Energy Minimization Studies Research Articles

Conserved water-mediated H-bonding dynamics of catalytic Asn 175 in plant thiol protease

The role of invariant water molecules in the activity of plant cysteine protease is ubiquitous in nature. On analysing the 11 different Protein DataBank (PDB) structures of plant thiol proteases, the two invariant water molecules W1 and W2 (W220 and W222 in the template 1PPN structure) were observed to form H-bonds with the O b atom of Asn 175. Extensive energy minimization and molecular dynamics simulation studies up to 2 ns on all the PDB and solvated structures clearly revealed the involvement of the H-bonding association of the two water molecules in fixing the orientation of the asparagine residue of the catalytic triad. From this study,it is suggested that H-bonding of the water molecule at the W1 invariant site better stabilizes the Asn residue at the active site of the catalytic triad.

Conformational Changes in the Selectivity Filter of the Open-State KcsA Channel: An Energy Minimization Study

Potassium channels switch between closed and open conformations and selectively conduct K + ions. There are at least two gates. The TM2 bundle at the intracellular site is the primary gate of KcsA, and rearrangements at the selectivity filter (SF) act as the second gate. The SF blocks ion flow via an inactivation process similar to C-type inactivation of voltage-gated K + channels. We recently generated the open-state conformation of the KcsA channel. We found no major, possibly inactivating, structural changes in the SF associated with this massive inner-pore rearrangement, which suggests that the gates might act independently. Here we energy-minimize the open state of wild-type and mutant KcsA, validating in silico structures of energy-minimized SFs by comparison with crystallographic structures, and use these data to gain insight into how mutation, ion depletion, and K + to Na + substitution influence SF conformation. Both E71 or D80 protonations/mutations and the presence/absence of protein-buried water molecule(s) modify the H-bonding network stabilizing the P-loops, spawning numerous SF conformations. We find that the inactivated state corresponds to conformations with a partially unoccupied or an entirely empty SF. These structures, involving modifications in all four P-loops, are stabilized by H-bonds between amide H and carbonyl O atoms from adjacent P-loops, which block ion passage. The inner portions of the P-loops are more rigid than the outer parts. Changes are localized to the outer binding sites, with innermost site S4 persisting in the inactivated state. Strong binding by Na + locally contracts the SF around Na +, releasing ligands that do not participate in Na + coordination, and occluding the permeation pathway. K + selectivity primarily appears to arise from the inability of the SF to completely dehydrate Na + ions due to basic structural differences between liquid water and the “quasi-liquid” SF matrix.

Molecular Simulations and Conformational Studies of Fucoseα1-3)Gal(β1-X)GlcNAc where X=3, 4, or 6 Oligosaccharides

Energy minimization and conformational studies of molecular ions generated by ESI (electrospray ionization) tandem mass spectrometry (MS/MS) can be used for the discrimination of stereoisomeric permethylated and sodium cationized trisaccharides. Sets of fucose-containing trisaccharides having different internal and terminal linkages have been synthesized to analyze the reducing terminal linkage positions using BT and IT fusion approaches. A detailed investigation has been undertaken on the conformational behaviors of four trisaccharide fragments from human milk and blood group determinants of Type 1 and Type 2, namely Fuc(α13)Gal(β1-3)GalNAc and Fuc(α1-3)Gal(β1-X)GlcNAc where X = 3, 4 and 6 using molecular modeling methods. Three dimensional rigid and adiabatic phi-psi-energy maps (Surfer program) describing the energy as a function of rotation around corresponding glycosidic linkages were calculated by SYBYL molecular modeling and MM4 force field programs conjunction with cleavage energies of ESI MS/MS for the side group orientations. This approach predicted conformational behaviors exhibited by isomer saccharides for future applications on biologically active glycoconjugates and to exploit a faster method of synthesizing a series of structural isomeric oligosaccharides.

