• Molecular dynamics simulation of humic substances ...

    2014-9-2 · Humic substances (HS) are complex mixtures of natural organic material which are found almost everywhere in the environment, and particularly in soils, sediments, and natural water. HS play key roles in many processes of paramount importance, such as plant growth, carbon storage, and the fate of contaminants in the environment. While most of the research …CELLULOSE CRYSTAL STRUCTURE AND FORCE FIELDS2010-10-15 · CELLULOSE CRYSTAL STRUCTURE AND FORCE FIELDS Malin Bergenstråhle,1,2 James Matthews3, Michael Crowley3 and John Brady2 1 Wallenberg Wood Science Center, KTH, Stockholm, Sweden 2 Dep of Food Science, Cornell University, Ithaca, NY, …

  • Enhancing the catalytic activity of a novel GH5 cellulase ...

    2018-3-22 · Cellulases of glycosyl hydrolase (GH) family 5 share a (β/α)8 TIM-barrel fold structure with eight βα loops surrounding the catalytic pocket. These loops exposed on the surface play a vital role in protein functions, primarily due to the interactions of some key amino acids with solvent and ligand molecules. It has been reported that motions of these loops facilitate …Revealing Origin of Decrease in Potency of Darunavir and ...2014-11-3 · Clinical inhibitors Darunavir (DRV) and Amprenavir (APV) are less effective on HIV-2 protease (PR2) than on HIV-1 protease (PR1). To identify molecular basis associated with the lower inhibition ...

  • Solution NMR refinement of a metal ion bound protein …

    2013-4-23 · Correctly calculating the structure of metal coordination sites in a protein during the process of nuclear magnetic resonance (NMR) structure determination and refinement continues to be a challenging task. In this study, we present an accurate and convenient means by which to include metal ions in the NMR structure determination process using molecular dynamics (MD) …Molecular dynamics simulation of humic substances ...2014-9-2 · Humic substances (HS) are complex mixtures of natural organic material which are found almost everywhere in the environment, and particularly in soils, sediments, and natural water. HS play key roles in many processes of paramount importance, such as plant growth, carbon storage, and the fate of contaminants in the environment. While most of the research …

  • Molecular dynamics simulation and free energy analysis of ...

    2021-9-6 · WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein, Comparison of simple potential functions for simulating liquid water, J Chem Phys 79:926–935, 1983. Crossref, ISI, Google Scholar 52.BCR‐ABL residues interacting with ponatinib are critical ...C hronic myeloid leukemia (CML) has historically represented one of the few "paradigm diseases" in the field of cancer research (1 – 3) deed, CML was one of the first malignancies associated with a known cytogenetic alteration (i.e., the Philadelphia chromosome) and a specific molecular hallmark (i.e., the BCR-ABL oncoprotein; refs.4, 5). ...

  • How phosphorylation influences E1 subunit pyruvate ...

    2018-10-2 · Pyruvate (PYR) dehydrogenase complex (PDC) is an enzymatic system that plays a crucial role in cellular metabolism as it controls the entry of carbon into the Krebs cycle. From a structural point ...(PDF) Adaptively Biased Molecular Dynamics: An Umbrella ...PDF | We discuss an adaptively biased molecular dynamics (ABMD) method for the computation of a free energy surface for a set of reaction coordinates.... | Find, read and cite all the research you ...

  • Possible allosteric binding site on Gyrase B, a key target ...

    2014-10-15 · Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935. doi:10.1063/1.445869. Article CAS Google ScholarMolecular dynamics simulation of humic substances ...2014-9-2 · Humic substances (HS) are complex mixtures of natural organic material which are found almost everywhere in the environment, and particularly in soils, sediments, and natural water. HS play key roles in many processes of paramount importance, such as plant growth, carbon storage, and the fate of contaminants in the environment. While most of the research …

  • (PDF) Adaptively Biased Molecular Dynamics: An Umbrella ...

    PDF | We discuss an adaptively biased molecular dynamics (ABMD) method for the computation of a free energy surface for a set of reaction coordinates.... | Find, read and cite all the research you ...The evolutionary process of mammalian determination ...2018-1-16 · The molecular evolution of the therian SRY gene. Fig. 1 shows the alignment of amino acid sequences of HMG domain in SRY genes. We use SOX1, SOX2 and SOX3 genes that are included in SOXB1 group, and it is believed that SRY and SOX3 genes originated from a common ancestral gene [13, 24].The sea squirt genome has only one gene of the SOXB1 …

  • Temperature artifacts in protein structures bias ligand ...

    X-ray crystallography is the gold standard to resolve conformational ensembles that are significant for protein function, ligand discovery, and computational methods development. However, relevant conformational states may be missed at common cryogenic (cryo) data-collection temperatures but can be populated 2021 Chemical Science HOT Article Collection 2021 …Peptide Gaussian accelerated molecular dynamics (Pep …2020-10-19 · Peptides mediate up to 40% of known protein–protein interactions in higher eukaryotes and play an important role in cellular signaling. However, it is challenging to simulate both binding and unbinding of peptides and calculate peptide binding free energies through conventional molecular dynamics, due to long biological timescales and extremely high …

  • Physics-based scoring of protein–ligand interactions ...

    2011-5-9 · The ability to accurately predict the interaction of a ligand with its receptor is a key limitation in computer-aided drug design approaches such as virtual screening and de novo design. In this article, we examine current strategies for a physics-based approach to scoring of protein–ligand affinity, as well as outlining recent developments in force fields and quantum …Extensive Numerical Tests of Leapfrog Integrator in Middle ...Accurate and efficient integration of the equations of motion is indispensable for molecular dynamics (MD) simulations. Despite the massive use of the conventional leapfrog (LF) integrator in modern computational tools within the framework of MD propagation, further development for better performance is still possible. The alternative version of LF in the middle thermostat …

  • Revealing Origin of Decrease in Potency of Darunavir and ...

    2014-11-3 · Clinical inhibitors Darunavir (DRV) and Amprenavir (APV) are less effective on HIV-2 protease (PR2) than on HIV-1 protease (PR1). To identify molecular basis associated with the lower inhibition ...How phosphorylation influences E1 subunit pyruvate ...2018-10-2 · Pyruvate (PYR) dehydrogenase complex (PDC) is an enzymatic system that plays a crucial role in cellular metabolism as it controls the entry of carbon into the Krebs cycle. From a structural point ...

  • Nancy A Madura

    Nancy Madura, Lantana, FL 132 Mayfield Rd, Lantana, FL 33462 Tel: 561-855-2057 Email: [email protected] ... Norma Steinbrecher 9551 N Belfort Cir Tamarac, FL 33321 . Dorothy Kramer 9541 N Belfort Cir Tamarac, FL 33321 . Eva Levy ...Temperature artifacts in protein structures bias ligand ...X-ray crystallography is the gold standard to resolve conformational ensembles that are significant for protein function, ligand discovery, and computational methods development. However, relevant conformational states may be missed at common cryogenic (cryo) data-collection temperatures but can be populated 2021 Chemical Science HOT Article Collection 2021 …

  • Physics-based scoring of protein–ligand interactions ...

    2011-5-9 · The ability to accurately predict the interaction of a ligand with its receptor is a key limitation in computer-aided drug design approaches such as virtual screening and de novo design. In this article, we examine current strategies for a physics-based approach to scoring of protein–ligand affinity, as well as outlining recent developments in force fields and quantum …Molecular dynamics simulation and free energy analysis of ...2021-9-6 · WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein, Comparison of simple potential functions for simulating liquid water, J Chem Phys 79:926–935, 1983. Crossref, ISI, Google Scholar 52.

  • Revealing Origin of Decrease in Potency of Darunavir and ...

