1
|
Hossain MA, Sarin R, Donnelly DP, Miller BC, Weiss A, McAlary L, Antonyuk SV, Salisbury JP, Amin J, Conway JB, Watson SS, Winters JN, Xu Y, Alam N, Brahme RR, Shahbazian H, Sivasankar D, Padmakumar S, Sattarova A, Ponmudiyan AC, Gawde T, Verrill DE, Yang W, Kannapadi S, Plant LD, Auclair JR, Makowski L, Petsko GA, Ringe D, Agar NYR, Greenblatt DJ, Ondrechen MJ, Chen Y, Yerbury JJ, Manetsch R, Hasnain SS, Brown RH, Agar JN. Evaluating protein cross-linking as a therapeutic strategy to stabilize SOD1 variants in a mouse model of familial ALS. PLoS Biol 2024; 22:e3002462. [PMID: 38289969 PMCID: PMC10826971 DOI: 10.1371/journal.pbio.3002462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 12/05/2023] [Indexed: 02/01/2024] Open
Abstract
Mutations in the gene encoding Cu-Zn superoxide dismutase 1 (SOD1) cause a subset of familial amyotrophic lateral sclerosis (fALS) cases. A shared effect of these mutations is that SOD1, which is normally a stable dimer, dissociates into toxic monomers that seed toxic aggregates. Considerable research effort has been devoted to developing compounds that stabilize the dimer of fALS SOD1 variants, but unfortunately, this has not yet resulted in a treatment. We hypothesized that cyclic thiosulfinate cross-linkers, which selectively target a rare, 2 cysteine-containing motif, can stabilize fALS-causing SOD1 variants in vivo. We created a library of chemically diverse cyclic thiosulfinates and determined structure-cross-linking-activity relationships. A pre-lead compound, "S-XL6," was selected based upon its cross-linking rate and drug-like properties. Co-crystallographic structure clearly establishes the binding of S-XL6 at Cys 111 bridging the monomers and stabilizing the SOD1 dimer. Biophysical studies reveal that the degree of stabilization afforded by S-XL6 (up to 24°C) is unprecedented for fALS, and to our knowledge, for any protein target of any kinetic stabilizer. Gene silencing and protein degrading therapeutic approaches require careful dose titration to balance the benefit of diminished fALS SOD1 expression with the toxic loss-of-enzymatic function. We show that S-XL6 does not share this liability because it rescues the activity of fALS SOD1 variants. No pharmacological agent has been proven to bind to SOD1 in vivo. Here, using a fALS mouse model, we demonstrate oral bioavailability; rapid engagement of SOD1G93A by S-XL6 that increases SOD1G93A's in vivo half-life; and that S-XL6 crosses the blood-brain barrier. S-XL6 demonstrated a degree of selectivity by avoiding off-target binding to plasma proteins. Taken together, our results indicate that cyclic thiosulfinate-mediated SOD1 stabilization should receive further attention as a potential therapeutic approach for fALS.
Collapse
Affiliation(s)
- Md Amin Hossain
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
- Department of Neurosurgery and Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richa Sarin
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Biogen Inc, Cambridge, Massachusetts, United States of America
| | - Daniel P. Donnelly
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Brandon C. Miller
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Alexandra Weiss
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Luke McAlary
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Department of Biochemistry & Systems Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Joseph P. Salisbury
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Jakal Amin
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Jeremy B. Conway
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Samantha S. Watson
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Jenifer N. Winters
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Yu Xu
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
| | - Novera Alam
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Rutali R. Brahme
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Haneyeh Shahbazian
- School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Durgalakshmi Sivasankar
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Swathi Padmakumar
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Aziza Sattarova
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
| | - Aparna C. Ponmudiyan
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Tanvi Gawde
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - David E. Verrill
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Wensheng Yang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Sunanda Kannapadi
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Leigh D. Plant
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
| | - Jared R. Auclair
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
| | - Lee Makowski
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, United States of America
| | - Gregory A. Petsko
- Ann Romney Center for Neurologic Diseases at Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Departments of Chemistry and Biochemistry, and Rosenstiel Center for Basic Medical Research, Brandeis University, Waltham, Massachusetts, United States of America
| | - Dagmar Ringe
- Departments of Chemistry and Biochemistry, and Rosenstiel Center for Basic Medical Research, Brandeis University, Waltham, Massachusetts, United States of America
| | - Nathalie Y. R. Agar
- Department of Neurosurgery and Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David J. Greenblatt
- School of Medicine, Tufts University, Boston, Massachusetts, United States of America
| | - Mary Jo Ondrechen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Yunqiu Chen
- Biogen Inc, Cambridge, Massachusetts, United States of America
| | - Justin J. Yerbury
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Roman Manetsch
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
| | - S. Samar Hasnain
- Molecular Biophysics Group, Department of Biochemistry & Systems Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Robert H. Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jeffrey N. Agar
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- Barnett Institute of Chemical and Biological Analysis, Boston, Massachusetts, United States of America
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, United States of America
| |
Collapse
|
2
|
Fushman D, Ringe D. Editorial overview: Biophysical methods: Exploring structures in motions, from biomolecules to cells, and how to drug them. Curr Opin Struct Biol 2022; 77:102494. [PMID: 36370534 DOI: 10.1016/j.sbi.2022.102494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- David Fushman
- Center for Biomolecular Structure & Organization, Department of Chemistry & Biochemistry, University of Maryland, College Park, MD 20742, USA.