Molecular Modeling of the Ternary Complex of Rusticyanin-Cytochrome c4-Cytochrome Oxidase: An Insight to Possible H-Bond Mediated Recognition and Electron Transfer Reaction in T.ferrooxidans

The metabolism of Thiobacillus ferrooxidans involves electron transfer from the Fe+2 ions in the extracellular environment to the terminal oxygen in the bacterial cytoplasm through a series of periplasmic proteins like Rusticyanin (RCy), Cytochrome (Cyt c4), and Cytochrome oxidase (CcO). The energy minimization and MD studies reveal the stabilization of the three redox proteins in their ternary complex through the direct and water mediated H-bonds and electrostatic interaction. The surface exposed polar residues of the three proteins, i.e., RCy (His 143, Thr 146, Lys 81, Glu 20), Cyt c4 (Asp 5, 15, 52, Ser 14, Glu 61), and CcO (Asp 135, Glu 126, 140, 142, Thr 177) formed the intermolecular hydrogen bonds and stabilized the ternary complex. The oxygen (Oεl) of Glu 126, 140, and 142 on subunit II of the CcO interact to the exposed side-chain and Ob atoms of the Asp 52 of Cyt c4 and Glu 20 and Leu 12 of RCy. The Asp 135 of subunit II also forms H-bond with the Nε atom of Lys 81 of RCy. The Oεl of Glu 61 of Cyt c4 is also H-bonded to Oγ atom of Thr 177 of CcO. Solvation followed by MD studies of the ternary protein complex revealed the presence of seven water molecules in the interfacial region of the interacting proteins. Three of the seven water molecules (W 79, W 437, and W 606) bridged the three proteins by forming the hydrogen bonded network (with the distances ∼ 2.10–2.95 Å) between the Lys 81 (RCy), Glu 61 (Cyt c4), and Asp 135 (CcO). Another water molecule W 603 was H-bonded to Tyr 122 (CcO) and interconnected the Lys 81 (RCy) and Asp 135 (CcO) through the water molecules W 606 and W 437. The other two water molecules (W 21 and W 455) bridged the RCy to Cyt c4 through H-bonds, whereas the remaining W 76 interconnected the His 53 (Cytc4) to Glu 126 (CcO) with distances ∼ 2.95–3.0 Å.

Homology modeling of 5-lipoxygenase and hints for better inhibitor design

Lipoxygenases (LOXs) are a group of enzymes involved in the oxygenation of polyunsaturated fatty acids. Among these 5-lipoxygenase (5-LOX) is the key enzyme leading to the formation of pharmacologically important leukotrienes and lipoxins, the mediators of inflammatory and allergic disorders. In view of close functional similarity to mammalian lipoxygenase, potato 5-LOX is used extensively. In this study, the homology modeling technique has been used to construct the structure of potato 5-LOX. The amino acid sequence identity between the target protein and sequence of template protein 1NO3 (soybean LOX-3) searched from NCBI protein BLAST was 63%. Based on the template structure, the protein model was constructed by using the Homology program in InsightII. The protein model was briefly refined by energy minimization steps and validated using Profile-3D, ERRAT and PROCHECK. The results showed that 99.3% of the amino acids were in allowed regions of Ramachandran plot, suggesting that the model is accurate and its stereochemical quality good. Like all LOXs, 5-LOX also has a two-domain structure, the small N-terminal beta-barrel domain and a larger catalytic domain containing a single atom of non-heme iron coordinating with His525, His530, His716 and Ile864. Asn720 is present in the fifth coordination position of iron. The sixth coordination position faces the open cavity occupied here by the ligands which are docked. Our model of the enzyme is further validated by examining the interactions of earlier reported inhibitors and by energy minimization studies which were carried out using molecular mechanics calculations. Four ligands, nordihydroguaiaretic acid (NDGA) having IC(50) of 1.5 microM and analogs of benzyl propargyl ethers having IC(50) values of 760 microM, 45 microM, and no inhibition respectively were selected for our docking and energy minimization studies. Our results correlated well with the experimental data reported earlier, which proved the quality of the model. This model generated can be further used for the design and development of more potent 5-LOX inhibitors.

