当前位置： SCI文献检索 > JOURNAL OF MOLECULAR MODELING期刊下所有文献 > Effects of local protein environment on the binding of diatomic molecules to heme in myoglobins. DFT and dispersion-corrected DFT studies.

Effects of local protein environment on the binding of diatomic molecules to heme in myoglobins. DFT and dispersion-corrected DFT studies.

Abstract：

:The heme-AB binding energies (AB = CO, O2) in a wild-type myoglobin (Mb) and two mutants (H64L, V68N) of Mb have been investigated in detail with both DFT and dispersion-corrected DFT methods, where H64L and V68N represent two different, opposite situations. Several dispersion correction approaches were tested in the calculations. The effects of the local protein environment were accounted for by including the five nearest surrounding residues in the calculated systems. The specific role of histidine-64 in the distal pocket was examined in more detail in this study than in other studies in the literature. Although the present calculated results do not change the previous conclusion that the hydrogen bonding by the distal histidine-64 residue plays a major role in the O2/CO discrimination by Mb, more details about the interaction between the protein environment and the bound ligand have been revealed in this study by comparing the binding energies of AB to a porphyrin and the various myoglobins. The changes in the experimental binding energies from one system to another are well reproduced by the calculations. Without constraints on the residues in geometry optimization, the dispersion correction is necessary, since it improves the calculated structures and energetic results significantly.

journal_name

J Mol Model

journal_title

Journal of molecular modeling

authors

Liao MS,Huang MJ,Watts JD

doi

10.1007/s00894-013-1864-2

subject

Has Abstract

pub_date

2013-08-01 00:00:00

pages

3307-23

issue

8

eissn

1610-2940

issn

0948-5023

journal_volume

19

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR MODELING文献大全
  • Reaction mechanism of CH3M≡MCH 3 (M=C, Si, Ge) with C2H4: [2+1] or [2+2] cycloaddition?

    abstract：:The mechanism of the cycloaddition reaction CH3M≡MCH3 (M=C, Si, Ge) with C2H4 has been studied at the CCSD(T)/6-311++G(d,p)//MP2/6-311++G(d,p) level. Vibrational analysis and intrinsic reaction coordinate (IRC), calculated at the same level, have been applied to validate the connection of the stationary points. The br...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-1882-0

    authors： Huo S,Li X,Zeng Y,Zheng S,Meng L

    更新日期：2013-09-01 00:00:00

  • Solvent accessible surface area approximations for rapid and accurate protein structure prediction.

    abstract：:The burial of hydrophobic amino acids in the protein core is a driving force in protein folding. The extent to which an amino acid interacts with the solvent and the protein core is naturally proportional to the surface area exposed to these environments. However, an accurate calculation of the solvent-accessible surf...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-009-0454-9

    authors： Durham E,Dorr B,Woetzel N,Staritzbichler R,Meiler J

    更新日期：2009-09-01 00:00:00

  • A joint theoretical and experimental characterization of two acene-thiophene derivatives.

    abstract：:Acene-thiophenes compounds have been used successfully as active materials in thin-film transistors and photodetectors. This work aims at obtaining an adequate theoretical framework to accurately characterize the optical and electronic properties of two such compounds: NaT2 and NaT3. This is done by comparing the resu...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3241-z

    authors： de Sousa LE,Mamiya AA,Kjelstrup-Hansen J,da Silva Filho DA

    更新日期：2017-02-01 00:00:00

  • Molecular modeling study on chemically diverse series of cyclooxygenase-2 selective inhibitors: generation of predictive pharmacophore model using catalyst.

    abstract：:Cyclooxygenase (COX) enzymes catalyse the biosynthesis of prostaglandins and thromboxane from arachidonic acid (AA). We summarize in this paper, the development of pharmacophores of a dataset of inhibitors for COX-2 by using the Catalyst/Hypogen module using six chemically diverse series of compounds. Training set con...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-008-0350-8

    authors： Chopra M,Gupta R,Gupta S,Saluja D

    更新日期：2008-11-01 00:00:00

  • New complete orthonormal sets of hyperspherical harmonics and their one-range addition and expansion theorems.

    abstract：:In this study, the complete orthonormal sets of phi(alpha)-momentum space orbitals (where alpha = 1, 0, -1, -2, ...) obtained from the psi(alpha)-ETO in coordinate representation (I.I. Guseinov, J. Mol. Model., 9 (2003) 135) are reduced to the complete orthonormal sets of hyperspherical harmonics (HSH) by means of a F...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-005-0093-8

    authors： Guseinov II

    更新日期：2006-09-01 00:00:00

  • Quantum chemical study of the isomerization of 24-methylenecycloartanol, a potential marker of olive oil refining.

