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Molecular Surface (molecular + surface)
Terms modified by Molecular Surface Selected AbstractsProton Transfer on the Molecular Surface of Proteins and Model SystemsISRAEL JOURNAL OF CHEMISTRY, Issue 2 2009Ran Friedman Proton transfer (PT) reactions take place on the molecular surface of proteins, membranes, ionic polymers, and other molecules. The rates of the reactions can be followed experimentally, while the atomistic details can be elucidated by molecular modeling. This manuscript gives a brief overview of the use of computer simulations and molecular modeling, in conjuction with experiments, to study PT reactions on the surface of solvated molecules. An integrative approach is discussed, where molecular dynamics simulations are performed with a protein, and quantum-mechanics-based calculations are performed on a small molecule. The simulation results allow the identification of the necessary conditions that yield PT reactions on the molecular surface. The reactions are efficient when they involve a donor and acceptor located a few Å apart and under the influence of a negative electrostatic field. In proton-pumping proteins, it is possible to identify such conditions a priori and locate proton-attracting antenna domains without the need to mutate each potential donor and acceptor. Based on density functional theory calculations, the arrangement of water molecules that interconnect the donor and acceptor moieties is suggested as the rate-limiting step for proton transfer on the molecular surface. [source] Bond-based 3D-chiral linear indices: Theory and QSAR applications to central chirality codificationJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2008Juan A. Castillo-Garit Abstract The recently introduced non-stochastic and stochastic bond-based linear indices are been generalized to codify chemical structure information for chiral drugs, making use of a trigonometric 3D-chirality correction factor. These improved modified descriptors are applied to several well-known data sets to validate each one of them. Particularly, Cramer's steroid data set has become a benchmark for the assessment of novel quantitative structure activity relationship methods. This data set has been used by several researchers using 3D-QSAR approaches such as Comparative Molecular Field Analysis, Molecular Quantum Similarity Measures, Comparative Molecular Moment Analysis, E-state, Mapping Property Distributions of Molecular Surfaces, and so on. For that reason, it is selected by us for the sake of comparability. In addition, to evaluate the effectiveness of this novel approach in drug design we model the angiotensin-converting enzyme inhibitory activity of perindoprilate's ,-stereoisomers combinatorial library, as well as codify information related to a pharmacological property highly dependent on the molecular symmetry of a set of seven pairs of chiral N -alkylated 3-(3-hydroxyphenyl)-piperidines that bind ,-receptors. The validation of this method is achieved by comparison with earlier publications applied to the same data sets. The non-stochastic and stochastic bond-based 3D-chiral linear indices appear to provide a very interesting alternative to other more common 3D-QSAR descriptors. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Molecular surface electrostatic potentials in relation to noncovalent interactions in biological systemsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2001Peter Politzer Abstract Noncovalent interactions are predominantly electrostatic in nature. It follows that an effective tool for their investigation and elucidation is the electrostatic potential on the molecular surface. We have shown that a variety of condensed phase macroscopic properties can be expressed quantitatively in terms of certain site-specific and global statistical quantities that characterize the overall pattern of the surface potential. We are now extending this approach to interactions in biological systems. Several applications will be discussed, including initial qualitative studies of dioxins, a series of anticonvulsants and some tetracyclines, the nucleotide bases, and a recent quantitative treatment of the anti-HIV activities of three groups of reverse transcriptase inhibitors. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001 [source] Proton Transfer on the Molecular Surface of Proteins and Model SystemsISRAEL JOURNAL OF CHEMISTRY, Issue 2 2009Ran Friedman Proton transfer (PT) reactions take place on the molecular surface of proteins, membranes, ionic polymers, and other molecules. The rates of the reactions can be followed experimentally, while the atomistic details can be elucidated by molecular modeling. This manuscript gives a brief overview of the use of computer simulations and molecular modeling, in conjuction with experiments, to study PT reactions on the surface of solvated molecules. An integrative approach is discussed, where molecular dynamics simulations are performed with a protein, and quantum-mechanics-based calculations are performed on a small molecule. The simulation results allow the identification of the necessary conditions that yield PT reactions on the molecular surface. The reactions are efficient when they involve a donor and