Structural changes in the molecular sheets along (hk0) planes derived from cellulose Iβ by molecular dynamics simulations

We studied the stability of molecular sheets with four cellotetraoses in an aqueous environment by molecular dynamics simulation to identify the molecular details of first structure as one of the possibilities in the course of crystallization of cellulose I. After simulation, the molecular sheets formed by van der Waals forces along the (11?0) and (110) crystal plane did not change their structures in an aqueous environment, whereas the other ones formed by hydrogen bonds along the (100) and (200) crystal plane changed into a van der Waals associated molecular sheet, similar to the former. These simulated molecular sheets formed by van der Waals forces were structurally stable in water because of their hydrophilic exterior and hydrophobic interior. Therefore, if the molecular sheet structures are formed in the real system, the sheets formed by van der Waals forces are probably the initial structure of crystallization. A close analysis indicated that these sheets could be classified into two groups in terms of the hydrogen bonding networks, camber angle, and main and side chain conformations. One group was the molecular sheets corresponding to the (110) after simulation. This sheet is probably rigid because intramolecular hydrogen bonds of the chains in the sheet are highly developed. The other group was the molecular sheets corresponding to (200), (100), and (11?0) crystal plane: the chains in these sheets seemed to be rather flexible due to their moderately developed intramolecular hydrogen bonds.     

Selective formation of stable triplexes including a TA or a CG interrupting site with new bicyclic nucleoside analogues (WNA)

Triplex-forming oligonucleotides (TFOs) are potential DNA-targeting molecules and would become powerful tools for genomic research. As the stabilization of the TFO is partially provided by hydrogen bonds to purine bases, the most stable triplexes form with homopurine/homopyrimidine sequences, and a pyrimidine base in the purine strand of the duplex interrupts triplex formation. If a TFO can recognize sequences including such an interrupting site, the target regions in the genome would be expanded to a greater extent. However, this problem has not been generally solved despite extensive studies. We have previously reported a new base analogue (WNA) constructed of three parts, a benzene ring, a heterocyclic ring, and a bicyclic skeleton to hold these two parts. In this study, we have further investigated modification of WNA systematically and determined two useful WNA analogues, WNA-beta T and WNA-beta C, for selective stabilization of triplexes at a TA and a CG interrupting site, respectively. The triplexes with WNA analogues have exhibited an interesting property in that they are more stable than natural-type triplexes even at low Mg(2+) concentration. From comparison of the results with H-WNA-beta T lacking benzene and those with WNA-H without thymine, it has been suggested that benzene is a major contributor for triplex stability and thymine provides selectivity. Thus, it has been successfully demonstrated that WNA-beta T/TA and WNA-beta C/CG combinations may expand triplex recognition codes in addition to the natural A/AT and G/GC base triplet codes. The results of this study will provide useful information for the design of new WNA analogues to overcome inherent problems for further expansion of triplex recognition codes.     

Hydrogen‐bonding interactions in the active site of a low molecular weight protein‐tyrosine phosphatase

Molecular dynamics simulation of the Michaelis complex, phospho‐enzyme intermediate, and the wild‐type and C12S mutant have been carried out to examine hydrogen‐bonding interactions in the active site of the bovine low molecular weight protein‐tyrosine phosphatase (BPTP). It was found that the S_γ atom of the nucleophilic residue Cys‐12 is ideally located at a position opposite from the phenylphosphate dianion for an inline nucleophilic substitution reaction. In addition, electrostatic and hydrogen‐bonding interactions from the backbone amide groups of the phosphate‐binding loop strongly stabilize the thiolate anion, making Cys‐12 ionized in the active site. In the phospho‐enzyme intermediate, three water molecules are found to form strong hydrogen bonds with the phosphate group. In addition, another water molecule can be identified to form bridging hydrogen bonds between the phosphate group and Asp‐129, which may act as the nucleophile in the subsequent phosphate hydrolysis reaction, with Asp‐129 serving as a general base. The structural difference at the active site between the wild‐type and C12S mutant has been examined. It was found that the alkoxide anion is significantly shifted toward one side of the phosphate binding loop, away from the optimal position enjoyed by the thiolate anion of the wild‐type enzyme in an S_N2 process. This, coupled with the high pK_a value of an alcoholic residue, makes the C12S mutant catalytically inactive. These molecular dynamics simulations provided details of hydrogen bonding interactions in the active site of BPTP, and a structural basis for further studies using combined quantum mechanical and molecular mechanical potential to model the entire dephosphorylation reaction by BPTP. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1192–1203, 2000     