    abstract：:Quantum chemical calculations on the isomerization of 24-methylenecycloartanol are described. An energetically viable mechanism, with a rate-determining protonation step, is proposed. This rearrangement may find applicability in tests for determining if an olive oil has been refined. ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-015-2652-y

    authors： Wedler HB,Pemberton RP,Lounnas V,Vriend G,Tantillo DJ,Wang SC

    更新日期：2015-05-01 00:00:00

  • The mechanism and kinetics of decomposition of 5-aminotetrazole.

    abstract：:The pathway and ab initio direct kinetics of the decomposition 5-aminotetrazole (5-ATZ) to HN(3) and NH(2)CN was investigated. Reactant, products and transition state were optimized with MP2 and B3LYP methods using 6-311G** and aug-cc-pVDZ basis sets. The intrinsic reaction coordinate curve of the reaction was calcula...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-008-0290-3

    authors： Zhang JG,Feng LN,Zhang SW,Zhang TL,Zheng HH

    更新日期：2008-05-01 00:00:00

  • Discovering the stacking landscape of a pyridine-pyridine system.

    abstract：:Extremely extensive calculations of potential energy surfaces for the parallel-displaced configuration of pyridine dimer systems have been carried out using a dispersion-corrected density functional. Instead of focusing on stationary geometries these calculations provide much deeper insight into the "landscape" of the...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3496-4

    authors： Sierański T

    更新日期：2017-11-09 00:00:00

  • A three-dimensional model of the human transglutaminase 1: insights into the understanding of lamellar ichthyosis.

    abstract：:The stratum corneum, the outer layer of the epidermis, serves as a protective barrier to isolate the skin from the external environment. Keratinocyte transglutaminase 1 (TGase 1) catalyzes amide crosslinking between glutamine and lysine residues on precursor proteins forming the impermeable layers of the epidermal cel...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-006-0144-9

    authors： Boeshans KM,Mueser TC,Ahvazi B

    更新日期：2007-01-01 00:00:00

  • A novel dimerization interface of cyclic nucleotide binding domain, which is disrupted in presence of cAMP: implications for CNG channels gating.

    abstract：:Cyclic nucleotide binding domain (CNBD) is a ubiquitous domain of effector proteins involved in signalling cascades of prokaryota and eukaryota. CNBD activation by cyclic nucleotide monophosphate (cNMP) is studied well in the case of several proteins. However, this knowledge is hardly applicable to cNMP-modulated cati...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1404-5

    authors： Gushchin IY,Gordeliy VI,Grudinin S

    更新日期：2012-09-01 00:00:00

  • Multiscale simulations of the structure and dynamics of stereoregular poly(methyl methacrylate)s.

    abstract：:The chain tacticity of a polymer is a key influence on its structure and dynamics, which ultimately determine its properties. While they have great potential to elucidate the influence of chain tacticity, all-atom molecular simulations are often restricted to short chains and small systems. In this work, two typical s...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2377-3

    authors： Wu C

    更新日期：2014-08-01 00:00:00

  • Architecture, electronic structure and stability of TM@Ge(n) (TM = Ti, Zr and Hf; n = 1-20) clusters: a density functional modeling.

    abstract：:The present study reports the geometry, electronic structure and properties of neutral and anionic transition metal (TM = Ti, Zr and Hf)) doped germanium clusters containing 1 to 20 germanium atoms within the framework of linear combination of atomic orbitals density functional theory under spin polarized generalized ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-011-1122-4

    authors： Kumar M,Bhattacharyya N,Bandyopadhyay D

    更新日期：2012-01-01 00:00:00

  • Insights into amprenavir resistance in E35D HIV-1 protease mutation from molecular dynamics and binding free-energy calculations.

    abstract：:Drug resistance is a very important factor contributing to the failure of current HIV therapies. The ability to understand the resistance mechanism of HIV-protease mutants may be useful in developing more effective and longer lasting treatment regimens. In this paper, we report the first computational study of the cli...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-006-0121-3

    authors： Meiselbach H,Horn AH,Harrer T,Sticht H

    更新日期：2007-02-01 00:00:00

  • Unsaturated trinuclear iron fluoroborylene complexes.