| | - Dagmar Ringe
- Departments of Biochemistry and Chemistry, Brandeis University, MS 029, 415 South Street, Waltham, MA 02454, USA.
| |
Collapse
|
3
|
Liu X, Garber A, Ryan J, Deshpande A, Ringe D, Pochapsky TC. A Model for the Solution Structure of Human Fe(II)-Bound Acireductone Dioxygenase and Interactions with the Regulatory Domain of Matrix Metalloproteinase I (MMP-I). Biochemistry 2020; 59:4238-4249. [PMID: 33135413 PMCID: PMC7768908 DOI: 10.1021/acs.biochem.0c00724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The metalloenzyme acireductone dioxygenase (ARD) shows metal-dependent physical and enzymatic activities depending upon the metal bound in the active site. The Fe(II)-bound enzyme catalyzes the penultimate step of the methionine salvage pathway, converting 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one (acireductone) into formate and the ketoacid precursor of methionine, 2-keto-4-thiomethyl-2-oxobutanoate, using O2 as the oxidant. If Ni(II) is bound, an off-pathway shunt occurs, producing 3-methylthiopropionate, formate, and carbon monoxide from the same acireductone substrate. The solution structure of the Fe(II)-bound human enzyme, HsARD, is described and compared with the structures of Ni-bound forms of the closely related mouse enzyme, MmARD. Potential rationales for the different reactivities of the two isoforms are discussed. The human enzyme has been found to regulate the activity of matrix metalloproteinase I (MMP-I), which is involved in tumor metastasis, by binding the cytoplasmic transmembrane tail peptide of MMP-I. Nuclear magnetic resonance titration of HsARD with the MMP-I tail peptide permits identification of the peptide binding site on HsARD, a cleft anterior to the metal binding site adjacent to a dynamic proline-rich loop.
Collapse
Affiliation(s)
- Xinyue Liu
- Department of Chemistry, Brandeis University, 415 South St., Waltham MA 02454-9110, USA
| | - Abigail Garber
- Department of Biochemistry, Brandeis University, 415 South St., Waltham MA 02454-9110, USA
| | - Julia Ryan
- Department of Biochemistry, Brandeis University, 415 South St., Waltham MA 02454-9110, USA
| | - Aditi Deshpande
- Department of Biochemistry, Brandeis University, 415 South St., Waltham MA 02454-9110, USA
| | - Dagmar Ringe
- Department of Chemistry, Brandeis University, 415 South St., Waltham MA 02454-9110, USA
- Department of Biochemistry, Brandeis University, 415 South St., Waltham MA 02454-9110, USA
- Rosenstiel Institute for Basic Biomedical Research, Brandeis University, 415 South St., Waltham MA 02454-9110 USA
| | - Thomas C. Pochapsky
- Department of Chemistry, Brandeis University, 415 South St., Waltham MA 02454-9110, USA
- Department of Biochemistry, Brandeis University, 415 South St., Waltham MA 02454-9110, USA
- Rosenstiel Institute for Basic Biomedical Research, Brandeis University, 415 South St., Waltham MA 02454-9110 USA
| |
Collapse
|
4
|
Ringe D, Kreinbring C, Wilson M, Kovalevsky A, Blakeley M, Fisher Z, Lazar L, Moulin A, Novak W, Petsko G. The missing atom in function: reliability of the determination of hydrogen positions in protein structures. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s0108767318099695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
5
|
Tu Y, Kreinbring CA, Hill M, Liu C, Petsko GA, McCune CD, Berkowitz DB, Liu D, Ringe D. Crystal Structures of Cystathionine β-Synthase from Saccharomyces cerevisiae: One Enzymatic Step at a Time. Biochemistry 2018; 57:3134-3145. [PMID: 29630349 DOI: 10.1021/acs.biochem.8b00092] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cystathionine β-synthase (CBS) is a key regulator of sulfur amino acid metabolism, taking homocysteine from the methionine cycle to the biosynthesis of cysteine via the trans-sulfuration pathway. CBS is also a predominant source of H2S biogenesis. Roles for CBS have been reported for neuronal death pursuant to cerebral ischemia, promoting ovarian tumor growth, and maintaining drug-resistant phenotype by controlling redox behavior and regulating mitochondrial bioenergetics. The trans-sulfuration pathway is well-conserved in eukaryotes, but the analogous enzymes have different enzymatic behavior in different organisms. CBSs from the higher organisms contain a heme in an N-terminal domain. Though the presence of the heme, whose functions in CBSs have yet to be elucidated, is biochemically interesting, it hampers UV-vis absorption spectroscopy investigations of pyridoxal 5'-phosphate (PLP) species. CBS from Saccharomyces cerevisiae (yCBS) naturally lacks the heme-containing N-terminal domain, which makes it an ideal model for spectroscopic studies of the enzymological reaction catalyzed and allows structural studies of the basic yCBS catalytic core (yCBS-cc). Here we present the crystal structure of yCBS-cc, solved to 1.5 Å. Crystal structures of yCBS-cc in complex with enzymatic reaction intermediates have been captured, providing a structural basis for residues involved in catalysis. Finally, the structure of the yCBS-cc cofactor complex generated by incubation with an inhibitor shows apparent off-pathway chemistry not normally seen with CBS.
