Items where Author is "Pang, Jiayun"

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5-aminomutase (OAM) activation of Co-C bond Active site cooperativity adenosylcobalamin (AdoCbl anionic polymers catalysis cationic drugs coenzyme B12)-dependent isomerase cofactor B12 Computational models d-ornithine 4 deep learning density functional calculations DFT calculations DHFR dihydrofolate reductase dimer domain conformational changes donor-acceptor distance drug discovery drug-polymer interactions enzyme catalysis enzyme kinetics enzyme mechanism Enzyme mechanisms enzyme models enzymes enzymes isotope effects ESOL solubility parameter FAD binding finetuning folding Fourier transform infrared (FTIR) spectroscopy Fukui indice H transfer H-tunnelling Hansen solubility parameter hexahydromethanocarbazole homolytic rupture hot-melt extrusion (HME) technique Hugging Face hydride transfer hydride transfer reaction hydrogen transfer hydrogen tunneling hydrophobic effect hydrostatic pressure hyperthermophile kinetic isotope effect kinetic isotope effects kinetics MD simulations Methanol intolerance miscibility mitochondria molecular dynamics Molecular dynamics simulation molecular embedding molecular mechanics molecular modelling morphinone reductase multiple reactive configurations NLP norbornene ONIOM(DFT:MM) palladium PETNR primary kinetic isotope effect (KIE) privileged structure promoting vibrations protein dynamics protein folding protein motions Protein stability protein–protein interaction QM/MM QSAR quantum chemistry quantum mechanics quinones radical reactions Rational design reaction barrier redox catalysis Rossmann domain secondary kinetic isotope effect simulation SMILES solid dispersions stopped-flow sulphydryl oxidase targeted MD simulations temperature-dependence Thermomyces lanuginosus lipase transfer learning tryptophan residue TTQ cofactor tunnelling zinc-dependent enzymes

Number of items: 112.

5-aminomutase (OAM)

Pang, Jiayun ORCID: 0000-0003-0689-8440 , Li, Xin, Morokuma, Keiji, Scrutton, Nigel S. and Sutcliffe, Michael J. (2011) Large-scale domain conformational change is coupled to the activation of the Co–C bond in the B₁₂-dependent enzyme ornithine 4,5-aminomutase: a computational study. Journal of the American Chemical Society, 134 (4). pp. 2367-2377. ISSN 0002-7863 (Print), 1520-5126 (Online) (doi:https://doi.org/10.1021/ja210417k)

activation of Co-C bond

Pang, Jiayun ORCID: 0000-0003-0689-8440 , Li, Xin, Morokuma, Keiji, Scrutton, Nigel S. and Sutcliffe, Michael J. (2011) Large-scale domain conformational change is coupled to the activation of the Co-C bond in the B12-dependent enzyme ornithine 4,5-aminomutase: a computational study. Journal of the American Chemical Society, 134 (4). pp. 2367-2377. ISSN 0002-7863 (Print), 1520-5126 (Online) (doi:https://doi.org/10.1021/ja210417k)

Active site cooperativity

Vivoli, Mirella, Pang, Jiayun ORCID: 0000-0003-0689-8440 and Harmer, Nicholas J. (2017) A half-site multimeric enzyme achieves its cooperativity without conformational changes. Scientific Reports, 7 (1):16529. ISSN 2045-2322 (Print), 2045-2322 (Online) (doi:https://doi.org/10.1038/s41598-017-16421-2)

adenosylcobalamin (AdoCbl

anionic polymers

Maniruzzaman, Mohammed, Morgan, David J., Mendham, Andrew P., Pang, Jiayun ORCID: 0000-0003-0689-8440 , Snowden, Martin J. ORCID: 0000-0002-1087-2692 and Douroumis, Dennis ORCID: 0000-0002-3782-0091 (2012) Drug–polymer intermolecular interactions in hot-melt extruded solid dispersions. International Journal of Pharmaceutics, 443 (1-2). pp. 199-208. ISSN 0378-5173 (doi:https://doi.org/10.1016/j.ijpharm.2012.11.048)

catalysis

Allemann, Rudolf K., Evans, Rhiannon M., Tey, Lai-hock, Maglia, Giovanni, Pang, Jiayun ORCID: 0000-0003-0689-8440 , Rodriguez, Robert, Shrimpton, Paul J. and Swanwick, Richard S. (2006) Protein motions during catalysis by dihydrofolate reductases. Philosophical Transactions of the Royal Society B: Biological Sciences, 361 (1472). pp. 1317-1321. ISSN 0962-8436 (Print), 1471-2970 (Online) (doi:https://doi.org/10.1098/rstb.2006.1865)

cationic drugs

coenzyme B12)-dependent isomerase

cofactor B12

Pang, Jiayun ORCID: 0000-0003-0689-8440 , Li, Xin, Morokuma, Keiji, Scrutton, Nigel S. and Sutcliffe, Michael J. (2011) Large-scale domain conformational change is coupled to the activation of the Co-C bond in the B12-dependent enzyme ornithine 4,5-aminomutase: a computational study. Journal of the American Chemical Society, 134 (4). pp. 2367-2377. ISSN 0002-7863 (Print), 1520-5126 (Online) (doi:https://doi.org/10.1021/ja210417k)

