An Effective Solvation Term Based on Atomic Occupancies for Use in Protein Simulations

Abstract

Several approaches to the treatment of solvent effects based on continuum models are reviewed and a new method based on occupied atomic volumes (occupancies) is proposed and tested. The new method describes protein-water interactions in terms of atomic solvation parameters, which represent the solvation free energy per unit of volume. These parameters were determined for six different atoms types, using experimental free energies of solvation. The method was implemented in the GROMOS and PRESTO molecular simulation program suites. Simulations with the solvation term require 20-50% more CPU time than the corresponding vacuum simulations and are approximately 20 times faster than explicit water simulations. The method and parameters were tested by carrying out 200 ps simulations of BPTI in water, in vacuo, and with the solvation term. The performance of the solvation term was assessed by comparing the structures and energies from the solvation simulations with the equivalent quantities derived from several BPTI crystal structures and from the explicit water and vacuum simulations. The model structures were evaluated in terms of exposed total surface, buried and exposed polar surfaces, secondary structure preservation, number of hydrogen bonds, energy contributions, and positional deviations from BPTI crystal structures. Vacuum simulations produced unrealistic structures with respect to all criteria applied. The structures resulting from the simulations with explicit water were closer to the 5PTI crystal structure, although part of the secondary structure dissolved. The simulations with the effective solvation term produce structures that are normal according to all evaluations and in most respects are remarkably similar to the 5PTI crystal structure despite considerable positional fluctuations during the simulations. The segments where the model and crystal structures differ are known to be flexible and the observed difference may be physically realistic. The effective solvation term based on occupancies is not only very efficient in terms of computer time but also results in meaningful structural properties for BPTI. It may therefore be generally useful in molecular dynamics of macromolecules.     

Protein surface roughness accounts for binding free energy of Plasmepsin II‐ligand complexes

The calculation of absolute binding affinities for protein‐inhibitor complexes remains as one of the main challenges in computational structure‐based ligand design. The present work explored the calculations of surface fractal dimension (as a measure of surface roughness) and the relationship with experimental binding free energies of Plasmepsin II complexes. Plasmepsin II is an attractive target for novel therapeutic compounds to treat malaria. However, the structural flexibility of this enzyme is a drawback when searching for specific inhibitors. Concerning that, we performed separate explicitly solvated molecular dynamics simulations using the available high‐resolution crystal structures of different Plasmepsin II complexes. Molecular dynamics simulations allowed a better approximation to systems dynamics and, therefore, a more reliable estimation of surface roughness. This constitutes a novel approximation in order to obtain more realistic values of fractal dimension, because previous works considered only x‐ray structures. Binding site fractal dimension was calculated considering the ensemble of structures generated at different simulation times. A linear relationship between binding site fractal dimension and experimental binding free energies of the complexes was observed within 20 ns. Previous studies of the subject did not uncover this relationship. Regression model, coined FD model, was built to estimate binding free energies from binding site fractal dimension values. Leave‐one‐out cross‐validation showed that our model reproduced accurately the absolute binding free energies for our training set (R² = 0.76; <|error|> =0.55 kcal/mol; SD_error = 0.19 kcal/mol). The fact that such a simple model may be applied raises some questions that are addressed in the article.     