acceptor located a few Å apart and under the influence of a negative electrostatic field. In proton-pumping proteins, it is possible to identify such conditions a priori and locate proton-attracting antenna domains without the need to mutate each potential donor and acceptor. Based on density functional theory calculations, the arrangement of water molecules that interconnect the donor and acceptor moieties is suggested as the rate-limiting step for proton transfer on the molecular surface. [source] Pattern recognition strategies for molecular surfaces: III.JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2004Binding site prediction with a neural network Abstract An algorithm for the identification of possible binding sites of biomolecules, which are represented as regions of the molecular surface, is introduced. The algorithm is based on the segmentation of the molecular surface into overlapping patches as described in the first article of this series.1 The properties of these patches (calculated on the basis of physical and chemical properties) are used for the analysis of the molecular surfaces of 7821 proteins and protein complexes. Special attention is drawn to known protein binding sites. A binding site identification algorithm is realized on the basis of the calculated data using a neural network strategy. The neural network is able to classify surface patches as protein,protein, protein,DNA, protein,ligand, or nonbinding sites. To show the capability of the algorithm, results of the surface analysis and the predictions are presented and discussed with representative examples. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 779,789, 2004 [source] Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvatureJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2002Oleg V. Tsodikov Abstract New computer programs, SurfRace and FastSurf, perform fast calculations of the solvent accessible and molecular (solvent excluded) surface areas of macromolecules. Program SurfRace also calculates the areas of cavities inaccessible from the outside. We introduce the definition of average curvature of molecular surface and calculate average molecular surface curvatures for each atom in a structure. All surface area and curvature calculations are analytic and therefore yield exact values of these quantities. High calculation speed of this software is achieved primarily by avoiding computationally expensive mathematical procedures wherever possible and by efficient handling of surface data structures. The programs are written initially in the language C for PCs running Windows 2000/98/NT, but their code is portable to other platforms with only minor changes in input-output procedures. The algorithm is robust and does not ignore either multiplicity or degeneracy of atomic overlaps. Fast, memory-efficient and robust execution make this software attractive for applications both in computationally expensive energy minimization algorithms, such as docking or molecular dynamics simulations, and in stand-alone surface area and curvature calculations. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 600,609, 2002 [source] Amino and cyano N atoms in competitive situations: which is the best hydrogen-bond acceptor?ACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2001A crystallographic database investigation The relative hydrogen-bond acceptor abilities of amino and cyano N atoms have been investigated using data retrieved from the Cambridge Structural Database and via ab initio molecular orbital calculations. Surveys of the CSD for hydrogen bonds between HX (X = N, O) donors, N,T,C,N (push,pull nitriles) and N,(Csp3)n,C,N molecular fragments show that the hydrogen bonds are more abundant on the nitrile than on the amino nitrogen. In the push,pull family, in which T is a transmitter of resonance effects, the hydrogen-bonding ability of the cyano nitrogen is increased by conjugative interactions between the lone pair of the amino substituent and the C,N group: a clear example of resonance-assisted hydrogen bonding. The strength of the hydrogen-bonds on the cyano nitrogen in this family follows the experimental order of hydrogen-bond basicity, as observed in solution through the pKHB scale. The number of hydrogen bonds established on the amino nitrogen is greater for aliphatic aminonitriles N,(Csp3)n,C,N, but remains low. This behaviour reflects the greater sensitivity of the amino nitrogen to steric hindrance and the electron-withdrawing inductive effect compared with the cyano nitrogen. Ab initio molecular orbital calculations (B3LYP/6-31+G** level) of electrostatic potentials on the molecular surface around each nitrogen confirm the experimental observations. [source] Structure of Arabidopsis chloroplastic monothiol glutaredoxin AtGRXcpACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2010Lenong Li Monothiol glutaredoxins (Grxs) play important roles in maintaining redox homeostasis in living cells and are conserved across species. Arabidopsis thaliana monothiol glutaredoxin AtGRXcp is critical for protection from oxidative stress in chloroplasts. The crystal structure of AtGRXcp has been determined at 2.4,Å resolution. AtGRXcp has a glutaredoxin/thioredoxin-like fold with distinct structural features that differ from those of dithiol Grxs. The structure reveals that the putative active-site motif CGFS is well defined and is located on the molecular surface and that a long groove extends to both sides of the catalytic Cys97. Structural comparison and molecular modeling suggest that glutathione can bind in this groove and form extensive interactions with conserved charged residues including Lys89, Arg126 and Asp152. Further comparative studies reveal that a unique loop with five additional residues adjacent to the active-site motif may be a key structural feature of monothiol Grxs and may influence their function. This study provides the first structural information on plant CGFS-type monothiol Grxs, allowing a better understanding of the redox-regulation mechanism mediated by these plant Grxs. [source] Systematic study on crystal-contact engineering of diphthine synthase: influence of mutations at crystal-packing regions on X-ray diffraction qualityACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2008Hisashi Mizutani It is well known that protein crystallizability can be influenced by site-directed mutagenesis of residues on the molecular surface of proteins, indicating that the intermolecular interactions in crystal-packing regions may play a crucial role in the structural regularity at atomic resolution of protein crystals. Here, a systematic examination was made of the improvement in the diffraction resolution of protein crystals on introducing a single mutation of a crystal-packing residue in order to provide more favourable packing interactions, using diphthine synthase from Pyrococcus horikoshii OT3 as a model system. All of a total of 21 designed mutants at 13 different crystal-packing residues yielded almost isomorphous crystals from the same crystallization conditions as those used for the wild-type crystals, which diffracted X-rays to 2.1,Å resolution. Of the 21 mutants, eight provided crystals with an improved resolution of 1.8,Å or better. Thus, it has been clarified that crystal quality can be improved by introducing a suitable single mutation of a crystal-packing residue. In the improved crystals, more intimate crystal-packing interactions than those in the wild-type crystal are observed. Notably, the mutants K49R and T146R yielded crystals with outstandingly improved resolutions of 1.5 and 1.6,Å, respectively, in which a large-scale rearrangement of packing interactions was unexpectedly observed despite the retention of the same isomorphous crystal form. In contrast, the mutants that provided results that were in good agreement with the designed putative structures tended to achieve only moderate improvements in resolution of up to 1.75,Å. These results suggest a difficulty in the rational prediction of highly effective mutations in crystal engineering. [source] Structure of Escherichia coli tryptophanaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2006Shao-Yang Ku Pyridoxal 5,-phosphate (PLP) dependent tryptophanase has been isolated from Escherichia coli and its crystal structure has been determined. The structure shares the same fold with and has similar quaternary structure to Proteus vulgaris tryptophanase and tyrosine-phenol lyase, but is found in a closed conformation when compared with these two enzymes. The tryptophanase structure, solved in its apo form, does not have covalent PLP bound in the active site, but two sulfate ions. The sulfate ions occupy the phosphoryl-binding site of PLP and the binding site of the ,-carboxyl of the natural substrate tryptophan. One of the sulfate ions makes extensive interactions with both the transferase and PLP-binding domains of the protein and appears to be responsible for holding the enzyme in its closed conformation. Based on the sulfate density and the structure of the P. vulgaris enzyme, PLP and the substrate tryptophan were modeled into the active site. The resulting model is consistent with the roles of Arg419 in orienting the substrate to PLP and acidifying the ,-proton of the substrate for ,-elimination, Lys269 in the formation and decomposition of the PLP quinonoid intermediate, Arg230 in orienting the substrate,PLP intermediates in the optimal conformation for catalysis, and His463 and Tyr74 in determining substrate specificity and suggests that the closed conformation observed in the structure could be induced by substrate binding and that significant conformational changes occur during catalysis. A catalytic mechanism for tryptophanase is proposed. Since E. coli tryptophanase has resisted forming diffraction-quality crystals for many years, the molecular surface of tryptophanase has been analyzed in various crystal forms and it was rationalized that strong crystal contacts occur on the flat surface of the protein and that the size of crystal contact surface seems to correlate with the diffraction quality of the crystal. [source] Morphology and the strength of intermolecular contacts in protein crystalsACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2003Yoshiki Matsuura The strengths of intermolecular contacts (macrobonds) and the areas occupied by each contact on the molecular surface were estimated in four polymorphic modifications of lysozyme crystals based on the bond strengths between individual atomic pairs belonging to the