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Article ; Online: New High-Throughput Screen Discovers Novel Ligands of Full-Length Nuclear Receptor LRH-1.

Malabanan, M Merced / Chapagain, Pratima / Haratipour, Zeinab / Choi, Woong Jae / Orun, Abigail R / Blind, Raymond D

ACS chemical biology

2023 Volume 18, Issue 5, Page(s) 1101–1114

Abstract: Nuclear receptor liver receptor homolog-1 (LRH-1, ...

Abstract	Nuclear receptor liver receptor homolog-1 (LRH-1,
MeSH term(s)	Humans ; Gene Expression Regulation ; Ligands ; Receptors, Cytoplasmic and Nuclear/metabolism ; Transcription Factors/metabolism
Chemical Substances	abamectin (5U8924T11H) ; Ligands ; Receptors, Cytoplasmic and Nuclear ; Transcription Factors ; NR5A2 protein, human
Language	English
Publishing date	2023-04-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1554-8937
ISSN (online)	1554-8937
DOI	10.1021/acschembio.2c00805
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Article ; Online: Inositol polyphosphate multikinase (IPMK) in transcriptional regulation and nuclear inositide metabolism.

Malabanan, M Merced / Blind, Raymond D

Biochemical Society transactions

2016 Volume 44, Issue 1, Page(s) 279–285

Abstract: Inositol polyphosphate multikinase (IPMK, ipk2, Arg(82), ArgRIII) is an inositide kinase with unusually flexible substrate specificity and the capacity to partake in many functional protein-protein interactions (PPIs). By merging these two activities, ... ...

Abstract	Inositol polyphosphate multikinase (IPMK, ipk2, Arg(82), ArgRIII) is an inositide kinase with unusually flexible substrate specificity and the capacity to partake in many functional protein-protein interactions (PPIs). By merging these two activities, IPMK is able to execute gene regulatory functions that are very unique and only now beginning to be recognized. In this short review, we present a brief history of IPMK, describe the structural biology of the enzyme and highlight a few recent discoveries that have shed more light on the role IPMK plays in inositide metabolism, nuclear signalling and transcriptional regulation.
MeSH term(s)	Animals ; Biocatalysis ; Cell Nucleus/metabolism ; Gene Expression Regulation ; Humans ; Inositol/metabolism ; Phosphotransferases (Alcohol Group Acceptor)/chemistry ; Phosphotransferases (Alcohol Group Acceptor)/metabolism ; Transcription, Genetic
Chemical Substances	Inositol (4L6452S749) ; Phosphotransferases (Alcohol Group Acceptor) (EC 2.7.1.-) ; inositol polyphosphate multikinase (EC 2.7.1.-)
Language	English
Publishing date	2016-02
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	184237-7
ISSN	1470-8752 ; 0300-5127
ISSN (online)	1470-8752
ISSN	0300-5127
DOI	10.1042/BST20150225
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Article ; Online: Enzyme Architecture: Amino Acid Side-Chains That Function To Optimize the Basicity of the Active Site Glutamate of Triosephosphate Isomerase.

Zhai, Xiang / Reinhardt, Christopher J / Malabanan, M Merced / Amyes, Tina L / Richard, John P

Journal of the American Chemical Society

2018 Volume 140, Issue 26, Page(s) 8277–8286

Abstract: We report pH rate profiles for ... ...

Abstract	We report pH rate profiles for k
MeSH term(s)	Amino Acids/chemistry ; Amino Acids/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Glutamic Acid/chemistry ; Glutamic Acid/metabolism ; Hydrogen-Ion Concentration ; Models, Molecular ; Molecular Structure ; Triose-Phosphate Isomerase/chemistry ; Triose-Phosphate Isomerase/metabolism
Chemical Substances	Amino Acids ; Glutamic Acid (3KX376GY7L) ; Triose-Phosphate Isomerase (EC 5.3.1.1)
Language	English
Publishing date	2018-06-21
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.8b04367
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Article ; Online: The Genetic Landscape of Familial Pulmonary Fibrosis.

Liu, Qi / Zhou, Yuan / Cogan, Joy D / Mitchell, Daphne B / Sheng, Quanhu / Zhao, Shilin / Bai, Youhuang / Ciombor, Kristen K / Sabusap, Carleen M / Malabanan, M Merced / Markin, Cheryl R / Douglas, Katrina / Ding, Guixiao / Banovich, Nicholas E / Nickerson, Deborah A / Blue, Elizabeth E / Bamshad, Michael J / Brown, Kevin K / Schwartz, David A /

Phillips, John A / Martinez-Barricarte, Ruben / Salisbury, Margaret L / Shyr, Yu / Loyd, James E / Kropski, Jonathan A / Blackwell, Timothy S

American journal of respiratory and critical care medicine

2023 Volume 207, Issue 10, Page(s) 1345–1357

Abstract: Rationale and Objectives: ...