基于高通量共聚焦激光扫描显微镜方法定量分析副溶血性弧菌生物被膜结构

【目的】副溶血性弧菌是水产品中常见的食源性致病菌,生物被膜的形成对副溶血性弧菌的环境生存和传播至关重要。这项工作的目的是评估临床和环境中分离出的44株副溶血性弧菌菌株形成的生物被膜的结构多样性。【方法】该研究基于共聚焦激光扫描显微镜的高通量方法,使用与高分辨率成像兼容的96孔微量滴定板,结合结构分析软件ISA-2来研究生物被膜形成和结构,分析22株食品与22株临床来源的副溶血性弧菌菌株形成的生物被膜结构参数(生物体积、平均厚度、粗糙系数)。【结果】CLSM图像显示,44株副溶血性弧菌菌株在培养48h后能够形成3D结构,进一步比较分析了临床来源菌株与环境来源菌株形成的生物被膜结构异同,发现临床菌株生物被膜的变异系数比环境菌株生物被膜的变异系数小,且同时携带tdh和trh两种毒力因子的菌株生物被膜变异性最小。凝聚层次聚类分析结果显示,副溶血性弧菌生物被膜可以分为致密且表面光滑(39%)、斑驳且表面粗糙(27%)、疏松且表面坑洼(34%),临床菌株易形成致密且表面光滑和斑驳且表面粗糙的生物被膜,而环境菌株易形成致密且表面光滑和疏松且表面坑洼的生物被膜。【结论】该研究深入了解了副溶血性弧菌生物...     

An analytical approach to the light transport in columnar phosphors. Detector Optical Gain,angular distribution and the CsI:Tl paradigm

PurposeAn analytical model has been developed for the light propagation in columnar phosphors, based on the optical photon propagation physical and geometrical principles.MethodsThis model accounts for the multiple reflections on the sides of the crystal column, as well as for the infinite forward and backward reflections of the propagated optical photon beams created in the crystal bulk. Additionally it considers the lateral propagated optical photon beams after multiple refractions from the neighbor columns and the optical photon attenuation inside the scintillator.The model was used to predict the Detector Optical Gain (DOG), and the angular distribution, of the columnar CsI:Tl scintillators, used in medical imaging.ResultsThe model was validated against CsI:Tl optical photon transmission published results and good agreement was observed. It was, also, found that the DOG is affected by the length of the columns, as well as the incident X-ray energy spectrum. The results of the angular distribution are in accordance with the theory that the longer crystal columns have more directional light distribution.ConclusionsThe results of DOG are in accordance with the use of short crystal columns for lower energies (mammography) and the use of long crystal columns for higher energies (general radiology). Angular distribution was found more directive for long crystal columns.     

Insights into the Substrate Specificity of a Thioesterase Rv0098 of Mycobacterium Tuberculosis through X-ray Crystallographic and Molecular Dynamics Studies

Abstract

The crystal structure of Rv0098, a long-chain fatty acyl-CoA thioesterase from Mycobacterium tuberculosis with bound dodecanoic acid at the active site provided insights into the mode of substrate binding but did not reveal the structural basis of substrate specificities of varying chain length. Molecular dynamics studies demonstrated that certain residues of the substrate binding tunnel are flexible and thus modulate the length of the tunnel. The flexibility of the loop at the base of the tunnel was also found to be important for determining the length of the tunnel for accommodating appropriate substrates. A combination of crystallographic and molecular dynamics studies thus explained the structural basis of accommodating long chain substrates by Rv0098 of M. tuberculosis.     

Structural Features of a Cold-adapted Alaskan Bacterial Lipase

Abstract

The three dimensional model of cold-adapted Alaskan psychrotroph Pseudomonas species (Strain B11-1) lipase has been constructed by homology modeling based on the crystal structure of acetyl esterase from Rhodococcus species and refined by molecular dynamics methods. Our model locates the substrate-binding cavity and further suggests that Ser-155, Asp-250, and His-280 are the members of the catalytic triad. Substrate specificity of the modeled lipase has been examined by docking experiments, which indicates that the ester of C₆ fatty acid has the highest affinity for the enzyme. Our model also identifies the oxyanion hole that plays an important role in the stabilization of the tetrahedral intermediate during catalysis. Comparison of this cold-adapted lipase with the crystal structure of a thermophilic Bacillus stearothermophilus P1 lipase supported the assumption that cold-adapted enzymes have a more flexible three-dimensional structure than their thermophilic counterparts. The conformational flexibility of this modeled cold-adapted lipase at low temperature probably originates from a combination of factors compared to its thermophilic counterpart, i.e., lower number of salt bridges and cation-π interactions, increase in the non-polar surface area exposed to solvent. Our study may help in understanding the structural features of a cold- adapted lipase and can further be used in engineering lipase that can function at or near extreme temperatures with considerable biotechnological potential.     