    2014-11-3 · Clinical inhibitors Darunavir (DRV) and Amprenavir (APV) are less effective on HIV-2 protease (PR2) than on HIV-1 protease (PR1). To identify molecular basis associated with the lower inhibition ...Atomistic De‐novo Inhibitor Generation‐Guided Drug ...2021-5-5 · Introduction. SARS-CoV-2, the cause of the COVID-19 pandemic, is a positive strand RNA beta-coronavirus with large sequence similarities to the SARS-CoV and BatCoV RATG13 RNA viruses. 1 Despite being known from at least early 2019 to as far back as 2006 as found in a report by Tang et al., 1 the virus, seemingly incurable and unstoppable, has grown to an …

  • 2012-5-7 ·  >> 2012, Vol. 28 >> Issue (09): 2191-2201. doi: 10.3866/PKU.WHXB201207063 1, 1, 1,2, 1, 1(PDF) FASCAPLYSIN as a Specific Inhibitor for CDK4 ...2012-8-14 · Citation: Shafiq MI, Steinbrecher T, Schmid R (2012) FASCAPLYSIN as a Specific Inhibitor for CDK4: Insights from Molecular Modelling. PLoS ONE 7(8): e42612. PLoS ONE 7(8): e42612. doi:10.1371 ...

  • Temperature artifacts in protein structures bias ligand ...

    X-ray crystallography is the gold standard to resolve conformational ensembles that are significant for protein function, ligand discovery, and computational methods development. However, relevant conformational states may be missed at common cryogenic (cryo) data-collection temperatures but can be populated 2021 Chemical Science HOT Article Collection 2021 …Distinct dissociation kinetics between ion pairs: Solvent ...2015-7-28 · Different ion pairs exhibit different dissociation kinetics; however, while the nature of this process is vital for understanding various molecular systems, the underlying mechanism remains unclear. In this study, to examine the origin of different kinetic rate constants for this process, molecular dynamics simulations were conducted for LiCl, NaCl, KCl, and CsCl in water.

  • Peptide Gaussian accelerated molecular dynamics (Pep …

    2020-10-19 · Peptides mediate up to 40% of known protein–protein interactions in higher eukaryotes and play an important role in cellular signaling. However, it is challenging to simulate both binding and unbinding of peptides and calculate peptide binding free energies through conventional molecular dynamics, due to long biological timescales and extremely high …Intrinsically disordered proteins access a range of ...IDPPs access a wide range of hysteretic phase behaviors. To investigate nonequilibrium phase behaviors in IDPs, we synthesized and characterized IDPPs by optical turbidity measurements [at 50 μM in phosphate-buffered saline (PBS)] over two to three cycles of heating and cooling (both at 1°C/min) around their critical cloud point temperatures.

  • Direct observation of ultrafast collective motions in CO ...

    Myoglobin is an α-helical hemoprotein. The CO-binding heme cofactor is coordinated by the proximal histidine residue (His 93), located in the F helix the distal pocket, the bound CO is in close contact with the residues Leu 29 and Phe 43, with His 64 and Val 68 located in the E helix, with the CD loop, and with the B helix () nsistent with the 150-fs pump-pulse duration, the …Enhancing the catalytic activity of a novel GH5 cellulase ...2018-3-22 · Cellulases of glycosyl hydrolase (GH) family 5 share a (β/α)8 TIM-barrel fold structure with eight βα loops surrounding the catalytic pocket. These loops exposed on the surface play a vital role in protein functions, primarily due to the interactions of some key amino acids with solvent and ligand molecules. It has been reported that motions of these loops facilitate …

  • Intrinsically disordered proteins access a range of ...

    IDPPs access a wide range of hysteretic phase behaviors. To investigate nonequilibrium phase behaviors in IDPs, we synthesized and characterized IDPPs by optical turbidity measurements [at 50 μM in phosphate-buffered saline (PBS)] over two to three cycles of heating and cooling (both at 1°C/min) around their critical cloud point temperatures.Peptide Gaussian accelerated molecular dynamics (Pep …2020-10-19 · Peptides mediate up to 40% of known protein–protein interactions in higher eukaryotes and play an important role in cellular signaling. However, it is challenging to simulate both binding and unbinding of peptides and calculate peptide binding free energies through conventional molecular dynamics, due to long biological timescales and extremely high …

  • EfavirenzHIV-1 ...