    abstract：:The unsaturated trinuclear iron fluoroborylene complexes Fe3(BF)3(CO) n (n = 7, 6) have been studied using density functional theory (DFT). Relatively complicated potential energy surfaces are found with nine and eight structures within 15 kcal mol-1 of the lowest energy structures for the Fe3(BF)3(CO)7 and Fe3(BF)3(C...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3301-4

    authors： Xu L,Li QS,King RB

    更新日期：2017-04-01 00:00:00

  • Theoretical determination of the effects of various linkages between trinitrobenzenes on energetic properties and sensitivity.

    abstract：:Density functional theory (DFT) has been applied to understand the influence of various linkages on the energetic properties and stability of the polynitro-biphenyl compounds. Structures were optimized using the B3PW91/6-31G(d,p) level, and the heats of formation (HOFs) were computed by employing the selected isodesmi...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-019-4201-6

    authors： Nirwan A,Devi A,Ghule VD

    更新日期：2019-09-15 00:00:00

  • Molecular basis of the beta-lactamase protein using comparative modelling, drug screening and molecular dynamics studies to understand the resistance of β-lactam antibiotics.

    abstract：:Beta-lactamase (ampC) in general causes the onset of antibiotic resistance in pathogenic bacteria against the β-lactam antibiotics. Morganella morganii which belongs to the Proteae tribe of the Enterobacteriaceae family is a Gram-negative bacillus. Gram-negative bacteria are the key problematic agents among the human ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-020-04459-5

    authors： Alazmi M

    更新日期：2020-07-07 00:00:00

  • The anti-fibrillogenic activity of tetracyclines on PrP 106-126: a 3D-QSAR study.

    abstract：:There is evidence that Tetracyclines are potentially useful drugs to treat prion disease, the fatal neurodegenerative disease in which cellular prion proteins change in conformation to become a disease-specific species (PrP(Sc)). Based on an in vitro anti-fibrillogenesis test, and using the peptide PrP106-126 in the p...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-008-0348-2

    authors： Cosentino U,Pitea D,Moro G,Saracino GA,Caria P,Varì RM,Colombo L,Forloni G,Tagliavini F,Salmona M

    更新日期：2008-10-01 00:00:00

  • First-principles simulations of the chemical functionalization of (5,5) boron nitride nanotubes.

    abstract：:We perform density functional theory studies to investigate structural and electronic properties of the (5,5) boron nitride nanotubes (BNNTs) with surfaces and ends functionalized by thiol (SH) and hydroxyl (OH) groups. The exchange-correlation energies are treated according to the functional of Hamprecht-Cohen-Tozer-...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-1782-3

    authors： Chigo Anota E,Cocoletzi GH

    更新日期：2013-06-01 00:00:00

  • Conformational and NMR study of some furan derivatives by DFT methods.

    abstract：:4'-substituted neutral/protonated furfurylidenanilines and trans-styrylfurans are able to exist in two different conformations related to the rotation around the furan ring-bridge double bond. In this work, the equilibrium geometry and the corresponding rotational barrier of the benzene ring for each furan derivative ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-1964-z

    authors： Santos-Carballal D,Suardíaz R,Crespo-Otero R,González L,Pérez CS

    更新日期：2013-10-01 00:00:00

  • Mesoscopic dynamics of colloids simulated with dissipative particle dynamics and fluid particle model.

    abstract：:We report results of numerical simulations of complex fluids, using a combination of discrete-particle methods. Our molecular modeling repertoire comprises three simulation techniques: molecular dynamics (MD), dissipative particle dynamics (DPD), and the fluid particle model (FPM). This type of model can depict multi-...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-001-0068-3

    authors： Dzwinel W,Yuen DA,Boryczko K

    更新日期：2002-01-01 00:00:00

  • Arm retraction and escape transition in semi-flexible star polymer under cylindrical confinement.

    abstract：:We studied the structure and dynamics of star-shaped polymers by means of coarse-grained molecular dynamics simulations and analysis of structural transitions of semi-flexible macromolecules confined in nano-channels. The conformation of star arms in narrow channels is given by the channel width, arm flexibility and n...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-015-2735-9

    authors： Račko D,Cifra P

    更新日期：2015-07-01 00:00:00

  • CO, CO2 and H2 adsorption on ZnO, CeO2, and ZnO/CeO2 surfaces: DFT simulations.

    abstract：:The adsorption of the molecules CO, CO2, and H2 on several ceria and zinc oxide surfaces was studied by means of periodical DFT calculations and compared with infrared frequency data. The stable CeO2(111), CeO2(331), and ZnO(0001) perfect faces were the first substrates considered. Afterwards, the same surfaces with o...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2270-0

    authors： Reimers WG,Baltanás MA,Branda MM

    更新日期：2014-06-01 00:00:00

  • Identification of novel, less toxic PTP-LAR inhibitors using in silico strategies: pharmacophore modeling, SADMET-based virtual screening and docking.