Synthesis of cyclobutane nucleoside analogues 3: Preparation of carbocyclic derivatives of oxetanocin

Abstract

A synthesis of cyclobutene nucleoside analogs in which the nucleobase is tethered by a methylene group is described. The coupling of 6-chloropurine with 3-hydroxymethyl-cyclobutanone proceeds via its triflate to give both N-7 and N-9 regioisomers with relative yields corresponding to the calculated charge distribution of the 6-chloropurinyl anion. The stereoselective reduction of the N-alkylated ketones yielded quantitatively one stereoisomer in each case. The structural assignments were based on spectroscopic data and single crystal X-ray diffraction. Attempts to photoexcite the N-7 and N-9 ketones in order to promote ring-expansion did not ensue. Preliminary evidence suggests a photodecarbonylation to cyclopropanes took place.     

Cancer stem cells CD133 inhibition and cytotoxicity of certain 3-phenylthiazolo[3,2-a]benzimidazoles: design,direct synthesis,crystal study and in vitro biological evaluation

Cancer stem cells (CSCs) have been objects of intensive study since their identification in 1994. Adopting a structural rigidification approach, a novel series of 3-phenylthiazolo[3,2-a]benzimidazoles 4a–d was designed and synthesised, in an attempt to develop potent anticancer agent that can target the bulk of tumour cells and CSCs. The anti-proliferative activity of the synthesised compounds was evaluated against two cell lines, namely; colon cancer HT-29 and triple negative breast cancer MDA-MB-468 cell lines. Also, their inhibitory activity against the cell surface expression of CD133 was examined. In particular, compound 4b emerged as a promising hit molecule as it manifested good antineoplastic potency against both tested cell lines (IC₅₀?=?9 and 12?μM, respectively), beside its ability to inhibit the cell surface expression of CD133 by 50% suggesting a promising potential of effectively controlling the tumour by eradicating the tumour bulk and inhibiting the proliferation of the CSCs. Moreover, compounds 4a and 4c showed moderate activity against HT-29 (IC₅₀?=?21 and 29?μM, respectively) and MDA-MB-468 (IC₅₀?=?23 and 24?μM, respectively) cell lines, while they inhibited the CD133 expression by 14% and 48%, respectively. Finally, a single crystal X-ray diffraction was recorded for compound 4d.     

Density functional theory study on (LiNH<Subscript>2</Subscript>)<Subscript>n</Subscript> (<Emphasis Type="Italic">n</Emphasis> = 1–5) clusters

Geometrical structures and relative stabilities of (LiNH₂)_n (n = 1–5) clusters were studied using density functional theory (DFT) at the B3LYP/6-31G* and B3LYP/6-31++G* levels. The electronic structures, vibrational properties, N–H bond dissociation energies (BDE), thermodynamic properties, bond properties and ionization potentials were analyzed for the most stable isomers. The calculated results show that the Li–N and Li–Li bonds can be formed more easily than those of the Li–H or N–H bonds in the clusters, in which NH₂ is bound to the framework of Li atomic clusters with fused rings. The average binding energies for each LiNH₂ unit increase gradually from 142 kJ mol⁻¹ up to about 180 kJ mol⁻¹ with increasing n. Natural bond orbital (NBO) analysis suggests that the bonds between Li and NH₂ are of strong ionicity. Three-center–two-electron Li–N–Li bonding exists in the (LiNH₂)₂ dimer. The N–H BDE values indicate that the change in N–H BDE values from the monomer a1 to the singlet-state clusters is small. The N–H bonds in singlet state clusters are stable, while the N–H bonds in triplet clusters dissociate easily. A study of their thermodynamic properties suggests that monomer a1 forms clusters (b1, c1, d2 and e1) easily at low temperature, and clusters with fewer numbers of rings tend to transfer to ones with more rings at low temperature. E _g, E _HOMO and E _av decrease gradually, and become constant. Ring-like (LiNH₂)_3,4 clusters possess higher ionization energy (VIE) and E _g, but lower values of E _HOMO. Ring-like (LiNH₂)_3,4 clusters are more stable than other types. A comparison of structures and spectra between clusters and crystal showed that the NH₂ moiety in clusters has a structure and spectral features similar to those of the crystal.     

