Protein strain in blue copper proteins studied by free energy perturbations.

Free energy perturbations have been performed on two blue copper proteins, plastocyanin and nitrite reductase. By changing the copper coordination geometry, force constants, and charges, we have estimated the maximum energy with which the proteins may distort the copper coordination sphere. By comparing this energy with the quantum chemical energy cost for the same perturbation on the isolated copper complex, various hypotheses about protein strain have been tested. The calculations show that the protein can only modify the copper-methionine bond length by a modest amount of energy-<5 kJ/mol-and they lend no support to the suggestion that the quite appreciable difference in the copper coordination geometry encountered in the two proteins is a result of the proteins enforcing different Cu-methionine bond lengths. On the contrary, this bond is very flexible, and neither the geometry nor the electronic structure change appreciably when the bond length is changed. Moreover, the proteins are rather indifferent to the length of this bond. Instead, the Cu(II) coordination geometries in the two proteins represent two distinct minima on the potential surface of the copper ligand sphere, characterized by different electronic structures, a tetragonal, mainly sigma-bonded, structure in nitrite reductase and a trigonal, pi-bonded, structure in plastocyanin. In vacuum, the structures have almost the same energy, and they are stabilized in the proteins by a combination of geometric and electrostatic interactions. Plastocyanin favors the bond lengths and electrostatics of the trigonal structure, whereas in nitrite reductase, the angles are the main discriminating factor. Proteins 1999;36:157-174.     

Density functional theory calculations on the thermodynamic properties of polynitrosoprismanes

A series of polynitrosoprismanes, C(6)H(6 - n )(NO)( n ) (n?=?1-6), considered as high energy density compounds (HEDCs), have been designed computationally. We calculated the electronic structures, the heats of formation, the specific enthalpies of combustion, the bond dissociation energies, and the strain energies of the title compounds using density functional theory (DFT) with the 6-311G** basis set. It was found that the ΔE (LUMO-HOMO) values of the title compounds decrease as the number of nitroso groups increase, and the energy gaps of the prismane derivatives are much lower than that of TATB. Their high positive heats of formation indicate that polynitrosoprismanes can store a great deal of energy. Furthermore, the HOFs for the nitrosoprismane series were observed to decrease until three nitroso groups were connected to the prismane skeleton. For the polynitrosoprismanes, the trigger bond was confirmed to be the C-C bond in the skeleton. According to our calculations, all nitrosoprismanes appear to have large strain energies, and these calculations can provide basic information that may prove useful for the molecular design of novel high energy density materials.     

Stereochemical studies on cyclic peptides. Part X. Conformational analysis of hydrogen bonded cyclic pentapeptides.

Conformational aspects of 4 leads to 1 hydrogen bonded cyclic pentapeptides are considered in this paper from the point of view of "contact criteria" and potential energy calculations. Three types of such hydrogen bonded conformations, designated A1, A2 and B, are possible, involving some amount of strain on the bond angles. The energy of hydrogen bonded cyclopentaglycyl is somewhat less than that of the five-fold symmetrical conformation. The stereochemical feasibility of introducing L- and D-alanyl resudues in these structures has also been studied and the possible types for different sequences of alanyl residues have been determined. The results are discussed further in the light of the limited data available from crystal structure and nuclear magnetic resonance studies on cyclic pentapeptides.     

Folding of the twisted beta-sheet in bovine pancreatic trypsin inhibitor

The dominant role of local interactions has been demonstrated for the formation of the strongly twisted antiparallel beta-sheet structure consisting of residues 18-35 in bovine pancreatic trypsin inhibitor. Conformational energy minimization has indicated that this beta-sheet has a strong twist even in the absence of the rest of the protein molecule. The twist is maintained essentially unchanged when energy minimization is carried out by starting from the native conformation. By starting from a nontwisted beta-sheet conformation of residues 18-35, a strongly twisted structure (higher in energy than the native) is obtained. The high twist of the native-like beta-sheet is a consequence of its amino acid sequence, but it is enhanced strongly by interchain interactions that operate within the beta-sheet. The existence of the twisted beta-sheet structure does not require the presence of a disulfide bond between residue 14 and residue 38. It actually may facilitate the formation of this bond. Therefore, it is likely that the beta-sheet structure forms during an earlier stage of folding than the formation of this disulfide bond. This study provides an example of the manner in which conformational energy calculations can be used to provide information about the probable pathway of the folding of a protein.     

