reaching 40 degrees C in pure D2O. A thermodynamic analysis of the data demonstrates that this result is due to an increasing enthalpy of unfolding in D2O vs. H2O. To provide a theoretical explanation for this result, we have used a model for hydration of (PPG)10 that we developed previously, in which inter-chain water bridges are formed between sterically crowded waters and peptide bond carbonyls. Energy minimizations were performed upon this model using hydrogen bond parameters for water, and altered hydrogen bond parameters that reproduced the differences in carbonyl oxygen-water oxygen distances found in small-molecule crystal structures containing oxygen-oxygen hydrogen bonds between organic molecules and H2O or D2O. It was found that using hydrogen bond parameters that reproduced the distance typical of hydrogen bonds to D2O resulted in a significant lowering of the potential energy of hydrated (PPG)10. This lowering of the energy involved energetic terms that were only indirectly related to the altered hydrogen bond parameters, and were therefore not artifactual; the intra-(PPG10) energy, plus the water-(PPG10) van der Waals energy (not including hydrogen bond interactions), were lowered enough to qualitatively account for the lower enthalpy of the triple-helical conformation, relative to the unfolded state, in D2O vs. H2O. This result indicates that the geometry of the carbonyl-D2O hydrogen bonds allows formation of good hydrogen bonds without making as much of an energetic sacrifice from other factors as in the case of hydration by H2O.     

Structural function of C-terminal amidation of endomorphin. Conformational comparison of mu-selective endomorphin-2 with its C-terminal free acid, studied by 1H-NMR spectroscopy, molecular calculation, and X-ray crystallography

To investigate the structural function of the C-terminal amide group of endomorphin-2 (EM2, H-Tyr-Pro-Phe-Phe-NH(2)), an endogenous micro-opioid receptor ligand, the solution conformations of EM2 and its C-terminal free acid (EM2OH, H-Tyr-Pro-Phe-Phe-OH) in TFE (trifluoroethanol), water (pH 2.7 and 5.2), and aqueous DPC (dodecylphosphocholine) micelles (pH 3.5 and 5.2) were investigated by the combination of 2D (1)H-NMR measurement and molecular modelling calculation. Both peptides were in equilibrium between the cis and trans rotamers around the Tyr--Pro w bond with population ratios of 1 : 1 to 1 : 2 in dimethyl sulfoxide, TFE and water, whereas they predominantly took the trans rotamer in DPC micelle, except in EM2OH at pH 5.2, which had a trans/cis rotamer ratio of 2 : 1. Fifty possible 3D conformers were generated for each peptide, taking different electronic states depending on the type of solvent and pH (neutral and monocationic forms for EM2, and zwitterionic and monocation forms for EM2OH) by the dynamical simulated annealing method, under the proton-proton distance constraints derived from the ROE cross-peak intensities. These conformers were then roughly classified into four groups of two open [reverse S (rS)- and numerical 7 (n7)-type] and two folded (F1- and F2-type) conformers according to the conformational pattern of the backbone structure. Most EM2 conformers in neutral (in TFE) and monocationic (in water and DPC micelles) forms adopted the open structure (mixture of major rS-type and minor n7-type conformers) despite the trans/cis rotamer form. On the other hand, the zwitterionic EM2OH in TFE, water and DPC micelles showed an increased population of F1- and F2-type folded conformers, the population of which varied depending on their electronic state and pH. Most of these folded conformers took an F1-type structure similar to that stabilized by an intramolecular hydrogen bond of (Tyr1)NH(3) (+)...COO(-)(Phe4), observed in its crystal structure. These results show that the substitution of a carboxyl group for the C-terminal amide group makes the peptide structure more flexible and leads to the ensemble of folded and open conformers. The conformational requirement of EM2 for binding to the micro-opioid receptor and the structural function of the C-terminal amide group are discussed on the basis of the present conformational features of EM2 and EM2OH and a possible model for binding to the micro-opioid receptor, constructed from the template structure of rhodopsin.     

Conformational analysis of genotoxic benzo[a]pyrene-7,8-dione-duplex DNA adducts using a molecular dynamics method (II)

The conformations of the benzo[a]pyrene-7,8-quinone (BPQ) modified oligonucleotide were investigated using molecular dynamic simulation. In the initial structures, the central guanine base was modified with BPQ resulting in the formation of four structurally distinguishable 10-(N2-deoxyguanosyl)-9,10-dihydro-9-hydroxy benzo[a]pyrene-7,8-dione adducts (BPQ-G3,4). Each of the oligonucleotide adduct consisted of two conformers, namely syn and anti conformations, depending on the rotation around the glycosidic bond between BPQ and the guanine base. The results revealed that the BPQ moiety was located in the major groove for all four syn conformers. The relative energies of these conformers were high, and the backbone largely deviated from the B-form. On the other hand, BPQ was located in the minor groove with relatively low energies, and backbone was retained in all of the anti conformer cases. The most conceivable BPQ-modified double stranded oligonucleotide structure was proposed from the energy calculation and the structural analysis.     