Kinetic and structural studies on the interactions of Torpedo californica acetylcholinesterase with two donepezil-like rigid analogues

Acetylcholinesterase inhibitors were introduced for the symptomatic treatment of Alzheimer’s disease (AD). Among the currently approved inhibitors, donepezil (DNP) is one of the most preferred choices in AD therapy. The X-ray crystal structures of Torpedo californica AChE in complex with two novel rigid DNP-like analogs, compounds 1 and 2, have been determined. Kinetic studies indicated that compounds 1 and 2 show a mixed-type inhibition against TcAChE, with K_i values of 11.12?±?2.88 and 29.86?±?1.12?nM, respectively. The DNP rigidification results in a likely entropy-enthalpy compensation with solvation effects contributing primarily to AChE binding affinity. Molecular docking evidenced the molecular basis for the binding of compounds 1 and 2 to the active site of β-secretase-1. Overall, these simplified DNP derivatives may represent new structural templates for the design of lead compounds for a more effective therapeutic strategy against AD by foreseeing a dual AChE and BACE-1 inhibitory activity.     

Molecular Dynamics Simulations of a Calmodulin-peptide Complex in Solution

Abstract

We have performed an 4-ns MD simulation of calmodulin complexed with a target peptide in explicit water, under realistic conditions of constant temperature and pressure, in the presence of a physiological concentration of counterions and using Ewald summation to avoid truncation of long-range electrostatic forces. During the simulation the system tended to perform small fluctuations around a structure similar to, but somewhat looser than the starting crystal structure. The calmodulin-peptide complex was quite rigid and did not exhibit any large amplitude domain motions such as previously seen in apo- and calcium-bound calmodulin. We analyzed the calmodulin-peptide interactions by calculating buried surface areas, CHARMM interaction energies and continuum model interaction free energies. In the trajectory, the protein surface area buried by contact with the peptide is 1373 Ų, approximately evenly divided between the calmodulin N-terminal, C-terminal and central linker regions. A majority of this buried surface, 803 ·A², comes from nonpolar residues, in contrast to the protein as a whole, for which the surface is made up of mostly polar and charged groups. Our continuum calculations indicate that the largest favorable contribution to pep- tide binding comes from burial of molecular surface upon complex formation. Electrostatic contributions are favorable but smaller in the trajectory structures, and actually unfavorable for binding in the crystal structure. Since nonpolar groups make up most of buried surface of the protein, our calculations suggest that the hydrophobic effect is the main driving force for binding the helical peptide to calmodulin, consistent with thermodynamic analysis of experimental data. Besides the burial of nonpolar surface area, secondary contributions to peptide binding come from burial of polar surface and electrostatic interactions. In the nonpolar interactions a crucial role is played by the nine methionines of calmodulin. In the electrostatic interactions the negatively charged protein residues and positively charged peptide residues play a dominant role.     