molecules in contact. It has been shown that the periodic bond chains of these macrobonds account for the morphology of protein crystals. The Coulombic contribution to the macrobond strength has also been estimated. Making use of the contact strengths and taking into account bond hydration, crystal,water interfacial energies were also estimated for different crystal faces. The areas of all contacts are mapped on the molecular surface, making use of a polar-coordinate representation of the contact. Comparing the locations of the intermolecular contacts in the different polymorphic crystal modifications, it is shown that these contacts can form a wide variety of patches on the molecular surface. The patches are located practically everywhere on the surface except for the inside of a concave active site. It is also shown that the contacts, which frequently involve water molecules, are formed by specific intermolecular hydrogen bonds on a background of non-specific attractive electrostatic interactions. Typical values of the macrobond strength are compared with the strength of association in other protein-complex systems. [source] Structural analysis of Tityus serrulatus Ts1 neurotoxin at atomic resolution: insights into interactions with Na+ channelsACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2003Carlos Basílio Pinheiro The structure of the Ts1 toxin from the Brazilian scorpion Tityus serrulatus was investigated at atomic resolution using X-ray crystallography. Several positively charged niches exist on the Ts1 molecular surface, two of which were found to coordinate phosphate ions present in the crystallization solution. One phosphate ion is bound to the conserved basic Lys1 residue at the Ts1 N-terminus and to residue Asn49. The second ion was found to be caged by residues Lys12, Trp54 and Arg56. Lys12 and Tyr/Trp54 residues are strictly conserved in all classical scorpion ,-neurotoxins. The cavity formed by these residues may represent a special scaffold required for interaction between ,-neurotoxins and sodium channels. The charge distribution on the Ts1 surface and the results of earlier chemical modification studies and side-directed mutagenesis experiments strongly indicate that the phosphate-ion positions mark plausible binding sites to the Na+ channel. The existence of two distinct binding sites on the Ts1 molecular surface provides an explanation for the competition between Ts1, depressant (LqhIT2) and excitatory (AaHIT) neurotoxins. [source] Structure of ribosomal protein L1 from Methanococcus thermolithotrophicus.ACTA CRYSTALLOGRAPHICA SECTION D, Issue 6-2 2002Functionally important structural invariants on the L1 surface The crystal structure of ribosomal protein L1 from the archaeon Methanococcus thermolithotrophicus has been determined at 2.7,Å resolution. The crystals belong to space group P212121, with unit-cell parameters a = 67.0, b = 70.1, c = 106.3,Å and two molecules per asymmetric unit. The structure was solved by the molecular-replacement method with AMoRe and refined with CNS to an R value of 18.9% and an Rfree of 25.4% in the resolution range 30,2.7,Å. Comparison of this structure with those obtained previously for two L1 proteins from other sources (the bacterium Thermus thermophilus and the archaeon M. jannaschii) as well as detailed analysis of intermolecular contacts in the corresponding L1 crystals reveal structural invariants on the molecular surface which are probably important for binding the 23S ribosomal RNA and protein function within the ribosome. [source] Do electrostatic interactions destabilize protein,nucleic acid binding?BIOPOLYMERS, Issue 2 2007Sanbo Qin Abstract The negatively charged phosphates of nucleic acids are often paired with positively charged residues upon binding proteins. It was thus counter-intuitive when previous Poisson,Boltzmann (PB) calculations gave positive energies from electrostatic interactions, meaning that they destabilize protein,nucleic acid binding. Our own PB calculations on protein,protein binding have shown that the sign and the magnitude of the electrostatic component are sensitive to the specification of the dielectric boundary in PB calculations. A popular choice for the boundary between the solute low dielectric and the solvent high dielectric is the molecular surface; an alternative is the van der Waals (vdW) surface. In line with results for protein,protein binding, in this article, we found that PB calculations with the molecular surface gave positive electrostatic interaction energies for two protein,RNA complexes, but the signs are reversed when the vdW surface was used. Therefore, whether destabilizing or stabilizing effects are predicted depends on the choice of the dielectric boundary. The two calculation protocols, however, yielded similar salt effects on the binding affinity. Effects of charge mutations differentiated the two calculation protocols; PB calculations with the vdW surface had smaller deviations overall from experimental data. © 2007 Wiley Periodicals, Inc. Biopolymers 86: 112,118, 2007. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Role of Kinases in Neuronal FunctionBIOTECHNOLOGY JOURNAL, Issue 8 2007Article first published online: 7 AUG 200 Cover illustration: Role of Cdk5 in neuronal function. Crystal structure of indirubin-38-monoxime in complex with Cdk5/p25 [1]. The inhibitor binds in the ATP-binding pocket of the catalytic subunit, mainly through hydrophobic interaction and two hydrogen bonds with Leu83. Indirubin-38-monoxime is shown as a ball-and-stick model, and the molecular surface of Cdk5/p25 is coloured according to electrostatic potential, with blue and red representing positive and negative potential, respectively. The figure was created with the program GRASP [2]. Courtesy of Claudia Crovace, Aldo Tarricone and Andrea Musacchio. [source] Dispersion-Oriented Soft Interaction in a Frustrated Lewis Pair and the Entropic Encouragement Effect in its FormationCHEMISTRY - A EUROPEAN JOURNAL, Issue 48 2009Woo Kim Abstract The origin of the stability of a frustrated Lewis pair (FLP) tBu3P:B(C6F5)3 is investigated computationally to demonstrate the importance of the dispersion interaction. To this end, the interaction between alkyl-substituted phosphines (Me3P and tBu3P) and hexafluorobenzene (C6F6) is first investigated. Driven by the lone-pair to ,-orbital interaction, the binding energy is found to be even larger than usual ,,, interaction energies between small aromatic compounds. This character, which is inherited to fluorophenyl-substituted B(C6F5)3 in the FLP, induces large flexibility in the FLP over the molecular surface of B(C6F5)3. This soft interaction, in turn, causes an entropic stabilization of the FLP formation in comparison with classical Lewis pairs based on close and tight PB dative bonds. It also suggests a diverse nature of the FLP when it is involved in chemical reactions. Even with the cooperative participation of the perfluorophenyl groups, a detailed inspection of the FLP interaction potential energy surface indicates that the boron atom is still the major interaction site for the pair formation. This non-negligible direct PB interaction, which is related also to the soft nature of the borane frontier orbital, is further supported by substantial spatial overlap between the frontier orbitals on the phosphine/borane fragments and their interaction energy estimations. [source] Computational Investigation of Hydrogen Adsorption by Alkali-Metal-Doped Organic Molecules: Role of AromaticityCHEMPHYSCHEM, Issue 2 2009Kancharlapally Srinivasu Abstract Hydrogen storage: Simple organic molecular systems (CnHn, n=4, 5, 6, 8) are proposed for hydrogen storage purposes based on the concept of aromaticity. The adsorption of hydrogen is attributed to pronounced charge transfer from the sodium atom (green, see picture) to the organic systems and the electrostatic interaction between the ion and hydrogen molecules. Theoretical studies on hydrogen adsorption in small organic molecular systems, such as cyclobutadiene (C4H4), the cyclopentadienyl radical (C5H5), benzene (C6H6), and cyclooctatetraene (C8H8) and their metal-doped modifications, are carried out. Our results reveal that the simple van der Waals surfaces of pure organic molecules are not good enough for hydrogen adsorption due to the weak interaction between hydrogen molecules and the organic molecular surface. However, doping of alkali-metal atoms in the above organic molecular systems increases their hydrogen adsorption ability significantly, mainly due to electron transfer from the metal atom to the carbon surface. This charged surface created around the metal atom is found to enhance the hydrogen adsorption capacity of the complex considerably, both in terms of interaction energy and the number of adsorbed hydrogen molecules, with a hydrogen adsorption capacity ranging from 10 to 12 wt,%. The role of aromaticity in such molecular systems is important in stabilizing these ionized organo-alkali-metal complexes. [source] Resonance Light Scattering Imaging Detection of Single Suprahelical Species of DNA Induced by Porphine-5,10,15,20-tetrakis(p -phenyltrimethylaminium)CHINESE JOURNAL OF CHEMISTRY, Issue 1 2006Xi-Dong Liu Abstract A resonance light scattering (RLS) imaging method was proposed based on imaging and measuring the RLS features of single suprahelical species of DNA, and its application to DNA assay was also investigated. In acidic medium, porphine-5,10,15,20-tetrakis(p -phenyltrimethylaminium) (PTPTMA), could stack along the molecular surface of DNA with the mode of long-range assembly to induce the formation of suprahelical species of DNA, resulting in strong RLS signals in the range of 450,510 nm. Under the excitation of 488 nm light beam of argon ion laser source, single suprahelical species could be observed with the aid of a common microscope due to the strong scattered light emitted by the suprahelical species. By capturing the RLS images of the single suprahelical species with a cooled charge coupled device (CCD) camera, and analyzing the RLS data, herein an RLS imaging method of DNA was proposed based on the linear relationship between the counts of suprahelical species in the detection focus plane and the concentration of DNA in nanograms. When 1.8??