Computational models

d-ornithine 4

deep learning

Pang, Jiayun ORCID: 0000-0003-0689-8440 , Pine, Alexander and Sulemana, Abdulai (2023) Using Natural Language Processing (NLP)-inspired molecular embedding approach to predict Hansen solubility parameters. Digital Discovery. ISSN 2635-098X (Online) (doi:https://doi.org/10.1039/d3dd00119a)

density functional calculations

Pang, Jiayun ORCID: 0000-0003-0689-8440 , Scrutton, Nigel S. and Sutcliffe, Michael J. (2014) Quantum mechanics/molecular mechanics studies on the mechanism of action of cofactor pyridoxal 5'-phosphate in ornithine 4,5-aminomutase. Chemistry - A European Journal, 20 (36). pp. 11390-11401. ISSN 0947-6539 (Print), 1521-3765 (Online) (doi:https://doi.org/10.1002/chem.201402759)

DFT calculations

Yin, Lina ORCID: 0000-0002-6734-521X , Guan, Ting, Cheng, Jie, Pan, Dongchao, Lu, Jinyang, Huang, Jiahui, Wu, Jiaqi, Chen, Xiaoli, You, Taiyun, Huo, Xuting, He, Yuting, Pang, Jiayun ORCID: 0000-0003-0689-8440 and Hu, Qingzhong ORCID: 0000-0002-8880-4948 (2022) Manipulations of phenylnorbornyl palladium species for multicomponent construction of a bridged polycyclic privileged scaffold. Communications Chemistry, 5 (1):140. ISSN 2399-3669 (Online) (doi:https://doi.org/10.1038/s42004-022-00759-4)

DHFR

Pang, Jiayun ORCID: 0000-0003-0689-8440 and Allemann, Rudolf K. (2006) Molecular dynamics simulation of thermal unfolding of Thermatoga maritima DHFR. Physical Chemistry Chemical Physics (PCCP), 9 (6). pp. 711-718. ISSN 1463-9076 (Print), 1463-9084 (Online) (doi:https://doi.org/10.1039/B611210B)

Pang, Jiayun ORCID: 0000-0003-0689-8440 , Pu, Jingzhi, Gao, Jiali, Truhlar, Donald G. and Allemann, Rudolf K. (2006) Hydride transfer reaction catalyzed by hyperthermophilic dihydrofolate reductase is dominated by quantum mechanical tunneling and is promoted by both inter- and intramonomeric correlated motions. Journal of the American Chemical Society, 128 (24). pp. 8015-8023. ISSN 0002-7863 (Print), 1520-5126 (Online) (doi:https://doi.org/10.1021/ja061585l)

dihydrofolate reductase

Hay, Sam, Pang, Jiayun ORCID: 0000-0003-0689-8440 , Monaghan, Phillip J., Wang, Xi, Evans, Rhiannon M., Sutcliffe, Michael J., Allemann, Rudolf K. and Scrutton, Nigel S. (2008) Secondary kinetic isotope effects as probes of environmentally-coupled enzymatic hydrogen tunneling reactions. ChemPhysChem, 9 (11). pp. 1536-1539. ISSN 1439-4235 (Print), 1439-7641 (Online) (doi:https://doi.org/10.1002/cphc.200800291)

dimer

domain conformational changes

Pang, Jiayun ORCID: 0000-0003-0689-8440 , Li, Xin, Morokuma, Keiji, Scrutton, Nigel S. and Sutcliffe, Michael J. (2011) Large-scale domain conformational change is coupled to the activation of the Co-C bond in the B12-dependent enzyme ornithine 4,5-aminomutase: a computational study. Journal of the American Chemical Society, 134 (4). pp. 2367-2377. ISSN 0002-7863 (Print), 1520-5126 (Online) (doi:https://doi.org/10.1021/ja210417k)