Abstract	Rationale and Objectives:
MeSH term(s)	Humans ; Pulmonary Fibrosis/genetics ; Endothelial Cells ; Lung Diseases, Interstitial/genetics ; Risk Factors ; Telomere ; Genetic Predisposition to Disease/genetics ; Receptors, Lysophosphatidic Acid/genetics
Chemical Substances	GPR87 protein, human ; Receptors, Lysophosphatidic Acid
Language	English
Publishing date	2023-01-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1180953-x
ISSN	1535-4970 ; 0003-0805 ; 1073-449X
ISSN (online)	1535-4970
ISSN	0003-0805 ; 1073-449X
DOI	10.1164/rccm.202204-0781OC
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Article ; Online: The acyl chains of phosphoinositide PIP3 alter the structure and function of nuclear receptor steroidogenic factor-1.

Bryant, Jamal M / Malabanan, M Merced / Vanderloop, Boden H / Nichols, Charles M / Haratipour, Zeinab / Poon, Katrina T / Sherrod, Stacy D / McLean, John A / Blind, Raymond D

Journal of lipid research

2021 Volume 62, Page(s) 100081

Abstract: Nuclear receptors are transcription factors that bind lipids, an event that induces a structural conformation of the receptor that favors interaction with transcriptional coactivators. The nuclear receptor steroidogenic factor-1 (SF-1, NR5A1) binds the ... ...

Abstract	Nuclear receptors are transcription factors that bind lipids, an event that induces a structural conformation of the receptor that favors interaction with transcriptional coactivators. The nuclear receptor steroidogenic factor-1 (SF-1, NR5A1) binds the signaling phosphoinositides PI(4,5)P2 (PIP2) and PI(3,4,5)P3 (PIP3), and our previous crystal structures showed how the phosphoinositide headgroups regulate SF-1 function. However, what role the acyl chains play in regulating SF-1 structure remains unaddressed. Here, we used X-ray crystallography with in vitro binding and functional assays to examine how the acyl chains of PIP3 regulate human SF-1 ligand-binding domain structure and function. Altering acyl chain length and unsaturation regulates apparent binding of all tested phosphoinositides to SF-1. Mass spectrometry-based lipidomics data suggest C16 and C18 phospholipids preferentially associate with SF-1 expressed ectopically in bacteria. We then solved the 2.5 Å crystal structure of SF-1 bound to dioleoyl PIP3(18:1/18:1) to compare it with a matched structure of SF-1 bound to dipalmitoyl PIP3(16:0/16:0). The dioleoyl-bound structure was severely disordered in a specific SF-1 region associated with pathogenic human polymorphisms and within the coactivator-binding region critical for SF-1 function while inducing increased sensitivity to protease digestion in solution. Validating these structural observations, in vitro functional studies showed dioleoyl PIP3 induced 6-fold poorer affinity of a peroxisome proliferator-activated receptor gamma coactivator 1-alpha coactivator peptide for SF-1 compared with dipalmitoyl PIP3. Together, these data suggest the chemical nature of the phosphoinositide acyl chains controls the ordered state of specific, clinically important structural regions in SF-1, regulating SF-1 function in vitro.
MeSH term(s)	Phosphatidylinositols
Chemical Substances	Phosphatidylinositols
Language	English
Publishing date	2021-04-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	80154-9
ISSN	1539-7262 ; 0022-2275
ISSN (online)	1539-7262
ISSN	0022-2275
DOI	10.1016/j.jlr.2021.100081
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Article ; Online: Reflections on the catalytic power of a TIM-barrel.

Richard, John P / Zhai, Xiang / Malabanan, M Merced

Bioorganic chemistry

2014 Volume 57, Page(s) 206–212

Abstract: The TIM-barrel fold is described and its propagation throughout the enzyme universe noted. The functions of the individual front loops of the eponymous TIM-barrel of triosephosphate isomerase are presented in a discussion of: (a) electrophilic catalysis, ...