    2015-9-14 ·  >> 2016, Vol. 32 >> Issue (2): 436-444. doi: 10.3866/PKU.WHXB201511302 EfavirenzHIV-1,*(),*()Enhancing the catalytic activity of a novel GH5 cellulase ...2018-3-22 · Cellulases of glycosyl hydrolase (GH) family 5 share a (β/α)8 TIM-barrel fold structure with eight βα loops surrounding the catalytic pocket. These loops exposed on the surface play a vital role in protein functions, primarily due to the interactions of some key amino acids with solvent and ligand molecules. It has been reported that motions of these loops facilitate …

  • Tino WOLTER | Karlsruhe Institute of Technology, Karlsruhe ...

    Tino Wolter. Thomas Steinbrecher. Marcus Elstner. Neurological glutamate receptors are among the most important and intensely studied protein ligand binding systems in …Distinct dissociation kinetics between ion pairs: Solvent ...2015-7-28 · Different ion pairs exhibit different dissociation kinetics; however, while the nature of this process is vital for understanding various molecular systems, the underlying mechanism remains unclear. In this study, to examine the origin of different kinetic rate constants for this process, molecular dynamics simulations were conducted for LiCl, NaCl, KCl, and CsCl in water.

  • Atomistic De‐novo Inhibitor Generation‐Guided Drug ...

    2021-5-5 · Introduction. SARS-CoV-2, the cause of the COVID-19 pandemic, is a positive strand RNA beta-coronavirus with large sequence similarities to the SARS-CoV and BatCoV RATG13 RNA viruses. 1 Despite being known from at least early 2019 to as far back as 2006 as found in a report by Tang et al., 1 the virus, seemingly incurable and unstoppable, has grown to an …Intrinsically disordered proteins access a range of ...IDPPs access a wide range of hysteretic phase behaviors. To investigate nonequilibrium phase behaviors in IDPs, we synthesized and characterized IDPPs by optical turbidity measurements [at 50 μM in phosphate-buffered saline (PBS)] over two to three cycles of heating and cooling (both at 1°C/min) around their critical cloud point temperatures.

  • Understanding the large solubility of lidocaine in 1-n ...

    2016-2-23 · Room temperature ionic liquids have been proposed as replacement solvents in a wide range of industrial separation processes. Here, we focus on the use of ionic liquids as solvents for the pharmaceutical compound lidocaine. We show that the solubility of lidocaine in seven common 1-n-butyl-3-methylimidazolium based ionic liquids is greatly enhanced relative …Physics-based scoring of protein–ligand interactions ...2011-5-9 · The ability to accurately predict the interaction of a ligand with its receptor is a key limitation in computer-aided drug design approaches such as virtual screening and de novo design. In this article, we examine current strategies for a physics-based approach to scoring of protein–ligand affinity, as well as outlining recent developments in force fields and quantum …

  • Molecular Dynamics Investigation of gluazo, a Photo ...

    2015-8-26 · Wolter T, Steinbrecher T, Elstner M. Computational study of synthetic agonist ligands of ionotropic glutamate receptors. PLoS ONE. 2013;8: e58774. View Article Google Scholar 19. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water.The covalent complex of Jo-In results from a long-lived ...2021-12-14 · The Jo/In system features two protein fragments (composed of 79 and 133 residues, respectively) capable of spontaneously and irreversibly crosslink through an isopeptide bond between side chains of K 191 of Jo and N 695 of In and involving Asp 600 of In as a proton shuttle []. Fig. 1 shows the 1 H, 15 N TROSY spectrum of the 15 N labelled Jo protein, free or …

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