Theoretical study of the discrimination between O(2) and CO by myoglobin

Combined quantum chemical and molecular mechanics geometry optimisations have been performed on myoglobin without or with O(2) or CO bound to the haem group. The results show that the distal histidine residue is protonated on the N(epsilon 2) atom and forms a hydrogen bond to the haem ligand both in the O(2) and the CO complexes. We have also re-refined the crystal structure of CO[bond]myoglobin by a combined quantum chemical and crystallographic refinement. Thereby, we probably obtain the most accurate available structure of the active site of this complex, showing a Fe[bond]C[bond]O angle of 171 degrees, and Fe[bond]C and C[bond]O bond lengths of 170-171 and 116-117 pm. The resulting structures have been used to calculate the strength of the hydrogen bond between the distal histidine residue and O(2) or CO in the protein. This amounts to 31-33 kJ/mol for O(2) and 2-3 kJ/mol for CO. The difference in hydrogen-bond strength is 21-22 kJ/mol when corrected for entropy effects. This is slightly larger than the observed discrimination between O(2) or CO by myoglobin, 17 kJ/mol. We have also estimated the strain of the active site inside the protein. It is 2-4 kJ/mol larger for the O(2) complex than for the CO complex, independent of which crystal structure the calculations are based on. Together, these results clearly show that myoglobin discriminates between O(2) and CO mainly by electrostatic interactions, rather than by steric strain.     

Investigation of Lignin-water interactions by molecular simulation

The results of molecular dynamics simulations of three lignin-water systems are presented. Static and dynamic properties of each system are compared to a benchmark system consisting entirely of water molecules. The significantly reduced mobility of water molecules local to lignin hydroxyl regions is attributed to hydrogen bond formation, while the slightly reduced mobility of water molecules in the vicinity of lignin methoxyl groups results from a hydrophobic effect that causes water molecules to structure themselves around these groups. The average diffusion of water in each system correlates with the number of methoxyl groups present in the system. As the number of methoxyls in the system increases, so too does the average diffusion constant of water in that system. The bulky methoxyl groups obstruct water from accessing lignin hydroxyl regions where hydrogen bond formation is anticipated and the hydrogen-bonded water lowers the average diffusion constant.     

Flexibility of 3',5' deoxyribonucleoside diphosphates

In 3',5' deoxyribonucleoside diphosphates, in addition to the nature of the base and the sugar puckering, there are six single bond rotations. However, from the analysis of crystal structure data on the constituents of nucleic acids, only three rotational angles, that are about glycosyl bond, about C4'-C5' and about C3'-O3' bonds, are flexible. For a given sugar puckering and a base, potential energy calculations using non-bonded, electrostatic and torsional functions were carried out by varying the three torsion angles. The energies are represented as isopotential energy surfaces. Since the availability of the real-time color graphics, it is possible to analyse these isopotential energy surfaces. The calculations were carried out for C3' exo and C3' endo puckerings for deoxyribose and also for four bases. These calculations throw more light not only on the allowed regions for the three rotational angles but also on the relationships among them. The dependence of base and the puckering of the sugar on these rotational angles and thereby the flexibility of the 3',5' deoxyribonucleoside diphosphates is discussed. From our calculations, it is now possible to follow minimum energy path for interconversion among various conformers.     

