Mark Kelly, PhD
Professional Researcher
Pharmaceutical Chemistry
School of Pharmacy

Publications (30)

Top publication keywords:
FluorineProtein Interaction Domains and MotifsHistone DemethylasesProtein EngineeringAdenosine TriphosphatasesMonomeric GTP-Binding ProteinsChromatinNuclear ProteinsMental Retardation, X-LinkedLigandsAllosteric RegulationCell Cycle ProteinsHypothermia, InducedProtein Structure, SecondaryComputer-Aided Design

• Identifying ligands for the PHD1 finger of KDM5A through high-throughput screening.
  RSC chemical biology 2023 Ortiz G, Longbotham JE, Qin SL, Zhang MY, Lee GM, Neitz RJ, Kelly MJS, Arkin MR, Fujimori DG
• Chromatin Sensing by the Auxiliary Domains of KDM5C Regulates Its Demethylase Activity and Is Disrupted by X-linked Intellectual Disability Mutations.
  Journal of molecular biology 2022 Ugur FS, Kelly MJS, Fujimori DG
• Probing the KRas Switch II Groove by Fluorine NMR Spectroscopy.
  ACS chemical biology 2022 Peacock DM, Kelly MJS, Shokat KM
• Systems-level effects of allosteric perturbations to a model molecular switch.
  Nature 2021 Perica T, Mathy CJP, Xu J, Jang G?, Zhang Y, Kaake R, Ollikainen N, Braberg H, Swaney DL, Lambright DG, Kelly MJS, Krogan NJ, Kortemme T
• Recognition of Histone H3 Methylation States by the PHD1 Domain of Histone Demethylase KDM5A.
  ACS chemical biology 2021 Longbotham JE, Kelly MJS, Fujimori DG