donor-acceptor distance

Pudney, Christopher R., McGrory, Tom, Lafite, Pierre, Pang, Jiayun ORCID: 0000-0003-0689-8440 , Hay, Sam, Leys, David, Sutcliffe, Michael J. and Scrutton, Nigel S. (2009) Parallel pathways and free-energy landscapes for enzymatic hydride transfer probed by hydrostatic pressure. ChemBioChem, 10 (8). pp. 1379-1384. ISSN 1439-4227 (Print), 1439-7633 (Online) (doi:https://doi.org/10.1002/cbic.200900071)

drug discovery

drug-polymer interactions

Maniruzzaman, Mohammed, Pang, Jiayun ORCID: 0000-0003-0689-8440 , Morgan, David J. and Douroumis, Dennis ORCID: 0000-0002-3782-0091 (2015) Molecular modelling as a predictive tool for the development of solid dispersions. Molecular Pharmaceutics, 12 (4). pp. 1040-1049. ISSN 1543-8384 (Print), 1543-8392 (Online) (doi:https://doi.org/10.1021/mp500510m)

enzyme catalysis

Heuts, Dominic P.H.M., Gummadova, Jennet O., Pang, Jiayun ORCID: 0000-0003-0689-8440 , Rigby, Stephen E.J. and Scrutton, Nigel S. (2011) Reaction of vascular adhesion protein-1 (VAP-1) with primary amines: mechanistic insights from isotope effects and quantitative structure-activity relationships. The Journal of Biological Chemistry, 286 (34). pp. 29584-93. ISSN 0021-9258 (Print), 1083-351X (Online) (doi:https://doi.org/10.1074/jbc.M111.232850)

Hay, Sam, Pudney, Christopher R., McGrory, Tom A., Pang, Jiayun ORCID: 0000-0003-0689-8440 , Sutcliffe, Michael J. and Scrutton, Nigel S. (2009) Barrier compression enhances an enzymatic hydrogen-transfer reaction. Angewandte Chemie International Edition, 48 (8). pp. 1452-1454. ISSN 1433-7851 (Print), 1521-3773 (Online) (doi:https://doi.org/10.1002/anie.200805502)

enzyme kinetics

enzyme mechanism

Hay, Sam, Pudney, Christopher, Hothi, Parvinder, Johannissen, Linus O., Masgrau, Laura, Pang, Jiayun ORCID: 0000-0003-0689-8440 , Leys, David, Sutcliffe, Michael J. and Scrutton, Nigel S. (2008) Atomistic insight into the origin of the temperature-dependence of kinetic isotope effects and H-tunnelling in enzyme systems is revealed through combined experimental studies and biomolecular simulation. Biochemical Society Transactions, 36 (1). pp. 16-21. ISSN 0300-5127 (Print), 1470-8752 (Online) (doi:https://doi.org/10.1042/BST0360016)

Enzyme mechanisms

enzyme models

enzymes

Pang, Jiayun ORCID: 0000-0003-0689-8440 , Scrutton, Nigel S., de Visser, Sam P. and Sutcliffe, Michael J. (2009) Assignment of the vibrational spectra of enzyme-bound tryptophan tryptophyl quinones using a combined QM/MM approach. The Journal of Physical Chemistry A, 114 (2). pp. 1212-1217. ISSN 1089-5639 (Print), 1520-5215 (Online) (doi:https://doi.org/10.1021/jp910161k)

Pang, Jiayun ORCID: 0000-0003-0689-8440 , Hay, Sam, Scrutton, Nigel S. and Sutcliffe, Michael J. (2008) Deep tunneling dominates the biologically important hydride transfer reaction from NADH to FMN in morphinone reductase. Journal of the American Chemical Society, 130 (22). pp. 7092-7097. ISSN 0002-7863 (Print), 1520-5126 (Online) (doi:https://doi.org/10.1021/ja800471f)

enzymes isotope effects

ESOL solubility parameter

FAD binding

Wang, Qi, Ang, Swee Kim, Ceh-Pavia, Efrain, Pang, Jiayun ORCID: 0000-0003-0689-8440 and Lu, Hui (2015) Role of tryptophan residues of Erv1: Trp95 and Trp183 are important for its folding and oxidase function. Bioscience Reports, 35 (4):e00244. ISSN 0144-8463 (Print), 1573-4935 (Online) (doi:https://doi.org/10.1042/BSR20150144)

finetuning

folding

Fourier transform infrared (FTIR) spectroscopy

Fukui indice

H transfer

Pang, Jiayun ORCID: 0000-0003-0689-8440 , Scrutton, Nigel S., de Visser, Sam P. and Sutcliffe, Michael J. (2010) New insights into the multi-step reaction pathway of the reductive half-reaction catalysed by aromatic amine dehydrogenase: a QM/MM study. ChemComm, 46 (18). pp. 3104-3106. ISSN 1359-7345 (Print), 1364-548X (Online) (doi:https://doi.org/10.1039/C003107K)