Monte Carlo and energy minimization studies of binary xylene adsorption in AEL and AFI networks

Adsorption of binary xylene mixtures in AEL and AFI networks was investigated using normal and biased GCMC simulations. Preferential o-xylene adsorption was evidenced in the simulations, as previously reported in single-component experimental data. In contrast to the FAU and MFI sieves, the AEL and AFI networks exhibit surprising azeotropic behavior. The selectivity switches from o-xylene to p-xylene at a gas phase mole fraction of ca. 0.5. Energy minimization was performed in the AlPO4-11 molecular sieve to determine the energy differences between the adsorption sites. The minimization study showed that AlPO4-11 has small adsorption energy differences between sites. The azeotropic behavior of the AEL and AFI networks can be explained using the two patch model proposed by Do and Do (Adsorption 5:319–329, 1999).

Studies on adsorption equilibrium of xylenes in AEL framework using biased GCMC and energy minimization

The adsorption of xylene isomers in AlPO 4-11 (AEL network) was investigated using biased grand canonical Monte Carlo (GCMC) simulations. Preferential o-xylene adsorption was predicted by the simulations, in agreement with previously reported experimental data. In AlPO 4-11 the selective adsorption behavior comes from the smaller length of the o-xylene molecule along the crystallographic c-axis compared to p-xylene. This is in contrast to AlPO 4-5 and AlPO 4-8, where the ortho-selectivity is caused by the characteristic face-to-face positioning of o-xylene. Energy minimization studies were also performed in a flexible AlPO 4-11 lattice to study the structural changes upon xylene adsorption. The energy minimization study showed that the AlPO 4-11 crystal distorts upon p- and o-xylene adsorption. The distortion mechanism is related to the strong interaction between xylene methyl groups and the sieve oxygen atoms in the O3 position in the wide region of the pore.

A new paradigm for electrostatic catalysis of radical reactions in vitamin B12 enzymes.

The catalytic power of enzymes containing coenzyme B(12) cofactor has been, in some respects, the "last bastion" for the strain hypothesis. The present work explores the origin of this effect by using simulation methods that overcome the sampling difficulties of previous energy minimization studies. It is found that the major part of the catalytic effect is due to the electrostatic interaction between the ribose and the protein, and that the strain contribution is very small. Remarkably, enzymes can use electrostatic effects even in a radical process, when the charge distribution of the reacting fragments does not change significantly during the reaction. Electrostatic catalysis can, in such cases, be obtained by attaching a polar group to the leaving fragment and designing an active site that interacts more strongly with this group in the product state than in the reactant state. The finding that evolution had to use this trick provides further evidence to the observation that it is extremely hard to catalyze enzymatic reactions by nonelectrostatic factors. The trick used by B(12) enzymes may, in fact, be a very powerful new strategy in enzyme design.

Toward the Prediction of Organic Hydrate Crystal Structures

Lattice energy minimization studies on four ordered crystal structures of ice and 22 hydrates of approximately rigid organic molecules (along with 11 corresponding anhydrate structures) were used to establish a model potential scheme, based on the use of a distributed multipole electrostatic model, that can reasonably reproduce the crystal structures. Transferring the empirical repulsion-dispersion potentials for organic oxygen and polar hydrogen atoms to water appears more successful for modeling ice phases than using common water potentials derived from liquid properties. Lattice energy differences are reasonable but quite sensitive to the exact conformation of water and the organic molecule used in the rigid molecule modeling. This potential scheme was used to test a new approach of predicting the crystal structure of 5-azauracil monohydrate (an isolated site hydrate) based on seeking dense crystal packings of 66 5-azauracil···water hydrogen-bonded clusters, derived from an analysis of hydrate hydrogen bond geometries involving the carbonyl- and aza-group acceptors in the Cambridge Structural Database. The known structure was found within 5 kJ mol(-1) of the global minimum in static lattice energy and as the third most stable structure, within 1 kJ mol(-1), when thermal effects at ambient temperature were considered. Thus, although the computational prediction of whether an organic molecule will crystallize in a hydrated form poses many challenges, the prediction of plausible structures for hydrogen-bonded monohydrates is now possible.