Abstract	The TIM-barrel fold is described and its propagation throughout the enzyme universe noted. The functions of the individual front loops of the eponymous TIM-barrel of triosephosphate isomerase are presented in a discussion of: (a) electrophilic catalysis, by amino acid side chains from loops 1 and 4, of abstraction of an α-carbonyl hydrogen from substrate dihydroxyacetone phosphate (DHAP) or d-glyceraldehyde 3-phosphate (DGAP). (b) The engineering of loop 3 to give the monomeric variant monoTIM and the structure and catalytic properties of this monomer. (c) The interaction between loops 6, 7 and 8 and the phosphodianion of DHAP or DGAP. (d) The mechanism by which a ligand-gated conformational change, dominated by motion of loops 6 and 7, activates TIM for catalysis of deprotonation of DHAP or DGAP. (e) The conformational plasticity of TIM, and the utilization of substrate binding energy to "mold" the distorted active site loops of TIM mutants into catalytically active enzymes. The features of the TIM-barrel fold that favor effective protein catalysis are discussed.
MeSH term(s)	Amino Acid Sequence ; Animals ; Crystallography, X-Ray ; Enzyme Activation ; Humans ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Triose-Phosphate Isomerase/chemistry ; Triose-Phosphate Isomerase/genetics ; Triose-Phosphate Isomerase/metabolism
Chemical Substances	Triose-Phosphate Isomerase (EC 5.3.1.1)
Language	English
Publishing date	2014-07-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	120080-x
ISSN	1090-2120 ; 0045-2068
ISSN (online)	1090-2120
ISSN	0045-2068
DOI	10.1016/j.bioorg.2014.07.001
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Article: Enzyme Architecture: Amino Acid Side-Chains That Function To Optimize the Basicity of the Active Site Glutamate of Triosephosphate Isomerase

Zhai, Xiang / Reinhardt, Christopher J / Malabanan, M. Merced / Amyes, Tina L / Richard, John P

Journal of the American Chemical Society. 2018 June 04, v. 140, no. 26

2018

Abstract: We report pH rate profiles for kcat and Km for the isomerization reaction of glyceraldehyde 3-phosphate catalyzed by wildtype triosephosphate isomerase (TIM) from three organisms and by ten mutants of TIM; and, for Ki for inhibition of this reaction by ... ...

Abstract	We report pH rate profiles for kcat and Km for the isomerization reaction of glyceraldehyde 3-phosphate catalyzed by wildtype triosephosphate isomerase (TIM) from three organisms and by ten mutants of TIM; and, for Ki for inhibition of this reaction by phosphoglycolate trianion (I3–). The pH profiles for Ki show that the binding of I3– to TIM (E) to form EH·I3– is accompanied by uptake of a proton by the carboxylate side-chain of E165, whose function is to abstract a proton from substrate. The complexes for several mutants exist mainly as E–·I3– at high pH, in which cases the pH profiles define the pKa for deprotonation of EH·I3–. The linear free energy correlation, with slope of 0.73 (r2 = 0.96), between kcat/Km for TIM-catalyzed isomerization and the disassociation constant of PGA trianion for TIM shows that EH·I3– and the transition state are stabilized by similar interactions with the protein catalyst. Values of pKa = 10–10.5 were estimated for deprotonation of EH·I3– for wildtype TIM. This pKa decreases to as low as 6.3 for the severely crippled Y208F mutant. There is a correlation between the effect of several mutations on kcat/Km and on pKa for EH·I3–. The results support a model where the strong basicity of E165 at the complex to the enediolate reaction intermediate is promoted by side-chains from Y208 and S211, which serve to clamp loop 6 over the substrate; I170, which assists in the creation of a hydrophobic environment for E165; and P166, which functions in driving the carboxylate side-chain of E165 toward enzyme-bound substrate.
Keywords	Gibbs free energy ; active sites ; catalysts ; catalytic activity ; glutamic acid ; glyceraldehyde 3-phosphate ; hydrophobicity ; isomerization ; models ; mutants ; mutation ; pH ; triose-phosphate isomerase
Language	English
Dates of publication	2018-0604
Size	p. 8277-8286.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.8b04367
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Article: Mechanistic Imperatives for Deprotonation of Carbon Catalyzed by Triosephosphate Isomerase: Enzyme-Activation by Phosphite Dianion.

Zhai, Xiang / Malabanan, M Merced / Amyes, Tina L / Richard, John P

Journal of physical organic chemistry

2014 Volume 27, Issue 4, Page(s) 269–276

Abstract: The mechanistic imperatives for catalysis of deprotonation of α-carbonyl carbon by triosephosphate isomerase (TIM) are discussed. There is a strong imperative to reduce the large thermodynamic barrier for deprotonation of carbon to form an enediolate ... ...