Thermodynamics of a 24-Mer Triple Helix Formation and Stability

In this work we report a thermodynamic characterization of stability and melting behaviour of two 24-mer DNA triplexes. The third strand, that binds the Watson-Crick double helix with Hoogsteen hydrogen bonds, contains 3′-3′ phosphodiester junction that determines the polarity inversion. The target double helix is composed of adjacent and alternate fragments of oligopurine-oligopyrimidine tracts. The two helices differ from the substitution of the cytosine, involved in the junction, with the thymine. Calorimetric data reported here provide a quantitative measure of the influence of pH and base modification on the stability of a DNA triplex. This revised version was published online in August 2006 with corrections to the Cover Date.     

From protein denaturant to protectant: comparative molecular dynamics study of alcohol/protein interactions

It is well known that alcohols can have strong effects on protein structures. For example, monohydric methanol and ethanol normally denature, whereas polyhydric glycol and glycerol protect, protein structures. In a recent combined theoretical and NMR experimental study, we showed that molecular dynamics simulations can be effectively used to understand the molecular mechanism of methanol denaturing protein. In this study, we used molecular dynamics simulations to investigate how alcohols with varied hydrophobicity and different numbers of hydrophilic groups (hydroxyl groups) exert effects on the structure of the model polypeptide, BBA5. First, we showed that methanol and trifluoroethanol (TFE) but not glycol or glycerol disrupt hydrophobic interactions. The latter two alcohols instead protect the assembly of the α- and β-domains of the polypeptide. Second, all four alcohols were shown to generally increase the stability of secondary structures, as revealed by the increased number of backbone hydrogen bonds formed in alcohol/water solutions compared to that in pure water, although individual hydrogen bonds can be weakened by certain alcohols, such as TFE. The two monohydric alcohols, methanol and TFE, display apparently different sequence-dependence in affecting the backbone hydrogen bond stability: methanol tends to enhance the stability of backbone hydrogen bonds of which the carbonyl groups are from polar residues, whereas TFE tends to stabilize those involving non-polar residues. These results demonstrated that subtle differences in the solution environment could have distinct consequences on protein structures.     

Helical molecular programming: supramolecular double helices by dimerization of helical oligopyridine-dicarboxamide strands

Helically preorganized oligopyridine-dicarboxamide strands are found to undergo dimerization into double helical supramolecular architectures. Dimerization of single helical strands with five or seven pyridine rings has been characterized by NMR and mass spectrometry in various solvent/ temperature conditions. Solution studies and stochastic dynamic simulations consistently show an increasing duplex stability with increasing strand length. The double helical structures of three different dimers was characterized in the solid phase by X-ray diffraction analysis. Both aromatic stacking and hydrogen bonding contribute the double helical arrangement of the oligopyridinedicarboxamide strand. Inter-strand interactions involve extensive face-to-face overlap between aromatic rings, which is not possible in the single helical monomers. Most hydrogen bonds occur within each strand of the duplex and stabilize its helical shape. Some inter-strand hydrogen bonds are found in the crystal structures. Dynamic studies by NMR as well as by molecular modeling computations yield structural and kinetic information on the double helices and on monomer-dimer interconversion. In addition, they reveal the presence of a spring-like extension/compression as well as rotational displacement motions.     