Molecular Dynamics Simulation of Polyamidoamine Dendrimer-Fullerene Conjugates:Generations Zero Through Four

Previously the synthesis of the polyamidoamine (PAMAM) (G4)-C60 conjugate with a molar ratio of 1 : 30 was reported. Because PAMAM G4 has sixty-four primary amine groups, it was hypothesized that approximately two surface amine groups react with each fullerene molecule to form the conjugates. A computational energy minimization study of various G4 PAMAM-fullerene conjugates containing 1 dendrimer but different amounts of fullerenes shows excellent stability for the 1 : 30 dendrimer to fullerene product. Attempts to prepare other PAMAM dendrimer-fullerene (C60) conjugates, using generations G0-G3 of PAMAM and C60 via the same procedure in pyridine were not successful, possibly due to solubility differences. The same computational techniques used to study the G4 conjugates were then used to determine (1) the stability of the G0-G3 conjugates (with a 2 : 1 primary amine to fullerene ratio), and (2) their solubility in pyridine compared to the (G4)-C60 conjugate. The findings allow for a better understanding of structure-property relationships of these nano-hybrid materials, through investigation of the molecular shape and radius of gyration. The findings reported herein may lead to improved syntheses of fullerene-dendrimer conjugates of various sizes and a better understanding of their nanoscopic structures and topographical influences.

Regioselective monobromination of substituted phenols in the presence of β-cyclodextrin

Cyclodextrin acts as a restricting nanovessel to enhance regioselectivity in bromination of substituted phenols such as 3-nitrophenol, 2-chlorophenol, 3-chlorophenol, and 4-chlorophenol. In contrast to solution bromination, cyclodextrin facilitates regioselective monobromination and formation of polybrominated products are substantially reduced. Selectivities in brominations are also observed in water and in the solid state. The observed results are rationalized on the basis of specific modes of inclusion of substituted phenols inside the cyclodextrin cavity and find strong support from energy minimization studies and 1H– 1H NOESY.

Intrinsic Amyloidogenic Behavior of Terminally Protected Alzheimer’s Aβ17–21 Peptide: Self-Aggregation and Amyloid-Like Fibril Formation

The terminally protected peptide Boc-Leu-Val-Phe-Phe-Ala-OMe bearing sequence similarity with the central hydrophobic cluster (CHC) of Alzheimer’s Aβ 17-21 peptide self-assembles to produce amyloid-like straight unbranched fibrils from organic solvents. The fibrils readily bind with a physiological dye Congo red (CR) and exhibits green gold birefringence under polarized light, a characteristic feature of amyloid plaque obtained from many neurodegenerative diseases. FTIR spectroscopy and in silico energy minimization study shed some light on the antiparallel supramolecular β-sheet aggregation of the peptide.

Structural and Functional Evidence for the Role of the TLR2 DD Loop in TLR1/TLR2 Heterodimerization and Signaling

The Toll/Interleukin-1 receptor (TIR) domain of the Toll-like receptors (TLRs) plays an important role in innate host defense signaling. The TIR-TIR platform formed by the dimerization of two TLRs promotes homotypic protein-protein interactions with additional cytoplasmic adapter molecules to form an active signaling complex resulting in the expression of pro- and anti-inflammatory cytokine genes. To generate a better understanding of the functional domains of TLR2 we performed a random mutagenesis analysis of the human TLR2 TIR domain and screened for TLR2/1 signaling-deficient mutants. Based upon the random mutagenesis results, we performed an alanine scanning mutagenesis of the TLR2 DD loop and part of the alphaD region. This resulted in the identification of four residues crucial for TLR2/1 signaling: Arg-748, Phe-749, Leu-752, and Arg-753. Computer-assisted energy minimization and docking studies indicated three regions of interaction in the TLR2/1 TIR-docked heterodimer. In Region I, residues Arg-748 and Phe-749 in TLR2 DD loop were involved in close contacts with Gly-676 in the TLR1 BB loop. Because this model suggested that steric hindrance would significantly alter the binding interactions between DD loop of TLR2 and BB loop of TLR1, Gly-676 in TLR1 was rationally mutated to Ala and Leu. As expected, in vitro functional studies involving TLR1 G676A and TLR1 G676L resulted in reduced PAM(3)CSK(4) mediated NF-kappaB activation lending support to the computerized predictions. Additionally, mutation of an amino acid residue (TLR2 Asp-730) in Region II also resulted in decreased activity in agreement with our model, providing new insights into the structure-function relationship of TLR2/1 TIR domains.