不同风化时间碳酸岩表面古菌群落结构与功能特征

【背景】古菌群落是碳酸岩表面微生物群落的重要成员,也是碳酸岩表面生物演替的先锋生物,能够促进碳酸岩风化和加快土壤形成,在生物地球化学循环中起重要作用。【目的】揭示在不同风化时间碳酸岩表面风化残积物中的古菌群落结构及生态功能。方法】采集19-213年风化时间段废弃碳酸岩墓碑表面风化残积物样品(n=18),基于宏基因组测序技术分析其古菌群落结构与功能特征。【结果】门水平上,优势门有广古菌门(Euryarchaeota),随后为奇古菌门(Thaumarchaeota)、未鉴定古菌门(unclassified Archaea)、深古菌门(Bathyarchaeota)和泉古菌门(Crenarchaeota);属水平上,优势属主要由甲烷八叠球菌属(Methanosarcina)、甲烷丝状菌属(Methanothrix)、Methanoperedens、氨氧化古菌属(Nitrosocosmicus)、亚硝化球菌属(Nitrososphaera)及其他未鉴定属组成;C/N、C/P、N/P是显著影响碳酸岩表面古菌群落的主要环境因子。进一步分析发现,碳酸岩表面古菌群落功能丰富,其中新陈代谢(metabo...     

Energy gaps of graphene clusters: the first-principles calculations based on high-throughput screening

Abstract

With the enumeration of the triangular lattice fragments, we have systematically investigated the graphene clusters (C_nH_m, n = 14 – 24) with various sizes and shapes, whose structural stabilities and electronic properties are studied by the Hückel molecular orbital (HMO) method and the first-principles calculation. According to the formation energies, we show the structural stabilities of the clusters are closely related to the shape and size, as well as the chemical potential of hydrogen. The energy gaps obtained from the HMO method are in the same trend with the ones calculated by the first-principles calculations, indicating the effective screening of the gap minimum and maximum in a fast speed. There is a general decreasing of the energy gaps with the size increment due to the quantum confinement, meanwhile, the gaps are also highly dependent on the shape of the clusters for those with the same number of carbon atom.     

Comparison of Protein Structures in Solution Using Local Conformations Derived from NMR Data: Application to Cytochrome c

Abstract

Structural comparisons of proteins in solution are often required to examine structure-functional relationships, study structural effects of mutations or distinguish between various forms of the same molecule under different conditions. A nuclear magnetic resonance (NMR) based probabilistic strategy is presented and used to study the structural differences between the two redox states of cytochrome C in solution. A probabilistic approach is employed to calculate the main chain conformations of horse ferro- and ferricytochrome C in solution, based on the published sequential d connectivity data. Conformational differences between the two oxidation states of horse cytochrome C in solution are found to be statistically significant. The largest changes in conformation are at residues Lys27, Thr28, Leu32, Gln42, Thr47, Tyr48, Thr49, Glu69, Lys72, Met80, Phe82, Ile85 and Lys86, all of which are close to the heme (within 14 Å of the heme iron in the high resolution Xray structure of tuna cytochrome c). We suggest that these conformational changes may modulate local dipole moments and hence influence the interactions of cytochrome C with its physiological redox partners during the electron transfer process. The oxidation state dependent conformational differences are found to be much greater in solution than in the crystalline state, and the solution and crystal structures differ significantly in regions close to the heme. These results suggest that the highly charged nature of cytochrome C makes this protein particularly sensitive to the ionic strength of its environment and leads to differences between crystal and solution structures in the same oxidation state. In such cases, crystal structures must be used with caution for modeling molecular interactions in vivo. More generally, this analysis indicates that the determination of accurate local conformations based on nmr data can provide useful information about structure-functional aspects of proteins in solution.     