Thermal and infrared spectroscopic studies on hydrogen‐bonding interactions between poly‐(ε‐caprolactone) and some dihydric phenols

The effects of three dihydric phenols on the thermal properties of poly‐(ε‐caprolactone) (PCL) were investigated by DSC. The thermal properties of PCL were found to be greatly modified by the addition of 4,4′‐dihydroxydiphenyl ether (DHDPE). When the content of DHDPE reached 40%, PCL that was a semicrystalline polymer in the pure state changed to a fully amorphous elastomer. Fourier transform infrared (FTIR) spectroscopy was also applied to investigate the specific interaction between PCL and DHDPE. The formations of intermolecular hydrogen bonds between the carbonyl groups of PCL and the hydroxyl groups of DHDPE were discovered. By applying the Beer–Lambert law and a curve‐fitting program, the fractions of hydrogen‐bonded carbonyl groups were quantitatively analyzed. Although one DHDPE molecule had the potentiality to form two hydrogen bonds with PCL chains, the values of the fraction of the hydroxyl group involved in the intermolecular hydrogen bond were so little that from a statistical point of view, the formation of two hydrogen bonds was very difficult for every DHDPE molecule. Both DSC and FTIR revealed that 4,4′‐dihydroxydiphenyl methane and 4,4′‐dihydroxyphenyl had the ability to form hydrogen bonds with PCL, which were strongly affected by the polarity of the group linking two hydroxyphenyls and the flexibility of the molecular chain. The stronger the polarity of the group and the better the flexibility of molecular chain, the more tendencies dihydric phenol had to form intermolecular hydrogen bonds with PCL. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 2108–2117, 2001     

Molecular dynamics study of the solvation of an alpha-helical transmembrane peptide by DMSO

A 10-ns molecular dynamics study of the solvation of a hydrophobic transmembrane helical peptide in dimethyl sulfoxide (DMSO) is presented. The objective is to analyze how this aprotic polar solvent is able to solvate three groups of amino acid residues (i.e., polar, apolar, and charged) that are located in a stable helical region of a transmembrane peptide. The 25-residue peptide (sMTM7) used mimics the cytoplasmic proton hemichannel domain of the seventh transmembrane segment (TM7) from subunit a of H(+)-V-ATPase from Saccharomyces cerevisiae. The three-dimensional structure of peptide sMTM7 in DMSO has been previously solved by NMR spectroscopy. The radial and spatial distributions of the DMSO molecules surrounding the peptide as well as the number of hydrogen bonds between DMSO and the side chains of the amino acid residues involved are extracted from the molecular dynamics simulations. Analysis of the molecular dynamics trajectories shows that the amino acid side chains are fully embedded in DMSO. Polar and positively charged amino acid side chains have dipole-dipole interactions with the oxygen atom of DMSO and form hydrogen bonds. Apolar residues become solvated by DMSO through the formation of a hydrophobic pocket in which the methyl groups of DMSO are pointing toward the hydrophobic side chains of the residues involved. The dual solvation properties of DMSO cause it to be a good membrane-mimicking solvent for transmembrane peptides that do not unfold due to the presence of DMSO.     

Strengths of hydrogen bonds involving phosphorylated amino acid side chains

Post-translational phosphorylation plays a key role in regulating protein function. Here, we provide a quantitative assessment of the relative strengths of hydrogen bonds involving phosphorylated amino acid side chains (pSer, pAsp) with several common donors (Arg, Lys, and backbone amide groups). We utilize multiple levels of theory, consisting of explicit solvent molecular dynamics, implicit solvent molecular mechanics, and quantum mechanics with a self-consistent reaction field treatment of solvent. Because the approximately 6 pKa of phosphate suggests that -1 and -2 charged species may coexist at physiological pH, hydrogen bonds involving both protonated and deprotonated phosphates for all donor-acceptor pairs are considered. Multiple bonding geometries for the charged-charged interactions are also considered. Arg is shown to be capable of substantially stronger salt bridges with phosphorylated side chains than Lys. A pSer hydrogen-bond acceptor tends to form more stable interactions than a pAsp acceptor. The effect of phosphate protonation state on the strengths of the hydrogen bonds is remarkably subtle, with a more pronounced effect on pAsp than on pSer.     