Experimental and theoretical DFT (B3LYP,X3LYP,CAM-B3LYP and M06-2X) study on electronic structure,spectral features,hydrogen bonding and solvent effects of 4-methylthiadiazole-5-carboxylic acid

Detailed structural, electronic and spectroscopic study of 4-methylthiadiazole-5-carboxylic acid, one of the simplest 1,2,3-thiadiazole derivatives has been performed using density functional theory at four different functionals (B3LYP, X3LYP, CAM-B3LYP and M06-2X). The two possible conformers and their dimeric forms have been investigated for the stability and hence for the calculation of molecular properties of the title compound. Vibrational analysis has been performed with the help of experimental FT-IR and FT-Raman spectra. NBO analysis has been performed to estimate the N–H—O=C hydrogen bond strength and to evaluate the intra and inter molecular charge transfer in the system. Intermolecular hydrogen-bond strength has also been computed using Atoms in Molecules (AIM) theory. To visualise spatial domain, key sites of electron transitions and electron density difference between ground as well as excited states, and their 2D and 3D plots have been computed. Solvent effect on the intermolecular hydrogen bonding have also been investigated using solvents of different polarities. Non-linear optical properties, molecular electrostatic potential surface map (MESP), thermodynamic potentials at different temperatures have also been computed and plotted.     

Effect of the 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole residue on the stability of DNA duplexes and triplexes.

3-Nitropyrrole (M) was introduced as a non-discriminating 'universal' base in nucleic acid duplexes by virtue of small size and a presumed tendency to stack but not hydrogen bond with canonical bases. However, the absence of thermally-induced hyperchromic changes by single-stranded deoxyoligomers in which M alternates with A or C residues shows that M does not stack strongly with A or C nearest neighbors. Yet, the insertion of a centrally located M opposite any canonical base in a duplex is sometimes even less destabilizing than that of some mismatches, and the variation in duplex stability is small. In triplexes, on the other hand, an M residue centrally located in the third strand reduces triplex stability drastically even when the X.Y target base pair is A.T or G. C in a homopurine. homopyrimidine segment. But, when the target duplex opposition is M-T and the third strand residue is T, the presence of M in the test triplet has little effect on triplex stability. Therefore, a lack of hydrogen bonding in an otherwise helix-compatible test triplet cannot be responsible for triplex destabilization when M is the third strand residue. Thus, M is non-discriminating and none-too-destabilizing in a duplex, but in a triplex it is extremely destabilizing when in the third strand.     

B3LYP/6-311++G** study of alpha- and beta-D-glucopyranose and 1,5-anhydro-D-glucitol: 4C1 and 1C4 chairs, (3,O)B and B(3,O) boats, and skew-boat conformations

Geometry optimization, at the B3LYP/6-311++G** level of theory, was carried out on 4C1 and 1C4 chairs, (3,O)B and B(3,O) boats, and skew-boat conformations of alpha- and beta-D-glucopyranose. Similar calculations on 1,5-anhydro-D-glucitol allowed examination of the effect of removal of the 1-hydroxy group on the energy preference of the hydroxymethyl rotamers. Stable minimum energy boat conformers of glucose were found, as were stable skew boats, all having energies ranging from approximately 4-15 kcal/mol above the global energy 4C1 chair conformation. The 1C4 chair electronic energies were approximately 5-10 kcal/mol higher than the 4C1 chair, with the 1C4 alpha-anomers being lower in energy than the beta-anomers. Zero-point energy, enthalpy, entropy, and relative Gibbs free energies are reported at the harmonic level of theory. The alpha-anomer 4C1 chair conformations were found to be approximately 1 kcal/mol lower in electronic energy than the beta-anomers. The hydroxymethyl gt conformation was of lowest electronic energy for both the alpha- and beta-anomers. The glucose alpha/beta anomer ratio calculated from the relative free energies is 63/37%. From a numerical Hessian calculation, the tg conformations were found to be approximately 0.4-0.7 kcal/mol higher in relative free energy than the gg or gt conformers. Transition-state barriers to rotation about the C-5-C-6 bond were calculated for each glucose anomer with resulting barriers to rotation of approximately 3.7-5.8 kcal/mol. No energy barrier was found for the path between the alpha-gt and alpha-gg B(3,O) boat forms and the equivalent 4C1 chair conformations. The alpha-tg conformation has an energy minimum in the 1S3 twist form. Other boat and skew-boat forms are described. The beta-anomer boats retained their starting conformations, with the exception of the beta-tg-(3,O)B boat that moved to a skew form upon optimization.     