Diproline Templates as Folding Nuclei in Designed Peptides. Conformational Analysis of Synthetic Peptide Helices Containing Amino Terminal Pro-Pro Segments

The effect of N-terminal diproline segments in nucleating helical folding in designed peptides has been studied in two model sequences Piv-Pro-Pro-Aib-Leu-Aib-Phe-OMe (1) and Boc-Aib-Pro-Pro-Aib-Val-Ala-Phe-OMe (2). The structure of 1 in crystals, determined by X-ray diffraction, reveals a helical (alphaR) conformation for the segment residues 2 to 5, stabilized by one 4-->1 hydrogen bond and two 5-->1 interactions. The N-terminus residue, Pro(1) adopts a polyproline II (P(II)) conformation. NMR studies in three different solvent systems support a conformation similar to that observed in crystals. In the apolar solvent CDCl3, NOE data favor the population of both completely helical and partially unfolded structures. In the former, the Pro-Pro segment adopts an alphaR-alphaR conformation, whereas in the latter, a P(II)-alphaR structure is established. The conformational equilibrium shifts in favor of the P(II)-alphaR structure in solvents like methanol and DMSO. A significant population of the Pro(1)-Pro(2) cis conformer is also observed. The NMR results are consistent with the population of at least three conformational states about Pro-Pro segment: trans alphaR-alphaR, trans P(II)-alphaR and cis P(II)-alphaR. Of these, the two trans conformers are in rapid dynamic exchange on the NMR time scale, whereas the interconversion between cis and trans form is slow. Similar results are obtained with peptide 2. Analysis of 462 diproline segments in protein crystal structures reveals 25 examples of the alphaR-alphaR conformation followed by a helix. Modeling and energy minimization studies suggest that both P(II)-alphaR and alphaR-alphaR conformations have very similar energies in the model hexapeptide 1.

On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions.

Reliable studies of enzymatic reactions by combined quantum mechanics/molecular mechanics (QM/MM) approaches, with an ab initio description of the quantum region, presents a major challenge to computational chemists. The main problem is the need for a very large computer time for the evaluation of the QM energy, which in turn makes it extremely challenging to perform proper configurational sampling. A seemingly reasonable alternative is to perform energy minimization studies of the type used in gas-phase ab initio studies. However, it is hard to see why such an approach should give reliable results in protein active sites. To examine the problems with energy minimization QM/MM approaches, we chose the hypothetical reaction of a metaphosphate ion with water in the Ras.GAP complex. This hypothetical reaction served as a simple benchmark reaction. The possible problems with the QM/MM minimization were explored by generating several protein configurations from long MD simulations and using energy minimization and scanning of the reaction coordinates to evaluate the corresponding potential energy surfaces of the reaction for each of these different protein configurations. Comparing these potential energy surfaces, we found major variations of the corresponding minima. Furthermore, the reaction energies and activation energies also varied significantly even for similar protein configurations. The specific coordination of a magnesium ion, present in the active center of the protein complex, turned out to influence the energetics of the reaction in a major way, where a direct coordination to the reactant leads to an increase of the activation energy by 17 kcal/mol. Apparently, using energy minimization to generate potential surfaces for an enzymatic reaction, while starting from a single protein structure, could lead to major errors in calculations of activation free energies and binding free energies. Thus we believe that extensive samplings of the configurational space of the protein are essential for meaningful determination of the energetics of enzymatic reactions. The possible relevance of our conclusion with regard to a recent study of the RasGAP reaction is discussed.