Abstract	The mechanistic imperatives for catalysis of deprotonation of α-carbonyl carbon by triosephosphate isomerase (TIM) are discussed. There is a strong imperative to reduce the large thermodynamic barrier for deprotonation of carbon to form an enediolate reaction intermediate; and, a strong imperative for specificity in the expression of the intrinsic phosphodianion binding energy at the transition state for the enzyme-catalyzed reaction. Binding energies of 2 and 6 kcal/mol, respectively, have been determined for formation of phosphite dianion complexes to TIM and to the transition state for TIM-catalyzed deprotonation of the truncated substrate glycolaldehyde [T. L. Amyes, J. P. Richard,
Language	English
Publishing date	2014-04-02
Publishing country	England
Document type	Journal Article
ZDB-ID	1475025-9
ISSN	1099-1395 ; 0894-3230
ISSN (online)	1099-1395
ISSN	0894-3230
DOI	10.1002/poc.3195
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Article ; Online: Mechanism for activation of triosephosphate isomerase by phosphite dianion: the role of a ligand-driven conformational change.

Malabanan, M Merced / Amyes, Tina L / Richard, John P

Journal of the American Chemical Society

2011 Volume 133, Issue 41, Page(s) 16428–16431

Abstract: ... in a small 6-fold decrease in k(cat)/K(m) for the reversible enzyme-catalyzed isomerization of glyceraldehyde ...

Abstract	The L232A mutation in triosephosphate isomerase (TIM) from Trypanosoma brucei brucei results in a small 6-fold decrease in k(cat)/K(m) for the reversible enzyme-catalyzed isomerization of glyceraldehyde 3-phosphate to give dihydroxyacetone phosphate. In contrast, this mutation leads to a 17-fold increase in the second-order rate constant for the TIM-catalyzed proton transfer reaction of the truncated substrate piece [1-(13)C]glycolaldehyde ([1-(13)C]-GA) in D(2)O, a 25-fold increase in the third-order rate constant for the reaction of the substrate pieces GA and phosphite dianion (HPO(3)(2-)), and a 16-fold decrease in K(d) for binding of HPO(3)(2-) to the free enzyme. Most significantly, the mutation also results in an 11-fold decrease in the extent of activation of the enzyme toward turnover of GA by bound HPO(3)(2-). The data provide striking evidence that the L232A mutation leads to a ca. 1.7 kcal/mol stabilization of a catalytically active loop-closed form of TIM (E(c)) relative to an inactive open form (E(o)). We propose that this is due to the relief, in L232A mutant TIM, of unfavorable steric interactions between the bulky hydrophobic side chain of Leu-232 and the basic carboxylate side chain of Glu-167, the catalytic base, which destabilize E(c) relative to E(o).
MeSH term(s)	Anions/chemistry ; Anions/metabolism ; Biocatalysis ; Crystallography, X-Ray ; Ligands ; Models, Molecular ; Molecular Structure ; Phosphites/chemistry ; Phosphites/metabolism ; Triose-Phosphate Isomerase/chemistry ; Triose-Phosphate Isomerase/metabolism ; Trypanosoma brucei brucei/enzymology
Chemical Substances	Anions ; Ligands ; Phosphites ; Triose-Phosphate Isomerase (EC 5.3.1.1)
Language	English
Publishing date	2011-09-28
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/ja208019p
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Article ; Online: A role for flexible loops in enzyme catalysis.

Malabanan, M Merced / Amyes, Tina L / Richard, John P

Current opinion in structural biology

2010 Volume 20, Issue 6, Page(s) 702–710

Abstract: Triosephosphate isomerase (TIM), glycerol 3-phosphate dehydrogenase, and orotidine 5'-monophosphate decarboxylase each use the binding energy from the interaction of phosphite dianion with a flexible phosphate gripper loop to activate a second, ... ...

Abstract	Triosephosphate isomerase (TIM), glycerol 3-phosphate dehydrogenase, and orotidine 5'-monophosphate decarboxylase each use the binding energy from the interaction of phosphite dianion with a flexible phosphate gripper loop to activate a second, phosphodianion-truncated, substrate towards enzyme-catalyzed proton transfer, hydride transfer, and decarboxylation, respectively. Studies on TIM suggest that the most important general effect of loop closure over the substrate phosphodianion, and the associated conformational changes, is to extrude water from the enzyme active site. This should cause a decrease in the effective active-site dielectric constant, and an increase in transition state stabilization from enhanced electrostatic interactions with polar amino acid side chains. The most important specific effect of these conformational changes is to increase the basicity of the carboxylate side chain of the active site glutamate base by its placement in a 'hydrophobic cage'.
MeSH term(s)	Amino Acid Sequence ; Biocatalysis ; Entropy ; Enzymes/chemistry ; Enzymes/metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Molecular Sequence Data ; Phosphates/chemistry ; Phosphates/metabolism ; Solvents/metabolism
Chemical Substances	Enzymes ; Phosphates ; Solvents
Language	English
Publishing date	2010-10-13
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2010.09.005
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