Stabilization of a Bimolecular Triplex by 3′‐S‐Phosphorothiolate Modifications: An NMR and UV Thermal Melting Investigation

Triplexes formed from oligonucleic acids are key to a number of biological processes. They have attracted attention as molecular biology tools and as a result of their relevance in novel therapeutic strategies. The recognition properties of single‐stranded nucleic acids are also relevant in third‐strand binding. Thus, there has been considerable activity in generating such moieties, referred to as triplex forming oligonucleotides (TFOs). Triplexes, composed of Watson–Crick (W–C) base‐paired DNA duplexes and a Hoogsteen base‐paired RNA strand, are reported to be more thermodynamically stable than those in which the third strand is DNA. Consequently, synthetic efforts have been focused on developing TFOs with RNA‐like structural properties. Here, the structural and stability studies of such a TFO, composed of deoxynucleic acids, but with 3′‐S‐phosphorothiolate (3′‐SP) linkages at two sites is described. The modification results in an increase in triplex melting temperature as determined by UV absorption measurements. ¹H NMR analysis and structure generation for the (hairpin) duplex component and the native and modified triplexes revealed that the double helix is not significantly altered by the major groove binding of either TFO. However, the triplex involving the 3′‐SP modifications is more compact. The 3′‐SP modification was previously shown to stabilise G‐quadruplex and i‐motif structures and therefore is now proposed as a generic solution to stabilising multi‐stranded DNA structures.     

Molecular dynamics study of 2rotaxanes: influence of solvation and cation on co-conformation

The conformational preference of a [2]rotaxane system has been examined by molecular dynamics simulations. The rotaxane wheel consists of two bridged binding components: a cis-dibenzo-18-crown-6 ether and a 1,3-phenyldicarboxamide, and the penetrating axle consists of a central isophthaloyl unit with phenyltrityl capping groups. The influence of solvation on the co-conformation of the [2]rotaxane was evaluated by comparing the conformational flexibility in two solvents: chloroform and dimethyl sulfoxide. Attention was also paid to the effect of cation binding on the dynamical properties of the [2]rotaxane. The conformational stability of the [2]rotaxane was calculated using a MM/PB-SA strategy, and the occurrence of specific motions was examined by essential dynamics analysis. The changes in the co-conformational properties in the two solvents and upon cation binding are discussed in light of the available NMR data. The results indicate that in chloroform solution the [2]rotaxane system exists as a mixture of co-conformational states including some that have hydrogen bonds between axle C=O and wheel NH groups. Analysis of the simulations allow us to hypothesize that the [2]rotaxane's circumrotation motion can occur as the result of a dynamic process that combines a preliminary axle sliding step that breaks these hydrogen bonds and a conformational change in the ester group more distant from the wheel. In contrast, no hydrogen-bonded co-conformation was found in dimethyl sulfoxide, which appears to be due to the preferential formation of hydrogen bonds between the wheel NH groups with solvent molecules. Moreover, the axle experiences notable changes in anisotropic shielding, which would explain why the NMR signals are broadened in this solvent. Insertion of a sodium cation into the crown ether reduces co-conformational flexibility due to an interaction of the axle with the cation. Overall, the results reveal how both solvent and ionic atmosphere can influence the co-conformational preferences of rotaxanes.     

Studies on the Extension of Sequence‐independence and the Enhancement of DNA Triplex Formation

A more elaborate sequence‐independent triple‐helix formation viability study was carried out and extended from a recombination‐like triple‐helical DNA motif of a previous study (J. Mol. Recognition 14, 122–139 (2001)). The intended triple‐helix was formed by mixing one part of a DNA hairpin duplex and one part of a single (or third) strand identical to one of the duplex strands and complementary to the other strand. In contrast to the common purine and pyrimidine motifs in triple‐stranded DNA, the strands of the recombination‐like motif are not monotonously built from pyrimidine only, or purine only, in the sequence. The stability of the recombination‐like motif triplexes with varying sequences was monitored by UV thermal melting curves. The results showed that the order of the stability of the R‐form DNA base triads (J. Mol. Biol., 239, 181–200 (1994)) is G*(G ○ C) > C*(C ○ G) > A*(A ○ T) >T*(T ○ A) (the Watson‐Crick base pair is denoted in the parentheses) in 200 mM NaCl, at pH 7. In an attempt to increase the stability of the triplex in the recombination‐like motif, we replaced cytidine by 5‐methylcytidine (^mC) of the third strand. There is a general trend that ^mC modification stabilizes the complex (<2 °C per ^mC). The complex is furthermore stabilized by Mg²⁺ ion. The Tm increases from 7 to 2 °C from less stable to highly stable triplex by 20 mM Mg²⁺ ion in solution.     

Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation

The cooperative folding and unfolding of a beta-hairpin structure are observed in explicit water at native folding conditions through self-guided molecular dynamics simulation. The folded structure agrees excellently with the NMR NOE data. After going through a fully hydrated state, the peptide folds into a beta-hairpin structure in a highly cooperative process. During the folding process it is observed that side chain interaction occurs first, while intrapeptide hydrogen bonds only form at the final stage. On the contrary, the unfolding process starts with the breaking of interstrand hydrogen bonds. Energetic analysis indicates that the driving force of the folding is the intrapeptide interaction, while the solvent interaction opposes the folding.     

Influence of sodium ions on the dynamics and structure of single-stranded DNA oligomers: a molecular dynamics study.

The effects of sodium counterion presence and chain length on the structure and dynamics of single DNA strands of polythymidylate were studied by means of molecular dynamics simulations. The importance of the base-base stacking phenomenon increases with the chain length and partially reduces the flexibility of the strand. Sodium ions directly interact with the phosphate groups and keto oxygens of the thymine bases, complexes showing lifetimes below 400 ps. Simultaneous phosphate and keto complexes were observed for one of the sodium ions with lifetimes around 1 ns. The implications of such complexes in the folding process experienced by the strand are considered. Structurally, cation inner- and outer-sphere complexes were observed in the coordination of phosphate groups. For the inner-sphere complexes, the structural information retrieved from the simulations is in very good agreement with experimental data. The diffusion properties of the sodium ions also reflect both types of coordination modes.     

Structure and dynamics of methanol in water: a quantum mechanical charge field molecular dynamics study

An ab initio quantum mechanical charge field molecular dynamics simulation was carried out for one methanol molecule in water to analyze the structure and dynamics of hydrophobic and hydrophilic groups. It is found that water molecules around the methyl group form a cage-like structure whereas the hydroxyl group acts as both hydrogen bond donor and acceptor, thus forming several hydrogen bonds with water molecules. The dynamic analyses correlate well with the structural data, evaluated by means of radial distribution functions, angular distribution functions, and coordination number distributions. The overall ligand mean residence time, τ identifies the methanol molecule as structure maker. The relative dynamics data of hydrogen bonds between hydroxyl of methanol and water molecules prove the existence of both strong and weak hydrogen bonds. The results obtained from the simulation are in excellent agreement with the experimental results for dilute solution of CH(3)OH in water. The overall hydration shell of methanol consists in average of 18 water molecules out of which three are hydrogen bonded.     

Hydrogen-bonding cooperativity: using an intramolecular hydrogen bond to design a carbohydrate derivative with a cooperative hydrogen-bond donor centre

Neighbouring groups can be strategically located to polarise HO.OH intramolecular hydrogen bonds in an intended direction. A group with a unique hydrogen-bond donor or acceptor character, located at hydrogen-bonding distance to a particular OH group, has been used to initiate the hydrogen-bond network and to polarise a HO.OH hydrogen bond in a predicted direction. This enhanced the donor character of a particular OH group and made it a cooperative hydrogen-bond centre. We have proved that a five-membered-ring intramolecular hydrogen bond established between an amide NH group and a hydroxy group (1,2-e,a), which is additionally located in a 1,3-cis-diaxial relationship to a second hydroxy group, can be used to select a unique direction on the six-membered-ring intramolecular hydrogen bond between the two axial OH groups, so that one of them behaves as an efficient cooperative donor. Talose derivative 3 was designed and synthesised to prove this hydrogen-bonding network by NMR spectroscopy, and the mannopyranoside derivatives 1 and 2 were used as models to demonstrate the presence in solution of the 1,2-(e,a)/five-membered-ring intramolecular hydrogen bond. Once a well-defined hydrogen-bond is formed between the OH and the amido groups of a pyranose ring, these hydrogen-bonding groups no longer act as independent hydrogen-bonding centres, but as hydrogen-bonding arrays. This introduces a new perspective on the properties of carbohydrate OH groups and it is important for the de novo design of molecular recognition processes, at least in nonpolar media. Carbohydrates 1-3 have shown to be efficient phosphate binders in nonpolar solvents owing to the presence of cooperative hydroxy centres in the molecule.     