In memoriam

Microcosm experiments were performed to identify the influence of bacterial cell surfaces on the morphology, mineralogy, size and solubility of CaCO₃ precipitated in response to the enzymatic hydrolysis of urea in an artificial groundwater (AGW) by the ureolytic bacteria, Bacillus pasteurii. In each microcosm, B. pasteurii were contained within a cellulose dialysis membrane (10 K Dalton MWCO), resulting in bacteria-inclusive and bacteria-free AGW solution. Urea hydrolysis by B. pasteurii resulted in the production of ammonium and an increase in pH in the whole AGW solution. This initiated predominantly rhombohedral calcite precipitation at the same critical saturation state ( S _critical = 12) in the B. pasteurii-inclusive and bacteria-free zone of the AGW, indicating the mineralogy and morphology of CaCO₃ precipitation is not controlled by B. pasteurii surfaces. However, the temporal evolution of distinctly different lognormal crystal-size-distributions in the B. pasteurii-inclusive and bacteria-free zone of the AGW resulted from identical changes in bulk solution chemistry. Specifically, B. pasteurii increased the size and size variance of crystals, and led to a greater crystal growth rate throughout the experiments, relative to bacteria-free AGW. Calculated crystal solubility (ln K _S0 ) was lower for crystals > 4000 nm in diameter, reflecting smaller molar surface areas. This suggests that the larger crystals generated in the presence of B. pasteurii have a lower affinity for re-dissolution than those generated in the bacteria-free AGW, which may act as a positive feedback to maintain larger crystal sizes in the presence of B. pasteurii. During ureolysis, higher bacterial concentrations may therefore generate larger and less soluble carbonate crystals. This has important implications for the adaptation of bacterial ureolysis as a method for precipitating calcium carbonate and co-precipitating metals and radionuclides in contaminated aquifers.     

Structural and molecular insights into novel surface‐exposed mucus adhesins from Lactobacillus reuteri human strains

The mucus layer covering the gastrointestinal tract is the first point of contact of the intestinal microbiota with the host. Cell surface macromolecules are critical for adherence of commensal bacteria to mucus but structural information is scarce. Here we report the first molecular and structural characterization of a novel cell‐surface protein, Lar_0958 from Lactobacillus reuteri JCM 1112^T, mediating adhesion of L. reuteri human strains to mucus. Lar_0958 is a modular protein of 133 kDa containing six repeat domains, an N‐terminal signal sequence and a C‐terminal anchoring motif (LPXTG). Lar_0958 homologues are expressed on the cell‐surface of L. reuteri human strains, as shown by flow‐cytometry and immunogold microscopy. Adhesion of human L. reuteri strains to mucus in vitro was significantly reduced in the presence of an anti‐Lar_0958 antibody and Lar_0958 contribution to adhesion was further confirmed using a L. reuteri ATCC PTA 6475 lar_0958 KO mutant (6475‐KO). The X‐ray crystal structure of a single Lar_0958 repeat, determined at 1.5 Å resolution, revealed a divergent immunoglobulin (Ig)‐like β‐sandwich fold, sharing structural homology with the Ig‐like inter‐repeat domain of internalins of the food borne pathogen Listeria monocytogenes. These findings provide unique structural insights into cell‐surface protein repeats involved in adhesion of Gram‐positive bacteria to the intestine.     

Evaluation of the conformational free energies of loops in proteins

In this paper we discuss the problem of including solvation free energies in evaluating the relative stabilities of loops in proteins. A conformational search based on a gas-phase potential function is used to generate a large number of trial conformations. As has been found previously, the energy minimization step in this process tends to pack charged and polar side chains against the protein surface, resulting in conformations which are unstable in the aqueous phase. Various solvation models can easily identify such structures. In order to provide a more severe test of solvation models, gas phase conformations were generated in which side chains were kept extended so as to maximize their interaction with the solvent. The free energies of these conformations were compared to that calculated for the crystal structure in three loops of the protein E. coli RNase H, with lengths of 7, 8, and 9 residues. Free energies were evaluated with a finite difference Poisson-Boltzmann (FDPB) calculation for electrostatics and a surface area-based term for nonpolar contributions. These were added to a gas-phase potential function. A free energy function based on atomic solvation parameters was also tested. Both functions were quite successful in selecting, based on a free energy criterion, conformations quite close to the crystal structure for two of the three loops. For one loop, which is involved in crystal contacts, conformations that are quite different from the crystal structure were also selected. A method to avoid precision problems associated with using the FDPB method to evaluate conformational free energies in proteins is described. © 1994 John Wiley & Sons, Inc.     

