Computational models, Enzyme mechanisms, Active site cooperativity, zinc-dependent enzymes, Fukui indice

Vivoli, Mirella, Pang, Jiayun ORCID: https://orcid.org/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:10.1038/s41598-017-16421-2)

DHFR, H transfer, tunnelling, protein motions

Pang, Jiayun ORCID: https://orcid.org/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:10.1021/ja061585l)

Fourier transform infrared (FTIR) spectroscopy, enzymes

Pang, Jiayun ORCID: https://orcid.org/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:10.1021/jp910161k)

H transfer, QM/MM, TTQ cofactor

Pang, Jiayun ORCID: https://orcid.org/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:10.1039/C003107K)

Hansen solubility parameter; NLP; molecular embedding; deep learning; ESOL solubility parameter; SMILES; transfer learning; finetuning,; Hugging Face

Pang, Jiayun ORCID: https://orcid.org/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:10.1039/d3dd00119a)

MD simulations, DHFR, hyperthermophile, folding, dimer

Pang, Jiayun ORCID: https://orcid.org/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:10.1039/B611210B)

Thermomyces lanuginosus lipase; Methanol intolerance; Molecular dynamics simulation; Rational design; Protein stability

Tong, Xiaoxue, Busk, Peter Kamp, Lange, Lene and Pang, Jiayun ORCID: https://orcid.org/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:10.1080/08927022.2015.1059938)

cofactor B12, targeted MD simulations, ONIOM(DFT:MM), domain conformational changes, activation of Co-C bond

Pang, Jiayun ORCID: https://orcid.org/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:10.1021/ja210417k)

d-ornithine 4,5-aminomutase (OAM), adenosylcobalamin (AdoCbl; coenzyme B12)-dependent isomerase, homolytic rupture, Rossmann domain

Pang, Jiayun ORCID: https://orcid.org/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:10.1021/ja210417k)

density functional calculations, enzyme catalysis, enzyme models, molecular mechanics, radical reactions

Pang, Jiayun ORCID: https://orcid.org/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:10.1002/chem.201402759)

enzyme catalysis, enzyme kinetics, enzymes isotope effects, quinones, QSAR

Heuts, Dominic P.H.M., Gummadova, Jennet O., Pang, Jiayun ORCID: https://orcid.org/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:10.1074/jbc.M111.232850)

enzyme catalysis, hydrogen transfer, molecular dynamics, quantum chemistry, reaction barrier

Hay, Sam, Pudney, Christopher R., McGrory, Tom A., Pang, Jiayun ORCID: https://orcid.org/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:10.1002/anie.200805502)

enzyme mechanism, H-tunnelling, kinetic isotope effect, protein dynamics, redox catalysis, temperature-dependence

Hay, Sam, Pudney, Christopher, Hothi, Parvinder, Johannissen, Linus O., Masgrau, Laura, Pang, Jiayun ORCID: https://orcid.org/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:10.1042/BST0360016)

hexahydromethanocarbazole; palladium; norbornene; privileged structure; DFT calculations; drug discovery

Yin, Lina ORCID: https://orcid.org/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: https://orcid.org/0000-0003-0689-8440 and Hu, Qingzhong ORCID: https://orcid.org/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:10.1038/s42004-022-00759-4)

hydride transfer reaction, morphinone reductase, primary kinetic isotope effect (KIE), enzymes

Pang, Jiayun ORCID: https://orcid.org/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:10.1021/ja800471f)

hydride transfer, hydrostatic pressure, donor-acceptor distance, MD simulations

Pudney, Christopher R., McGrory, Tom, Lafite, Pierre, Pang, Jiayun ORCID: https://orcid.org/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:10.1002/cbic.200900071)

hydrogen transfer, kinetic isotope effects, protein dynamics, catalysis, enzymes

Allemann, Rudolf K., Evans, Rhiannon M., Tey, Lai-hock, Maglia, Giovanni, Pang, Jiayun ORCID: https://orcid.org/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:10.1098/rstb.2006.1865)

hydrogen transfer, promoting vibrations, PETNR,

Pudney, Christopher R., Hay, Sam, Levy, Colin, Pang, Jiayun ORCID: https://orcid.org/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:10.1021/ja908469m)

morphinone reductase, multiple reactive configurations, hydrogen tunneling

Pudney, Christopher R., Hay, Sam, Pang, Jiayun ORCID: https://orcid.org/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:10.1021/ja074463h)

organic reaction prediction, AI, language models, finetuning, byte-level tokenisation

Pang, Jiayun ORCID: https://orcid.org/0000-0003-0689-8440 and Vulic, Ivan (2024) Specialising and analysing instruction-tuned and byte-level language models for organic reaction prediction. Faraday Discussions. ISSN 1359-6640 (Print), 1364-5498 (Online) (doi:10.1039/D4FD00104D)

protein–protein interaction, hydrophobic effect, stopped-flow, kinetics, simulation

Ivanova, Ekaterina, Pang, Jiayun ORCID: https://orcid.org/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:10.1002/prot.23224)

secondary kinetic isotope effect, hydrogen transfer, dihydrofolate reductase

Hay, Sam, Pang, Jiayun ORCID: https://orcid.org/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:10.1002/cphc.200800291)

solid dispersions, cationic drugs, anionic polymers, hot-melt extrusion (HME) technique

Maniruzzaman, Mohammed, Morgan, David J., Mendham, Andrew P., Pang, Jiayun ORCID: https://orcid.org/0000-0003-0689-8440, Snowden, Martin J. ORCID: https://orcid.org/0000-0002-1087-2692 and Douroumis, Dennis ORCID: https://orcid.org/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:10.1016/j.ijpharm.2012.11.048)

solid dispersions, quantum mechanics, molecular modelling, miscibility, drug-polymer interactions

Maniruzzaman, Mohammed, Pang, Jiayun ORCID: https://orcid.org/0000-0003-0689-8440, Morgan, David J. and Douroumis, Dennis ORCID: https://orcid.org/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:10.1021/mp500510m)

sulphydryl oxidase, FAD binding, tryptophan residue, protein folding, mitochondria

Wang, Qi, Ang, Swee Kim, Ceh-Pavia, Efrain, Pang, Jiayun ORCID: https://orcid.org/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:10.1042/BSR20150144)