Crystal Structure of BRL 42715, C6-(N1-Methyl-1,2,3-triazolylmethylene)penem, in Complex withEnterobactercloacae908R β-Lactamase: Evidence for a Stereoselective Mechanism from Docking Studies

BRL 42715, C6-(N1-methyl-1,2,3-triazolylmethylene)penem, is an active-site-directed inactivator of bacterial beta-lactamases. The crystal structure of Enterobacter cloacae 908R class C beta-lactamase in complex with BRL 42715, docking, and energy minimization studies explain stereoselectivity of the binding of C6-(heterocyclic methylene)penems against class C beta-lactamase.

Azepinone as a conformational constraint in the design of κ-opioid receptor agonists

A new class of κ-opioid receptor agonists is described. The design of these agents was based upon energy minimization and structural overlay studies of the generic azepin-2-one structure 3 with the crystal structure of arylacetamide κ agonist 1, ICI 199441. The most active compound identified was ligand 4a ( K i = 0.34 nM), which demonstrated potent antinociceptive activity after oral administration in rodents.

Synthesis, structure solution, characterization, and catalytic properties of TNU-10: a high-silica zeolite with the STI topology.

A high-silica zeolite (Si/Al = 7.1) with the STI framework topology, denoted TNU-10, has been synthesized in the presence of 1,4-bis(N-methylpyrrolidinium)butane and Na(+) cations as structure-directing agents, and its structure in the proton form has been refined against laboratory powder X-ray data in space group Fmmm (a = 13.533(1) A, b = 17.925(2) A, c = 17.651(2) A). The space group symmetry is supported by electron diffraction and energy minimization studies. The as-made and proton form of TNU-10 are extensively characterized by elemental and thermal analyses, scanning electron microscopy, N(2) adsorption, multinuclear solid-state NMR, IR, and temperature-programmed desorption of ammonia, and the location of the organic structure-directing agent in the channel system is determined by molecular modeling. The catalytic properties of H-TNU-10 and Co-TNU-10 are evaluated for the skeletal isomerization of 1-butene to isobutene and the selective reduction of NO with methane, respectively. When compared to H-ferrierite, a low selectivity to isobutene is observed for H-TNU-10. However, it is found that Co-TNU-10 exhibits a maximum NO conversion of 93% at 823 K under conditions of high concentrations of methane (16,000 ppm) and water vapor (10%) and in the presence of 2.6% O(2), which is considerable higher than even the value (74%) obtained from Co-ferrierite, known as the best catalyst for this reaction, under the identical conditions.

A study of the cu clusters using gray-coded genetic algorithms and differential evolution

Energy minimization studies were carried out for a number of Cu clusters using binary and Gray-coded genetic algorithms along with real coded differential evolution, and their optimized ground state geometries are presented. The potential energy function is constructed using a two-body interaction methodology, involving both attractive and repulsive pair-potential terms. The results obtained through the evolutionary algorithms are compared against those obtained earlier using a Monte Carlo technique.

Vibrational and thermal studies of p-methylaniline complexes with Ni(II), Zn(II) and Cd(II) iodides

The complexes of general formula [MI 2( p-methylaniline) n ] ( n=2, M=Zn and Cd; n=4, M=Ni) have been prepared and characterized by their FT-infrared (IR) spectra, FT-Raman spectra, thermal analyses, elemental analyses and UV-Vis electronic absorption spectra. The observed IR and Raman bands of the complexes have been assigned as compared with the free p-methylaniline (pMA). The influence of the transition metals on the pMA vibrational bands has been investigated. The results of thermogravimetry (TG) and differential scanning calorimeter (DSC) have been discussed. The IR and Raman spectral studies and the energy minimization studies with B88-PW91/DZVP level density functional theory (DFT) and semiempirical MNDO/d calculations show that the four-coordinate [ZnI 2(pMA) 2] and [CdI 2(pMA) 2] complexes belong to C 2v point group.