    abstract：:Human leukocyte antigen-related (PTP-LAR) is a receptor-like transmembrane phosphatase and a potential target for diabetes, obesity and cancer. In the present study, a sequence of in silico strategies (pharmacophore mapping, a 3D database searching, SADMET screening, and docking and toxicity studies) was performed to ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-011-1037-0

    authors： Ajay D,Sobhia ME

    更新日期：2012-01-01 00:00:00

  • Structural model of an antistasin/notch-like fusion protein from the cocoon wall of the aquatic leech, Theromyzon tessulatum.

    abstract：:The aquatic leech, Theromyzon tessulatum, secretes a proteinaceous cocoon with extraordinary physical properties (e.g., proteolytic, thermal resiliency). The deduced amino acid sequence of a major protein (Tcp-Theromyzon cocoon protein) from the T. tessulatum cocoon wall has been used to model the endogenous structure...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-006-0107-1

    authors： Mason TA,McIlroy PJ,Shain DH

    更新日期：2006-09-01 00:00:00

  • Comparative evaluation of NANO transport properties for DNA nucleobase based molecular junction devices.

    abstract：:The feasibility of electron transport conduction through a guanine base of DNA was investigated and then compared with another component of DNA, i.e., cytosine. A mathematical approach based on the jellium model using non-equilibrium Green's function combined with semi empirical extended Huckel theory was applied usin...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-018-3856-8

    authors： Vohra R,Sawhney RS

    更新日期：2018-11-01 00:00:00

  • Three applications of path integrals: equilibrium and kinetic isotope effects, and the temperature dependence of the rate constant of the [1,5] sigmatropic hydrogen shift in (Z)-1,3-pentadiene.

    abstract：:Recent experiments have confirmed the importance of nuclear quantum effects even in large biomolecules at physiological temperature. Here we describe how the path integral formalism can be used to describe rigorously the nuclear quantum effects on equilibrium and kinetic properties of molecules. Specifically, we expla...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-010-0711-y

    authors： Zimmermann T,Vaníček J

    更新日期：2010-11-01 00:00:00

  • Theoretical study on cooperative effects between X⋯N and X⋯Carbene halogen bonds (X = F,Cl,Br and I).

    abstract：:Quantum chemical calculations are performed to study the interplay between halogen⋯nitrogen and halogen⋯carbene interactions in NCX⋯NCX⋯CH2 complexes, where X = F, Cl, Br and I. Molecular geometries and interaction energies of dyads and triads are investigated at the MP2/aug-cc-pVTZ level of theory. It is found that t...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-1983-9

    authors： Esrafili MD,Mohammdain-Sabet F,Esmailpour P

    更新日期：2013-11-01 00:00:00

  • Relationship between mutation of serine residue at 315th position in M. tuberculosis catalase-peroxidase enzyme and Isoniazid susceptibility: an in silico analysis.

    abstract：:Remarkable advances have been made in the drug therapy of tuberculosis. However much remains to be learned about the molecular and structural basis of drug resistance in Mycobacterium tuberculosis. It is known that, activation of Isoniazid (INH) is mediated by Mycobacterium tuberculosis catalase-peroxidase (MtBKatG) a...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-010-0785-6

    authors： Purohit R,Rajendran V,Sethumadhavan R

    更新日期：2011-04-01 00:00:00

  • Mechanisms on electrical breakdown strength increment of polyethylene by acetophenone and its analogues addition: a theoretical study.

    abstract：:A theoretical investigation is completed on the mechanism of electrical breakdown strength increment of polyethylene. It is shown that it is one of the most important factors for increasing electrical breakdown strength of polyethylene through keto-enol isomerization of acetophenone and its analogues at the ground sta...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-1946-1

    authors： Zhang H,Shang Y,Zhao H,Han B,Li Z

    更新日期：2013-10-01 00:00:00

  • Double-layer carbon nanocapsules with radioiodine content and its interaction with calcium, phosphorus, and strontium.

    abstract：:First principles calculations have been performed for C60@C180 carbon double-layer endofullerenes with up to: three diatomic radioiodine molecules (131I2), two potassium radio-iodide (K131I), and three sodium radio-iodide (Na131I) inside. The plane-wave pseudopotential (PP) method within the general gradient approxima...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3538-y

    authors： Valderrama A,Reynoso R,Gómez RW,Quintana M,Romero M

    更新日期：2017-12-04 00:00:00