H-tunnelling

Hansen solubility parameter

hexahydromethanocarbazole

homolytic rupture

hot-melt extrusion (HME) technique

Hugging Face

hydride transfer

hydride transfer reaction

hydrogen transfer

Pudney, Christopher R., Hay, Sam, Levy, Colin, Pang, Jiayun ORCID: 0000-0003-0689-8440 , Sutcliffe, Michael J., Leys, David and Scrutton, Nigel S. (2009) Evidence to support the hypothesis that promoting vibrations enhance the rate of an enzyme catalyzed H-tunneling reaction. Journal of the American Chemical Society, 131 (47). pp. 17072-17073. ISSN 0002-7863 (Print), 1520-5126 (Online) (doi:https://doi.org/10.1021/ja908469m)

hydrogen tunneling

Pudney, Christopher R., Hay, Sam, Pang, Jiayun ORCID: 0000-0003-0689-8440 , Costello, Claire, Leys, David, Sutcliffe, Michael J. and Scrutton, Nigel S. (2007) Mutagenesis of morphinone reductase induces multiple reactive configurations and identifies potential ambiguity in kinetic analysis of enzyme tunneling mechanisms. Journal of the American Chemical Society, 129 (45). pp. 13949-13956. ISSN 0002-7863 (Print), 1520-5126 (Online) (doi:https://doi.org/10.1021/ja074463h)

hydrophobic effect

Ivanova, Ekaterina, Pang, Jiayun ORCID: 0000-0003-0689-8440 , Jowitt, Thomas A., Yan, Guanhua, Warwicker, Jim, Sutcliffe, Michael J. and Lu, Hui (2011) Temperature-dependent study reveals that dynamics of hydrophobic residues plays an important functional role in the mitochondrial Tim9–Tim10 complex. Proteins: Structure, Function, and Bioinformatics, 80 (2). pp. 602-615. ISSN 0887-3585 (Print), 1097-0134 (Online) (doi:https://doi.org/10.1002/prot.23224)

hydrostatic pressure

hyperthermophile

kinetic isotope effect

kinetic isotope effects

kinetics

MD simulations

Methanol intolerance

Tong, Xiaoxue, Busk, Peter Kamp, Lange, Lene and Pang, Jiayun ORCID: 0000-0003-0689-8440 (2016) New insights into the molecular mechanism of methanol-induced inactivation of Thermomyces lanuginosus lipase: A molecular dynamics simulation study. Molecular Simulation, 42 (5). pp. 434-445. ISSN 0892-7022 (Print), 1029-0435 (Online) (doi:https://doi.org/10.1080/08927022.2015.1059938)

miscibility

mitochondria

molecular dynamics

Molecular dynamics simulation

molecular embedding

molecular mechanics

molecular modelling

morphinone reductase

multiple reactive configurations

NLP

norbornene

ONIOM(DFT:MM)

Pang, Jiayun ORCID: 0000-0003-0689-8440 , Li, Xin, Morokuma, Keiji, Scrutton, Nigel S. and Sutcliffe, Michael J. (2011) Large-scale domain conformational change is coupled to the activation of the Co-C bond in the B12-dependent enzyme ornithine 4,5-aminomutase: a computational study. Journal of the American Chemical Society, 134 (4). pp. 2367-2377. ISSN 0002-7863 (Print), 1520-5126 (Online) (doi:https://doi.org/10.1021/ja210417k)

palladium

PETNR

primary kinetic isotope effect (KIE)

privileged structure

promoting vibrations

protein dynamics

protein folding

protein motions

Protein stability

protein–protein interaction

QM/MM

QSAR

quantum chemistry

quantum mechanics

quinones

radical reactions

Rational design

reaction barrier

redox catalysis

Rossmann domain

secondary kinetic isotope effect

simulation

SMILES

solid dispersions

stopped-flow

sulphydryl oxidase

targeted MD simulations

Pang, Jiayun ORCID: 0000-0003-0689-8440 , Li, Xin, Morokuma, Keiji, Scrutton, Nigel S. and Sutcliffe, Michael J. (2011) Large-scale domain conformational change is coupled to the activation of the Co-C bond in the B12-dependent enzyme ornithine 4,5-aminomutase: a computational study. Journal of the American Chemical Society, 134 (4). pp. 2367-2377. ISSN 0002-7863 (Print), 1520-5126 (Online) (doi:https://doi.org/10.1021/ja210417k)

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