N+注入选育白腐菌及其降解油菜秸秆木质纤维素的研究

以白腐菌WY01为出发菌,利用N＋注入技术选育出一株遗传性状稳定的漆酶高产诱变菌株WY02,经过60 d的发酵培养,其产酶量由出发菌的13.75 U/g增加到52.5 U/g,即产酶量提高了2.82倍;诱变菌株WY02对油菜秸秆中的木质素、半纤维素和纤维素的降解率分别为54.1%,39.1%,32.8%,用红外光谱法（IR）分析经诱变菌株降解后的油菜秸秆中木质素官能团的变化,用于阐明诱变菌株对油菜秸秆中木质素的生物降解机制。结果表明：油菜秸秆经白腐菌诱变菌株降解后,其木质素含量明显降低。木质素与苯环相连的C=O键、木质素侧链上CH2结构以及木质素单体（紫丁香基和愈创木基）被部分降解,木质素的苯环结构遭到一定程度的破坏。     

Conformational preferences of cyclopropyl peptides. Crystal structure of (E)-DL-1-benzamido-1-methoxycarbonyl-2-chlorcyclopropane (BCP)

Crystal structure analysis of (E)-DL-1-benzamido-1-methoxycarbonyl-2-chlorocyclopropane (C12H12NO3Cl) is reported. The phi' (about N1-C1 bond) and psi' (about C1-C11 bond) torsional angles for this compound are -62.5 degrees and -33.0 degrees, respectively, and are close to the phi, psi values of the 3(10) helix and the alpha-helix. Semi-empirical potential energy calculations are performed on a cyclopropyl dipeptide which is a special case of alpha,alpha-disubstituted dipeptide where the alpha-carbon and the two substituent carbon atoms form a 3-membered ring. Our calculations show that different types of helics: alpha-, gamma-, pi-, omega-, 3(10-) and delta-helices, are energetically favorable. Another interesting possibility is the formation of a cyclic pentapeptide with five-fold symmetry. The effect of substitutions on C beta atom are also studied with the help of potential energy maps. Selective substitutions on C beta atom may be used effectively to restrict either phi or psi values into a very narrow range.     

Quantum mechanical electronic structure calculation reveals orientation dependence of hydrogen bond energy in proteins

Hydrogen bond plays a unique role in governing macromolecular interactions with exquisite specificity. These interactions govern the fundamental biological processes like protein folding, enzymatic catalysis, molecular recognition. Despite extensive research work, till date there is no proper report available about the hydrogen bond's energy surface with respect to its geometric parameters, directly derived from proteins. Herein, we have deciphered the potential energy landscape of hydrogen bond directly from the macromolecular coordinates obtained from Protein Data Bank using quantum mechanical electronic structure calculations. The findings unravel the hydrogen bonding energies of proteins in parametric space. These data can be used to understand the energies of such directional interactions involved in biological molecules. Quantitative characterization has also been performed using Shannon entropic calculations for atoms participating in hydrogen bond. Collectively, our results constitute an improved way of understanding hydrogen bond energies in case of proteins and complement the knowledge‐based potential. Proteins 2017; 85:1046–1055. © 2017 Wiley Periodicals, Inc.     

On the role of strain in blue copper proteins

Theoretical investigations of the structure and function of the blue copper proteins are described. We have studied the optimum vacuum geometry of oxidised and reduced copper sites, the relative stability of trigonal and tetragonal Cu(II) structures, the relation between the structure and electronic spectra, the reorganisation energy, and reduction potentials. Our calculations give no support to the suggestion that strain plays a significant role in the function of these proteins; on the contrary, our results show that the structures encountered in the proteins are close to their optimal vacuum geometries (within 7 kJ/mol). We stress the importance of defining what is meant by strain and of quantifying strain energies or forces in order to make strain hypotheses testable.     

The Fe-CO bond energy in myoglobin: a QM/MM study of the effect of tertiary structure

The Fe-CO bond dissociation energy (BDE) in myoglobin (Mb) has been calculated with B3LYP quantum mechanics/molecular mechanics methods for 22 different Mb conformations, generated from molecular dynamics simulations. Our average BDE of 8.1 kcal/mol agrees well with experiment and shows that Mb weakens the Fe-CO bond by 5.8 kcal/mol; the calculations provide detailed atomistic insight into the origin of this effect. BDEs for Mb conformations with the R carbonmonoxy tertiary structure are on average 2.6 kcal/mol larger than those with the T deoxy tertiary structure, suggesting two functionally distinct allosteric states. This allostery is partly explained by the reduction in distal cavity steric crowding as Mb moves from its T to R tertiary structure.     