An adjacent arginine, and the phosphorylated tyrosine in the c-Met receptor target sequence, dictates the orientation of c-Cbl binding

Previously, we have demonstrated that the tyrosine phosphorylated hepatocyte growth factor receptor (Met) binds to the c-Cbl phosphotyrosine-recognition, tyrosine kinase binding (TKB) domain in a reverse orientation compared to other c-Cbl binding partners. A Met peptide with the DpYR motif changed to RpYD (MetRD) retains a similar TKB binding affinity as the native Met peptide. However, the TKB: MetRD complex crystal structure reveals a complete reversal of the binding orientation. Collated data indicates that both binding and orientation is dictated by the phosphorylated tyrosine and an adjacent arginine forming intra-peptide hydrogen bonds and aligning unidirectionally with complementary charges in the phosphotyrosine binding pocket of c-Cbl.

Structured summary

c-Cbl and MetRDbind: shown by x-ray crystallography (view interaction)c-Cbl and MetRDbind: shown by mass spectrometry studies of complexes (view interaction)c-Cblbind to Met: shown by surface plasmon resonance (view interactions 1,2)     

Reliable computational design of biological-inorganic materials to the large nanometer scale using Interface-FF

Abstract

The function of nanomaterials and biomaterials greatly depends on understanding nanoscale recognition mechanisms, crystal growth and surface reactions. The Interface Force Field (IFF) and surface model database are the first collection of transferable parameters for inorganic and organic compounds that can be universally applied to all materials. IFF uses common energy expressions and achieves best accuracy among classical force fields due to rigorous validation of structural and energetic properties of all compounds in comparison to perpetually valid experimental data. This paper summarises key aspects of parameterisation, including atomic charges and transferability of parameters and current coverage. Examples of biomolecular recognition at metal and mineral interfaces, surface reactions of alloys, as well as new models for graphitic materials and pi-conjugated molecules are described. For several metal–organic interfaces, a match in accuracy of computed binding energies between of IFF and DFT results is demonstrated at ten million times lower computational cost. Predictive simulations of biomolecular recognition of peptides on phosphate and silicate surfaces are described as a function of pH. The use of IFF for reactive molecular dynamics is illustrated for the oxidation of Mo₃Si alloys at high temperature, showing the development of specific porous silica protective layers. The introduction of virtual pi electrons in graphite and pi-conjugated molecules enables improvements in property predictions by orders of magnitude. The inclusion of such molecule-internal polarity in IFF can reproduce cation–pi interactions, pi-stacking in graphite, DNA bases, organic semiconductors and the dynamics of aqueous and biological interfaces for the first time.     

Identification and analysis of long-range electrostatic effects in proteins by computer modeling:Aspartate transcarbamylase

While ion pairs are readily identified in crystal structures, longer range electrostatic interactions cannot be identified from the three-dimensional structure alone. These interactions are likely to be important in large, multisubunit proteins that are regulated by allosteric interactions. In this paper, we show that these interactions are readily detected by electrostatic modeling, using, as an example, unliganded Escherichia coli aspartate transcarbamylase, a widely studied allosteric enzyme with 12 subunits and a molecular weight of 310 kD. The Born, dipolar, and site-site interaction terms of the free energy of protonation of the 810 titratable sites in the holoenzyme were calculated using the multigrid solution of the nonlinear Poisson-Boltzmann equation. Calculated titration curves are in good agreement with experimental titration curves, and the structural asymmetry observed in the crystal structure is readily apparent in the calculated free energies and pK_1/2 values. Most of the residues with pK_1/2 values that differ substantially from those of model compounds are buried in the low dielectric medium of the protein, particularly at the intersubunit interfaces. The dependence of the site-site interaction free energies on distance is complex, with a steep dependence at distances less than 5 Å and a more shallow dependence at longer distances. Interactions over distances of 6 to 15 Å require a bridging residue and are often not apparent in the structure. The network of interactions between ionizable groups extends across and between subunits and provides a potential mechanism for transmitting long-range structural effects and allosteric signals. © 1996 Wiley-Liss, Inc.