<Superscript>1</Superscript>H NMR study on microstructure of a novel acrylamide/methacrylic acid template copolymer in aqueous solution

A novel acrylamide/methacrylic acid template copolymer was prepared using polyallylammonium chloride (PAAC) as a template. This copolymer contains acrylamide (PAM), phenoxy acrylate (POA), and acylic acid (PAA) blocks. The investigation by high resolution nuclear magnetic resonance (¹H NMR) shows that intramolecular hydrogen bonds between the PAM and PAA blocks lead to compact molecular arrangement at quite low pH values, and the motion of the phenoxy side chain of the POA blocks is somewhat restricted. With the increase in pH value of the solution, the carboxylic acid of the PAA block gradually dissociates, which weakens hydrogen bonds between the PAM and PAA blocks. The decrease in D _w, self-diffusion coefficient of water, indicates the growth in aggregate size of the template copolymer. The cross peaks between amide protons and backbone protons shown in 2D nuclear overhauser spectroscopy (NOESY) spectra imply the existence of the intermolecular hydrogen bonding interaction between PAM and PAA blocks. After the carboxylic acid of the PAA block is completely dissociated in alkaline solution, the electrostatic repulsion of the carboxylic ion makes the molecular chain of the copolymer exhibit more outstretched. Consequently, the phenoxy groups (the side chain of the POA block) have more space to move.     

A hydrogen-bonding-modulated molecular rotor: environmental effect in the conformational stability of peptidomimetic macrocyclic cyclophanes

The conformational behavior of 16- to 18-membered ring peptidomimetic p-cyclophanes 1a,b-3a,b has been studied by NMR. The cycles bearing 16 and 17 atoms showed a dynamic process within the NMR time scale, produced by the rotation of the aromatic p-diphenylene moiety with respect to the macrocyclic main plane. The temperature dependence of 1H NMR spectra has been studied in order to get activation parameters of the energetic barrier for the process (VT-NMR and line shape analysis). The rate of the movement clearly depends on the macrocyclic ring size and the nature of the peptidomimetic side chain. Entropic and enthalpic contributions to the free energy of activation are discussed. The rotation of the aromatic ring is closely related to the intramolecular hydrogen bonding pattern, as suggested by temperature factors of NH chemical shifts (DeltadeltaNH/DeltaT) and molecular modeling. The interconnected roles of the solvation and the intramolecular H-bonds have been established by measurements (VT-NMR and DeltadeltaNH/DeltaT) in environments of different polarities and H-bonding abilities. We concluded that the conformational stability of the systems directly depends on the stability of the intramolecular H-bonding pattern. We finally showed how one of these peptidomimetics behaves as a methanol-dependent artificial molecular rotor. In this simple molecular device, the well-defined molecular rotation is tuned by the competition between intramolecular hydrogen bonds and interactions with the solvent.     

Glucose–Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA

Noncovalent forces rule the interactions between biomolecules. Inspired by a biomolecular interaction found in aminoglycoside–RNA recognition, glucose‐nucleobase pairs have been examined. Deoxyoligonucleotides with a 6‐deoxyglucose insertion are able to hybridize with their complementary strand, thus exhibiting a preference for purine nucleobases. Although the resulting double helices are less stable than natural ones, they present only minor local distortions. 6‐Deoxyglucose stays fully integrated in the double helix and its OH groups form two hydrogen bonds with the opposing guanine. This 6‐deoxyglucose‐guanine pair closely resembles a purine‐pyrimidine geometry. Quantum chemical calculations indicate that glucose‐purine pairs are as stable as a natural T‐A pair.     

Dual recognition of a C-G pyrimidine-purine inversion site: synthesis and binding properties of triplex forming oligonucleotides containing 2′-aminoethoxy-5-methyl-1H-pyrimidin-2-one ribonucleosides

The synthesis of a new ribonucleoside analogue, which combines two modifications, namely a 2′-aminoethoxy side-chain on the ribose and a 5-methyl-1H-pyrimidin-2-one (^4HT) unit as a base replacement, is presented. This building block was incorporated into triplex forming oligonucleotides and the binding properties to CG inversion sites in DNA duplex targets were studied. The data clearly show that the ^4HT base selectively recognizes the CG base-pair, while the aminoethoxy chain adds to the overall stability of the triple helix.