Theoretical study of the surface properties of poly(dimethylsiloxane) and poly(tetrafluoroethylene)

Molecular dynamics (MD) simulations of poly(dimethylsiloxane) (PDMS) and poly(tetrafluoroethylene) (PTFE) were carried out to determine their surface properties and energies. This study helps to gain better insight into the molecular modeling of PDMS and PTFE, in particular how different approaches affect calculations of surface energy. Current experimental and theoretical data were used to further understand the surface properties of PDMS and PTFE as well as to validate and verify results obtained from the combination of density functional theory (DFT) calculations (including periodic boundary conditions) and MD simulations. Detailed analysis of the structure and electronic properties (by calculation of the projected density of states) of the bulk and surface models of PDMS and PTFE was performed. The sensitivity of the surface energy calculation of these two polymers to the chemistry and model preparation was indicated. The balance between the molecular density, weight (which also reflects bond orientation in the surface region), bond flexibility, and intramolecular interactions including bond stretching was revealed to govern the results obtained. In modeling, the structural organization of polymer near a given surface (types and number of end groups and broken bonds due to application of different cut offs of the periodic structure) also significantly affects the final results. Besides the structural differences, certain simulation parameters, such the DFT functionals and simulation boxes utilized, play an important role in determining surface energy. The models used here were shown to be sufficient due to their good agreement with experimental and other theoretical data related to surface properties and surface energies.     

Cellulose-Lignin Interactions (A Computational Study)

Within a broader program of study of the molecular structure of plant cell walls, molecular dynamics calculations were used to explore the character of the motion of lignin model compounds near a cellulose surface. Model cellulose microfibrils, which have a large number of hydroxyl groups on the surface, appear to have a net attractive interaction with the lignin models examined in this study. The lignin monomer coniferyl alcohol rapidly adsorbed onto the surface from a water layer after it was released 13 A from the surface. The major long-range force responsible for this adsorption is likely electrostatic. The attractive interaction is sufficient to restrict the motion of coniferyl alcohol when it is within 1 A of the surface and to orient the phenyl ring parallel to the surface. The [beta]-O-4-linked trimer also was observed to adsorb onto the surface with two of its phenyl rings parallel to the surface. These results suggest a mechanism by which the polysaccharide component of the plant cell wall could influence the structure of lignin. Furthermore, they provide a rationalization of the experimental observation that polysaccharides can change the course of dehydrogenation polymerization of cinnamyl alcohols.     

Computation of mixed phosphatidylcholine-cholesterol bilayer structures by energy minimization.

The energetically preferred structures of dimyristoylphosphatidylcholine (DMPC)-cholesterol bilayers were determined at a 1:1 mole ratio. Crystallographic symmetry operations were used to generate planar bilayers of cholesterol and DMPC. Energy minimization was carried out with respect to bond rotations, rigid body motions, and the two-dimensional lattice constants. The lowest energy structures had a hydrogen bond between the cholesterol hydroxyl and the carbonyl oxygen of the sn-2 acyl chain, but the largest contribution to the intermolecular energy was from the nonbonded interactions between the flat alpha surface of cholesterol and the acyl chains of DMPC. Two modes of packing in the bilayer were found; in structure A (the global minimum), unlike molecules are nearest neighbors, whereas in structure B (second lowest energy) like-like intermolecular interactions predominate. Crystallographic close packing of the molecules in the bilayer was achieved, as judged from the molecular areas and the bilayer thickness. These energy-minimized structures are consistent with the available experimental data on mixed bilayers of lecithin and cholesterol, and may be used as starting points for molecular dynamics or other calculations on bilayers.     

Study of conformations of the adenosine phosphates. I: Adenosine monophosphate (AMP)

Theoretical studies of the AMP molecule are made in a free and isolated environment with extended Mickel theory (EHT) using the experimentally observed bond lengths and angles, and the experimentally observed torsion angles as a starting conformation. Four torsional degrees of freedom were assumed and all AMP atoms were included in the calculations. Results show that the AMP structure corresponds to an EHT minimum energy configuration when the molecule is isolated from the crystal atoms. This is in contrast with results reported for ATP in the succeeding paper and is attributed to the fact that AMP is crystallized as a free acid. A global minimum, corresponding to a more open structure, is calculated to be more stable than the crystalline form and is lower in energy by 0·05 eV.     