MM3 potential energy surfaces of the 2-linked glucosyl trisaccharides alpha-kojitriose and beta-sophorotriose

The adiabatic potential energy surfaces (PES) of two trisaccharides with 2-linkages (alpha-kojitriose and beta-sophorotriose) were obtained using the MM3 force field, and are represented by a single 3D contour map for which the energy is plotted against the two psi glycosidic angles. In spite of the proximity of the positions where the two monosaccharidic units are linked to the central monosaccharide, an almost independent behavior of both linkages was found for the alpha-linked trisaccharide alpha-kojitriose, i.e., the surfaces are those expected from the maps of the disaccharide containing the same linkage. A slight shift of the position of the global minimum is found to occur, due to a hydrogen bond between the third and first monosaccharide units, which also leads to an increase in flexibility. On the other hand, for the beta-linked trisaccharide beta-sophorotriose, the surface is sharply different from that expected by observation of the disaccharide map. Some of the expected minima cannot appear unless a serious deformation of the phi and/or psi angles is produced. Furthermore, the global minimum corresponds to a combination of different conformations for each of the linkages, whereas another minimum with only slightly higher energy has both glycosidic linkages in a conformation less favored for the disaccharide, though close to that predicted in crystal diffraction studies.     

An insight into the inhibitory selectivity of 4-(Pyrazol- 4-yl)-pyrimidines to CDK4 over CDK2

Revealing selectivity mechanism of cyclin-dependent kinases (CDK) and their inhibitors is an important issue to develop potential anticancer drugs. The substituted 4-(Pyrazol-4-yl)-pyrimidines are potent inhibitors of CDK4 but not of the highly homologous CDK2. In order to reveal the inhibitory selectivity of these inhibitors to CDK4 over CDK2, we select one of substituted 4-(Pyrazol-4-yl)-pyrimidines as a representative (marked as A1 hereunder) and perform molecular docking, molecular dynamics simulations and binding free energy analysis for CDK4/A1 and CDK2/A1, respectively. The electrostatic and van der Waals (vdW) interactions of the A1 inhibitor with CDK4/CDK2 are discussed. The computed binding free energies based on the MM-PBSA method are consistent with experimental bioactivity ranking of A1 inhibitor to CDK4/CDK2. On the other hand, the conformational characteristics of CDK2 and CDK4 induced by A1 inhibitor are analysed and revealed. Results demonstrate that the vdW interactions considerably contribute to binding of CDK4/CDK2 with A1 inhibitor and are similar in size. The hydrogen bonding between A1 inhibitor and CDK4/CDK2 is considerably favourable to the binding, in which the hydrogen bond between the NH group of the pyrazole group of A1 and the residue Asp158 of CDK4 plays a crucial role in inhibitory selectivity of A1 inhibitor to CDK4 over CDK2. The electrostatic interaction energy differences between the corresponding residues of CDK4/A1 and CDK2/A1 confirm the above inference. The conformational changes of CDK2 and CDK4 induced by A1 inhibitor influence the selectivity of A1 inhibitor to CDK4/CDK2.     

Differential Stability of the Triple Helix of (Pro-Pro-Gly)10 in H2O and D2O: Thermodynamic and Structural Explanations

Abstract

(Pro-Pro-Gly)₁₀ [(PPG₁₀)], a collagen-like polypeptide, forms a triple-helical, polyproline-II structure in aqueous solution at temperatures somewhat lower than physiological, with a melting temperature of 24.5°C. In this article, we present circular dichroism spectra that demonstrate an increase of the melting temperature with the addition of increasing amounts of D₂O to an H₂O solution of (PPG)₁₀, with the melting temperature reaching 40°C in pure D₂O. A thermodynamic analysis of the data demonstrates that this result is due to an increasing enthalphy of unfolding in D₂O vs. H₂O. To provide a theoretical explanation for this result, we have used a model for hydration of (PPG)₁₀ that we developed previously, in which inter-chain water bridges are formed between sterically crowded waters and peptide bond carbonyls. Energy minimizations were performed upon this model using hydrogen bond parameters for water, and altered hydrogen bond parameters that reproduced the differences in carbonyl oxygen-water oxygen distances found in small-molecule crystal structures containing oxygen-oxygen hydrogen bonds between organic molecules and H₂O or D₂O. It was found that using hydrogen bond parameters that reproduced the distance typical of hydrogen bonds to D₂O resulted in a significant lowering of the potential energy of hydrated (PPG)₁₀. This lowering of the energy involved energetic terms that were only indirectly related to the altered hydrogen bond parameters, and were therefore not artifactual; the intra-(PPG₁₀) energy, plus the water-(PPG₁₀) van der Waals energy (not including hydrogen bond interactions), were lowered enough to qualitatively account for the lower enthalpy of the triple-helical conformation, relative to the unfolded state, in D₂O vs. H₂O. This result indicates that the geometry of the carbonyl-D₂O hydrogen bonds allows formation of good hydrogen bonds without making as much of an energetic sacrifice from other factors as in the case of hydration by H₂O.