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• Expanding the space of protein geometries by computational design of de novo fold families.
  Science (New York, N.Y.) 2020 Pan X, Thompson MC, Zhang Y, Liu L, Fraser JS, Kelly MJS, Kortemme T
• Computational design of a modular protein sense-response system.
  Science (New York, N.Y.) 2019 Glasgow AA, Huang YM, Mandell DJ, Thompson M, Ritterson R, Loshbaugh AL, Pellegrino J, Krivacic C, Pache RA, Barlow KA, Ollikainen N, Jeon D, Kelly MJS, Fraser JS, Kortemme T
• Neural JNK3 regulates blood flow recovery after hindlimb ischemia in mice via an Egr1/Creb1 axis.
  Nature communications 2019 Kant S, Craige SM, Chen K, Reif MM, Learnard H, Kelly M, Caliz AD, Tran KV, Ramo K, Peters OM, Freeman M, Davis RJ, Keaney JF
• A Cell-Penetrating Scorpion Toxin Enables Mode-Specific Modulation of TRPA1 and Pain.
  Cell 2019 Lin King JV, Emrick JJ, Kelly MJS, Herzig V, King GF, Medzihradszky KF, Julius D
• HDAC inhibition in glioblastoma monitored by hyperpolarized 13 C MRSI.
  NMR in biomedicine 2018 Radoul M, Najac C, Viswanath P, Mukherjee J, Kelly M, Gillespie AM, Chaumeil MM, Eriksson P, Delos Santos R, Pieper RO, Ronen SM
• The centrosomin CM2 domain is a multi-functional binding domain with distinct cell cycle roles.
  PloS one 2018 Citron YR, Fagerstrom CJ, Keszthelyi B, Huang B, Rusan NM, Kelly MJS, Agard DA
• A 31-residue peptide induces aggregation of tau's microtubule-binding region in cells.
  Nature chemistry 2017 Stöhr J, Wu H, Nick M, Wu Y, Bhate M, Condello C, Johnson N, Rodgers J, Lemmin T, Acharya S, Becker J, Robinson K, Kelly MJS, Gai F, Stubbs G, Prusiner SB, DeGrado WF
• Allosteric Indole Amide Inhibitors of p97: Identification of a Novel Probe of the Ubiquitin Pathway.
  ACS medicinal chemistry letters 2015 Alverez C, Bulfer SL, Chakrasali R, Chimenti MS, Deshaies RJ, Green N, Kelly M, LaPorte MG, Lewis TS, Liang M, Moore WJ, Neitz RJ, Peshkov VA, Walters MA, Zhang F, Arkin MR, Wipf P, Huryn DM
• Allosteric N-WASP activation by an inter-SH3 domain linker in Nck.
  Proceedings of the National Academy of Sciences of the United States of America 2015 Okrut J, Prakash S, Wu Q, Kelly MJ, Taunton J
• A Fragment-Based Ligand Screen Against Part of a Large Protein Machine: The ND1 Domains of the AAA+ ATPase p97/VCP.
  Journal of biomolecular screening 2015 Chimenti MS, Bulfer SL, Neitz RJ, Renslo AR, Jacobson MP, James TL, Arkin MR, Kelly MJ
• Histone demethylase KDM5A is regulated by its reader domain through a positive-feedback mechanism.
  Nature communications 2015 Torres IO, Kuchenbecker KM, Nnadi CI, Fletterick RJ, Kelly MJ, Fujimori DG
• Biophysical methods for identifying fragment-based inhibitors of protein-protein interactions.
  Methods in molecular biology (Clifton, N.J.) 2015 Pfaff SJ, Chimenti MS, Kelly MJ, Arkin MR
• Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone.
  Journal of molecular biology 2014 Street TO, Zeng X, Pellarin R, Bonomi M, Sali A, Kelly MJ, Chu F, Agard DA
• 13C NMR metabolomic evaluation of immediate and delayed mild hypothermia in cerebrocortical slices after oxygen-glucose deprivation.
  Anesthesiology 2013 Liu J, Segal MR, Kelly MJ, Pelton JG, Kim M, James TL, Litt L
• 1H nuclear magnetic resonance brain metabolomics in neonatal mice after hypoxia-ischemia distinguished normothermic recovery from mild hypothermia recoveries.
  Pediatric research 2013 Liu J, Sheldon RA, Segal MR, Kelly MJ, Pelton JG, Ferriero DM, James TL, Litt L
• Design of a phosphorylatable PDZ domain with peptide-specific affinity changes.
  Structure (London, England : 1993) 2012 Smith CA, Shi CA, Chroust MK, Bliska TE, Kelly MJS, Jacobson MP, Kortemme T
• Metabolomics of oxidative stress in recent studies of endogenous and exogenously administered intermediate metabolites.
  International journal of molecular sciences 2011 Liu J, Litt L, Segal MR, Kelly MJ, Pelton JG, Kim M
• Radically different amyloid conformations dictate the seeding specificity of a chimeric Sup35 prion.
  Journal of molecular biology 2011 Foo CK, Ohhashi Y, Kelly MJ, Tanaka M, Weissman JS
• Outcome-related metabolomic patterns from 1H/31P NMR after mild hypothermia treatments of oxygen-glucose deprivation in a neonatal brain slice model of asphyxia.
  Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism 2010 Liu J, Litt L, Segal MR, Kelly MJ, Yoshihara HA, James TL
• Cofilin is a pH sensor for actin free barbed end formation: role of phosphoinositide binding.
  The Journal of cell biology 2008 Frantz C, Barreiro G, Dominguez L, Chen X, Eddy R, Condeelis J, Kelly MJ, Jacobson MP, Barber DL
• Exogenous ethyl pyruvate versus pyruvate during metabolic recovery after oxidative stress in neonatal rat cerebrocortical slices.
  Anesthesiology 2007 Zeng J, Liu J, Yang GY, Kelly MJ, James TL, Litt L
• The structural basis of yeast prion strain variants.
  Nature 2007 Toyama BH, Kelly MJ, Gross JD, Weissman JS
• Parallel beta-helix proteins required for accurate capsule polysaccharide synthesis and virulence in the yeast Cryptococcus neoformans.
  Eukaryotic cell 2007 Liu OW, Kelly MJ, Chow ED, Madhani HD
• Pyruvate improves recovery after PARP-1-associated energy failure induced by oxidative stress in neonatal rat cerebrocortical slices.
  Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism 2006 Zeng J, Yang GY, Ying W, Kelly M, Hirai K, James TL, Swanson RA, Litt L
• Using 31P NMR spectroscopy at 14.1 Tesla to investigate PARP-1 associated energy failure and metabolic rescue in cerebrocortical slices.
  Journal of bioenergetics and biomembranes 2004 Zeng J, Hirai K, Yang GY, Ying W, Swanson RA, Kelly M, Mayer M, James TL, Litt L