µmol/L PTPTMA was employed, both calf thymus DNA (ct DNA) and fish sperm DNA (fs DNA) in the range of 25,1100 ng/mL could be detected with the limits of detection lower than 25 ng/mL (3,). Four synthetic samples were detected satisfactorily with relative standard deviations less than 5.1%. [source] Structures of Cytochrome b5 Mutated at the Charged Surface-Residues and Their Interactions with Cytochrome c,CHINESE JOURNAL OF CHEMISTRY, Issue 11 2002Jlan Wu Abstract Glu44, Glu48, Ghi56 and Asp60 are the negatively charged residues located at the molecular surface of cytochrome b5. Two mutants of cytochrome b5 were prepared, in which two or all of these four residues were mutated to alanines. The mutations give rise to slightly positive shifts of the redox potentials of cytochrome b5 and obvious decrease of the cytochrome b5 -cytochrome c binding constants and electron transfer rates. The crystal structures of the two mutants were determined at 0.18 nm resolution, showing no alteration in overall structures and exhibiting slight changes in the local conformations around the mutation sites as compared with the wild-type protein. Based on the crystal structure of the quadruple-site mutant, a model for the binding of this mutant with cytochrome c is proposed, which involves the salt bridges from Glu37, Glu38 and heme propionate of cytochrome b5 to three lysines of cytochrome c and can well account for the properties and behaviors of this mutant. [source] Computational characterization of nucleotide bases: Molecular surface electrostatic potentials and local ionization energies, and local polarization energiesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3-4 2001Jane S. Murray Abstract Electrostatic potentials and local ionization energies have been computed at the HF/6-31G* level on the molecular surfaces of the five nucleotide bases. The potentials are analyzed in terms of their most positive and negative values as well as several statistically defined quantities that reflect their patterns over the entire surface. Considerable charge separation and variability are found for all five molecules. The results are consistent with the base pairing that is known to occur. The observed reactive behavior toward electrophiles can be interpreted in terms of the complementary roles of the surface potential and the local electron lability. Local polarization energies, corresponding to a test charge being placed at specific points above the molecules, are also calculated (HF/6-31+G*), and their relationship to the local ionization energies is examined. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 83: 245,254, 2001 [source] Pattern recognition strategies for molecular surfaces: III.JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2004Binding site prediction with a neural network Abstract An algorithm for the identification of possible binding sites of biomolecules, which are represented as regions of the molecular surface, is introduced. The algorithm is based on the segmentation of the molecular surface into overlapping patches as described in the first article of this series.1 The properties of these patches (calculated on the basis of physical and chemical properties) are used for the analysis of the molecular surfaces of 7821 proteins and protein complexes. Special attention is drawn to known protein binding sites. A binding site identification algorithm is realized on the basis of the calculated data using a neural network strategy. The neural network is able to classify surface patches as protein,protein, protein,DNA, protein,ligand, or nonbinding sites. To show the capability of the algorithm, results of the surface analysis and the predictions are presented and discussed with representative examples. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 779,789, 2004 [source] Nonclassical forces: Seemingly insignificant but a powerful tool to control macromolecular structuresJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 14 2008Michiya Fujiki Abstract Strong chemical forces such as covalent and ionic bonds are responsible for building discrete molecules, nature dwells on noncovalent forces weaker by three orders in magnitude, like the hydrophobic effect, hydrogen bonding, and van der Waals forces. Despite being weak, they possess the potential to drive spontaneous folding or unfolding of proteins and nucleic acids and the recognition between complimentary molecular surfaces. The power of these forces lies in the cooperativity with which they act, thereby generating a cumulative effect of many bonding interactions occurring together. Many ongoing research aims to translate the potential of these forces to the synthetic world to create desired structures with specific chemical functions. Achieving this offers unlimited opportunities for designing and synthesizing the most complex structures with specific applications. This highlight aims to reflect the critical role these noncovalent forces play in controlling macromolecular structures, which hold immense untapped potential for applications defying conventions, and briefly touches on the concept of homochirality in nature based on chiral and weak noncovalent interactions in synthetic nonpolar Si-catenated polymers. It sheds some light on the discovery and characterization of Si/F-C interactions in fluoroalkylated polysilanes in chemosensing of fluoride ions and nitroaromatics with a great sensitivity and selectivity. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4637,4650, 2008 [source] | |||||||||||||||||||||||||