{"entity": "researcher", "timestamp": "2026-08-22T06:57:29.865Z", "family": "van der Kamp", "given": "Marc W", "initials": "MW", "orcid": "0000-0002-8060-3359", "affiliations": ["Department of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e09f39776374aeca06c0a767d62bfac.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e09f39776374aeca06c0a767d62bfac"}}, "publications": [{"entity": "publication", "iuid": "519b285dd47440b999323898a773c73b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/519b285dd47440b999323898a773c73b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/519b285dd47440b999323898a773c73b"}}, "title": "Correction to \"Loop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases\".", "authors": [{"family": "Crean", "given": "Rory M", "initials": "RM"}, {"family": "Biler", "given": "Michal", "initials": "M", "orcid": "0000-0003-3809-6928", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4e9f22f57e441cb9028720d6a4b2bfa.json"}}, {"family": "Corbella", "given": "Marina", "initials": "M", "orcid": "0000-0001-9209-868X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/53c414fb66534c3cbf91d3a3de055196.json"}}, {"family": "Calixto", "given": "Ana R", "initials": "AR", "orcid": "0000-0002-1123-0413", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/91f7bbeb7f3245449679931f97d21eb8.json"}}, {"family": "van der Kamp", "given": "Marc W", "initials": "MW", "orcid": "0000-0002-8060-3359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e09f39776374aeca06c0a767d62bfac.json"}}, {"family": "Hengge", "given": "Alvan C", "initials": "AC", "orcid": "0000-0002-5696-2087", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/43fb9bec035e46c4a63263aded78a78b.json"}}, {"family": "Kamerlin", "given": "Shina C L", "initials": "SCL", "orcid": "0000-0002-3190-1173", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4540c85432f4cdf952b0ef7cfe1d875.json"}}], "type": "published erratum", "published": "2022-06-08", "journal": {"title": "Journal of the American Chemical Society", "issn": "1520-5126", "volume": "144", "issue": "22", "pages": "10091-10093", "issn-l": "0002-7863"}, "abstract": null, "doi": "10.1021/jacs.2c04624", "pmid": "35609280", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11027752"}], "notes": [], "created": "2026-08-21T11:37:56.469Z", "modified": "2026-08-21T11:37:56.639Z"}, {"entity": "publication", "iuid": "7858c9014b094f75b3cc6bd6595f5398", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7858c9014b094f75b3cc6bd6595f5398.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7858c9014b094f75b3cc6bd6595f5398"}}, "title": "Reliable In Silico Ranking of Engineered Therapeutic TCR Binding Affinities with MMPB/GBSA.", "authors": [{"family": "Crean", "given": "Rory M", "initials": "RM"}, {"family": "Pudney", "given": "Christopher R", "initials": "CR", "orcid": "0000-0001-6211-0086", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e46df883c623428aba5d01bcf59c1895.json"}}, {"family": "Cole", "given": "David K", "initials": "DK"}, {"family": "van der Kamp", "given": "Marc W", "initials": "MW", "orcid": "0000-0002-8060-3359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e09f39776374aeca06c0a767d62bfac.json"}}], "type": "journal article", "published": "2022-02-14", "journal": {"title": "J Chem Inf Model", "issn": "1549-960X", "volume": "62", "issue": "3", "pages": "577-590", "issn-l": "1549-9596"}, "abstract": "Accurate and efficient in silico ranking of protein-protein binding affinities is useful for protein design with applications in biological therapeutics. One popular approach to rank binding affinities is to apply the molecular mechanics Poisson-Boltzmann/generalized Born surface area (MMPB/GBSA) method to molecular dynamics (MD) trajectories. Here, we identify protocols that enable the reliable evaluation of T-cell receptor (TCR) variants binding to their target, peptide-human leukocyte antigens (pHLAs). We suggest different protocols for variant sets with a few (\u22644) or many mutations, with entropy corrections important for the latter. We demonstrate how potential outliers could be identified in advance and that just 5-10 replicas of short (4 ns) MD simulations may be sufficient for the reproducible and accurate ranking of TCR variants. The protocols developed here can be applied toward in silico screening during the optimization of therapeutic TCRs, potentially reducing both the cost and time taken for biologic development.", "doi": "10.1021/acs.jcim.1c00765", "pmid": "35049312", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9097153"}], "notes": [], "created": "2026-08-21T11:32:58.073Z", "modified": "2026-08-21T11:32:58.145Z"}, {"entity": "publication", "iuid": "79b28f5d35424275a9aeec9755d5895e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/79b28f5d35424275a9aeec9755d5895e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/79b28f5d35424275a9aeec9755d5895e"}}, "title": "Chemical Mapping Exposes the Importance of Active Site Interactions in Governing the Temperature Dependence of Enzyme Turnover.", "authors": [{"family": "Winter", "given": "Samuel D", "initials": "SD"}, {"family": "Jones", "given": "Hannah B L", "initials": "HBL"}, {"family": "R\u0103s\u0103dean", "given": "Dora M", "initials": "DM"}, {"family": "Crean", "given": "Rory M", "initials": "RM"}, {"family": "Danson", "given": "Michael J", "initials": "MJ"}, {"family": "Panto\u015f", "given": "G