{"entity": "researcher", "timestamp": "2026-08-25T13:20:44.637Z", "family": "Richard", "given": "John P", "initials": "JP", "orcid": "0000-0002-0440-2387", "affiliations": ["Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ab612d1767343bb93df821f17ee8b2a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ab612d1767343bb93df821f17ee8b2a"}}, "publications": [{"entity": "publication", "iuid": "a0c3ca2da05c4affb945030276588494", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a0c3ca2da05c4affb945030276588494.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a0c3ca2da05c4affb945030276588494"}}, "title": "Uncovering the Role of Key Active-Site Side Chains in Catalysis: An Extended Br\u00f8nsted Relationship for Substrate Deprotonation Catalyzed by Wild-Type and Variants of Triosephosphate Isomerase.", "authors": [{"family": "Kulkarni", "given": "Yashraj S", "initials": "YS"}, {"family": "Amyes", "given": "Tina L", "initials": "TL"}, {"family": "Richard", "given": "John P", "initials": "JP", "orcid": "0000-0002-0440-2387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ab612d1767343bb93df821f17ee8b2a.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": "2019-10-09", "journal": {"title": "Journal of the American Chemical Society", "issn": "1520-5126", "volume": "141", "issue": "40", "pages": "16139-16150", "issn-l": "0002-7863"}, "abstract": "We report results of detailed empirical valence bond simulations that model the effect of several amino acid substitutions on the thermodynamic (\u0394G\u00b0) and kinetic activation (\u0394G\u29e7) barriers to deprotonation of dihydroxyacetone phosphate (DHAP) and d-glyceraldehyde 3-phosphate (GAP) bound to wild-type triosephosphate isomerase (TIM), as well as to the K12G, E97A, E97D, E97Q, K12G/E97A, I170A, L230A, I170A/L230A, and P166A variants of this enzyme. The EVB simulations model the observed effect of the P166A mutation on protein structure. The E97A, E97Q, and E97D mutations of the conserved E97 side chain result in \u22641.0 kcal mol-1 decreases in the activation barrier for substrate deprotonation. The agreement between experimental and computed activation barriers is within \u00b11 kcal mol-1, with a strong linear correlation between \u0394G\u29e7 and \u0394G\u00b0 for all 11 variants, with slopes \u03b2 = 0.73 (R2 = 0.994) and \u03b2 = 0.74 (R2 = 0.995) for the deprotonation of DHAP and GAP, respectively. These Br\u00f8nsted-type correlations show that the amino acid side chains examined in this study function to reduce the standard-state Gibbs free energy of reaction for deprotonation of the weak \u03b1-carbonyl carbon acid substrate to form the enediolate phosphate reaction intermediate. TIM utilizes the cationic side chain of K12 to provide direct electrostatic stabilization of the enolate oxyanion, and the nonpolar side chains of P166, I170, and L230 are utilized for the construction of an active-site cavity that provides optimal stabilization of the enediolate phosphate intermediate relative to the carbon acid substrate.", "doi": "10.1021/jacs.9b08713", "pmid": "31508957", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7032883"}], "notes": [], "created": "2026-08-21T11:38:07.805Z", "modified": "2026-08-21T11:38:07.867Z"}, {"entity": "publication", "iuid": "9da599539dcc490d9254b7717a2f2c6c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9da599539dcc490d9254b7717a2f2c6c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9da599539dcc490d9254b7717a2f2c6c"}}, "title": "Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies.", "authors": [{"family": "Mydy", "given": "Lisa S", "initials": "LS"}, {"family": "Cristobal", "given": "Judith R", "initials": "JR"}, {"family": "Katigbak", "given": "Roberto D", "initials": "RD"}, {"family": "Bauer", "given": "Paul", "initials": "P"}, {"family": "Reyes", "given": "Archie C", "initials": "AC", "orcid": "0000-0001-9955-393X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6997fdbb25584d06b5cc06f01502634d.json"}}, {"family": "Kamerlin", "given": "Shina Caroline Lynn", "initials": "SCL", "orcid": "0000-0002-3190-1173", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4540c85432f4cdf952b0ef7cfe1d875.json"}}, {"family": "Richard", "given": "John P", "initials": "JP", "orcid": "0000-0002-0440-2387", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ab612d1767343bb93df821f17ee8b2a.json"}}, {"family": "Gulick", "given": "Andrew M", "initials": "AM", "orcid": "0000-0003-4238-7453", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f8626a9ae1664fcbadbe90237c87cd1b.json"}}], "type": "journal article", "published": "2019-02-26", "journal": {"title": "Biochemistry", "issn": "1943-295X", "volume": "58", "issue": "8", "pages": "1061-1073", "issn-l": "0006-2960"}, "abstract": "Human liver glycerol 3-phosphate dehydrogenase ( hlGPDH) catalyzes the reduction of dihydroxyacetone phosphate (DHAP) to form glycerol 3-phosphate, using the binding energy associated with the nonreacting phosphodianion of the substrate to properly orient the enzyme-substrate complex within the active site. Herein, we report the crystal structures for unliganded, binary E\u00b7NAD, and ternary E\u00b7NAD\u00b7DHAP complexes of wild type hlGPDH, illustrating a new position of DHAP, and probe the kinetics of multiple mutant enzymes with natural and truncated substrates. Mutation of Lys120, which is positioned to donate a proton to the carbonyl of DHAP, results in similar increases in the activation barrier to hlGPDH-catlyzed reduction of DHAP and to phosphite dianion-activated reduction of glycolaldehyde, illustrating that these transition states show similar interactions with the cationic K120 side chain. The K120A mutation results in a 5.3 kcal/mol transition state destabilization, and 3.0 kcal/mol of the lost transition state stabilization is rescued by 1.0 M ethylammonium cation. The 6.5 kcal/mol increase in the activation barrier observed for the D260G mutant hlGPDH-catalyzed reaction represents a 3.5 kcal/mol weakening of transition state stabilization by the K120A side chain and a 3.0 kcal/mol weakening of the interactions with other residues. The interactions, at the enzyme active site, between the K120 side chain and the Q295 and R269 side chains were likewise examined by double-mutant analyses. These results provide strong evidence that the enzyme rate acceleration is due mainly or exclusively to transition state stabilization by electrostatic interactions with polar amino acid side chains.", "doi": "10.1021/acs.biochem.8b01103", "pmid": "30640445", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1006787"}, {"db": "pmc", "key": "PMC6450551"}], "notes": [], "created": "2026-08-21T11:32:45.066Z", "modified": "2026-08-21T11:32:45.325Z"}]}