Theoretical investigation on detonation performances and thermodynamic stabilities of the prismane derivatives

Based on DFT-B3LYP/6-311G** method, the molecular geometric structures of polynitramineprismanes are fully optimized. The detonation performances, energy gaps, strain energies, as well as their stability were investigated to look for high energy density compounds (HEDCs). Our results show that all polynitramineprismanes have high and positive heat of formation. To construct the relationship between stabilities and structures, energy gaps and bond dissociation energies are calculated, and these results show that the energy gaps of prismane derivatives are much higher than that of TATB (0.1630). In addition, the C-C bonds on cage are confirmed as trigger bond in explosive reaction. All polynitramineprismanes have large strain energies, and the strain energies of all compounds are slightly smaller than prismane, which indicated that the strain energies were somewhat released compared to prismane. Considering the quantitative criteria of HEDCs, hexanitramineprismane is a good candidate of high energy compounds.     

Histidine protonation states are key in the LigI catalytic reaction mechanism

Lignin is one of the world's most abundant organic polymers, and 2-pyrone-4,6-dicarboxylate lactonase (LigI) catalyzes the hydrolysis of 2-pyrone-4,6-dicarboxylate (PDC) in the degradation of lignin. The pH has profound effects on enzyme catalysis and therefore we studied this in the context of LigI. We found that changes of the pH mostly affects surface residues, while the residues at the active site are more subject to changes of the surrounding microenvironment. In accordance with this, a high pH facilitates the deprotonation of the substrate. Detailed free energy calculations by the empirical valence bond (EVB) approach revealed that the overall hydrolysis reaction is more likely when the three active site histidines (His31, His33 and His180) are protonated at the ? site, however, protonation at the δ site may be favored during specific steps of the reaction. Our studies have uncovered the determinant role of the protonation state of the active site residues His31, His33 and His180 in the hydrolysis of PDC.     

Catalytic Efficiency of some Mediators in Laccase-Catalyzed Alcohol Oxidation

The enzyme laccase oxidises phenolic groups of lignin but not the non-phenolic ones. Redox mediators activate laccase towards the non-phenolic groups, particularly the benzyl alcohols. The oxidation step is performed by the oxidised form of the mediator, generated on its interaction with laccase. The oxidised mediator can follow an electron transfer, a radical hydrogen atom transfer or an ionic mechanism in the oxidation of the non-phenolic subunits. Support for these conclusions is provided by (i) investigating the product pattern with suitable probe substrates, (ii) measuring the intramolecular kinetic isotope effect. Determination of electrochemical properties and bond dissociation energies via semiempirical calculations enabled us to rationalise the origin of the different mechanistic behaviour of the mediators. Finally, a comparison of different laccase-mediator-systems (LMS), when applied to the delignification of wood pulp, indicates violuric acid as the most efficient mediator, in an oxidation that is selectively directed towards lignin only.     

Catalytic Efficiency of some Mediators in Laccase-Catalyzed Alcohol Oxidation

The enzyme laccase oxidises phenolic groups of lignin but not the non-phenolic ones. Redox mediators activate laccase towards the non-phenolic groups, particularly the benzyl alcohols. The oxidation step is performed by the oxidised form of the mediator, generated on its interaction with laccase. The oxidised mediator can follow an electron transfer, a radical hydrogen atom transfer or an ionic mechanism in the oxidation of the non-phenolic subunits. Support for these conclusions is provided by (i) investigating the product pattern with suitable probe substrates, (ii) measuring the intramolecular kinetic isotope effect. Determination of electrochemical properties and bond dissociation energies via semiempirical calculations enabled us to rationalise the origin of the different mechanistic behaviour of the mediators. Finally, a comparison of different laccase-mediator-systems (LMS), when applied to the delignification of wood pulp, indicates violuric acid as the most efficient mediator, in an oxidation that is selectively directed towards lignin only.