Dan", "initials": "GD"}, {"family": "Katona", "given": "Gergely", "initials": "G"}, {"family": "Prentice", "given": "Erica", "initials": "E", "orcid": "0000-0001-7417-7296", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c35c332a9b634fc68afcf3c5f8e1b936.json"}}, {"family": "Arcus", "given": "Vickery L", "initials": "VL"}, {"family": "van der Kamp", "given": "Marc W", "initials": "MW", "orcid": "0000-0002-8060-3359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e09f39776374aeca06c0a767d62bfac.json"}}, {"family": "Pudney", "given": "Christopher R", "initials": "CR", "orcid": "0000-0001-6211-0086", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e46df883c623428aba5d01bcf59c1895.json"}}], "type": "journal article", "published": "2021-12-17", "journal": {"title": "ACS Catal", "issn": "2155-5435", "volume": "11", "issue": "24", "pages": "14854-14863", "issn-l": "2155-5435"}, "abstract": "Uncovering the role of global protein dynamics in enzyme turnover is needed to fully understand enzyme catalysis. Recently, we have demonstrated that the heat capacity of catalysis, \u0394C P \u2021, can reveal links between the protein free energy landscape, global protein dynamics, and enzyme turnover, suggesting that subtle changes in molecular interactions at the active site can affect long-range protein dynamics and link to enzyme temperature activity. Here, we use a model promiscuous enzyme (glucose dehydrogenase from Sulfolobus solfataricus) to chemically map how individual substrate interactions affect the temperature dependence of enzyme activity and the network of motions throughout the protein. Utilizing a combination of kinetics, red edge excitation shift (REES) spectroscopy, and computational simulation, we explore the complex relationship between enzyme-substrate interactions and the global dynamics of the protein. We find that changes in \u0394C P \u2021 and protein dynamics can be mapped to specific substrate-enzyme interactions. Our study reveals how subtle changes in substrate binding affect global changes in motion and flexibility extending throughout the protein.", "doi": "10.1021/acscatal.1c04679", "pmid": "34956689", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8689651"}], "notes": [], "created": "2026-08-20T08:08:59.537Z", "modified": "2026-08-21T11:35:08.836Z"}, {"entity": "publication", "iuid": "7b87917c4e4f4d47993d8f528607accc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7b87917c4e4f4d47993d8f528607accc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7b87917c4e4f4d47993d8f528607accc"}}, "title": "Loop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases.", "authors": [{"family": "Crean", "given": "Rory M", "initials": "RM"}, {"family": "Biler", "given": "Michal", "initials": "M"}, {"family": "van der Kamp", "given": "Marc W", "initials": "MW", "orcid": "0000-0002-8060-3359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e09f39776374aeca06c0a767d62bfac.json"}}, {"family": "Hengge", "given": "Alvan C", "initials": "AC", "orcid": "0000-0002-5696-2087", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/43fb9bec035e46c4a63263aded78a78b.json"}}, {"family": "Kamerlin", "given": "Shina C L", "initials": "SCL", "orcid": "0000-0002-3190-1173", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4540c85432f4cdf952b0ef7cfe1d875.json"}}], "type": "journal article", "published": "2021-03-17", "journal": {"title": "Journal of the American Chemical Society", "issn": "1520-5126", "volume": "143", "issue": "10", "pages": "3830-3845", "issn-l": "0002-7863"}, "abstract": "Protein tyrosine phosphatases (PTPs) play an important role in cellular signaling and have been implicated in human cancers, diabetes, and obesity. Despite shared catalytic mechanisms and transition states for the chemical steps of catalysis, catalytic rates within the PTP family vary over several orders of magnitude. These rate differences have been implied to arise from differing conformational dynamics of the closure of a protein loop, the WPD-loop, which carries a catalytically critical residue. The present work reports computational studies of the human protein tyrosine phosphatase 1B (PTP1B) and YopH from Yersinia pestis, for which NMR has demonstrated a link between their respective rates of WPD-loop motion and catalysis rates, which differ by an order of magnitude. We have performed detailed structural analysis, both conventional and enhanced sampling simulations of their loop dynamics, as well as empirical valence bond simulations of the chemical step of catalysis. These analyses revealed the key residues and structural features responsible for these differences, as well as the residues and pathways that facilitate allosteric communication in these enzymes. Curiously, our wild-type YopH simulations also identify a catalytically incompetent hyper-open conformation of its WPD-loop, sampled as a rare event, previously only experimentally observed in YopH-based chimeras. The effect of differences within the WPD-loop and its neighboring loops on the modulation of loop dynamics, as revealed in this work, may provide a facile means for the family of PTP enzymes to respond to environmental changes and regulate their catalytic activities.", "doi": "10.1021/jacs.0c11806", "pmid": "33661624", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8031367"}], "notes": [], "created": "2026-08-21T11:37:51.587Z", "modified": "2026-08-21T11:37:51.656Z"}]}