Collapse
Affiliation(s)
- Yupeng Tu
- Department of Biochemistry , Brandeis University , Waltham , Massachusetts 02454 , United States
| | - Cheryl A Kreinbring
- Department of Biochemistry , Brandeis University , Waltham , Massachusetts 02454 , United States
| | - Megan Hill
- Department of Biology , Brandeis University , Waltham , Massachusetts 02454 , United States
| | - Cynthia Liu
- Department of Biochemistry , Brandeis University , Waltham , Massachusetts 02454 , United States
| | - Gregory A Petsko
- Department of Neurology and Neuroscience , Weill Cornell Medical College , New York , New York 10021 , United States
| | - Christopher D McCune
- Department of Biochemistry , University of Nebraska , Lincoln , Nebraska 68588 , United States
| | - David B Berkowitz
- Department of Biochemistry , University of Nebraska , Lincoln , Nebraska 68588 , United States
| | - Dali Liu
- Department of Chemistry and Biochemistry , Loyola University Chicago , Chicago , Illinois 60660 , United States
| | - Dagmar Ringe
- Department of Biochemistry , Brandeis University , Waltham , Massachusetts 02454 , United States.,Department of Chemistry , Brandeis University , Waltham , Massachusetts 02454 , United States.,Rosenstiel Basic Medical Sciences Research Center , Brandeis University , Waltham , Massachusetts 02454 , United States
| |
Collapse
|
6
|
Mascarenhas R, Le HV, Clevenger KD, Lehrer HJ, Ringe D, Kelleher NL, Silverman RB, Liu D. Correction to Selective Targeting by a Mechanism-Based Inactivator against Pyridoxal 5′-Phosphate-Dependent Enzymes: Mechanisms of Inactivation and Alternative Turnover. Biochemistry 2017; 56:5844-5845. [DOI: 10.1021/acs.biochem.7b00961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
7
|
Mascarenhas R, Le HV, Clevenger KD, Lehrer HJ, Ringe D, Kelleher NL, Silverman RB, Liu D. Selective Targeting by a Mechanism-Based Inactivator against Pyridoxal 5'-Phosphate-Dependent Enzymes: Mechanisms of Inactivation and Alternative Turnover. Biochemistry 2017; 56:4951-4961. [PMID: 28816437 DOI: 10.1021/acs.biochem.7b00499] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Potent mechanism-based inactivators can be rationally designed against pyridoxal 5'-phosphate (PLP)-dependent drug targets, such as ornithine aminotransferase (OAT) or γ-aminobutyric acid aminotransferase (GABA-AT). An important challenge, however, is the lack of selectivity toward other PLP-dependent, off-target enzymes, because of similarities in mechanisms of all PLP-dependent aminotransferase reactions. On the basis of complex crystal structures, we investigate the inactivation mechanism of OAT, a hepatocellular carcinoma target, by (1R,3S,4S)-3-amino-4-fluorocyclopentane-1-carboxylic acid (FCP), a known inactivator of GABA-AT. A crystal structure of OAT and FCP showed the formation of a ternary adduct. This adduct can be rationalized as occurring via an enamine mechanism of inactivation, similar to that reported for GABA-AT. However, the crystal structure of an off-target, PLP-dependent enzyme, aspartate aminotransferase (Asp-AT), in complex with FCP, along with the results of attempted inhibition assays, suggests that FCP is not an inactivator of Asp-AT, but rather an alternate substrate. Turnover of FCP by Asp-AT is also supported by high-resolution mass spectrometry. Amid existing difficulties in achieving selectivity of inactivation among a large number of PLP-dependent enzymes, the obtained results provide evidence that a desirable selectivity could be achieved, taking advantage of subtle structural and mechanistic differences between a drug-target enzyme and an off-target enzyme, despite their largely similar substrate binding sites and catalytic mechanisms.
Collapse
Affiliation(s)
- Romila Mascarenhas
- Department of Chemistry and Biochemistry, Loyola University Chicago , Chicago, Illinois 60660, United States
| | - Hoang V Le
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, and Center for Molecular Innovation and Drug Discovery, Northwestern University , Evanston, Illinois 60208, United States.,Department of BioMolecular Sciences and Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi , University, Mississippi 38677, United States
| | - Kenneth D Clevenger
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, and Center for Molecular Innovation and Drug Discovery, Northwestern University , Evanston, Illinois 60208, United States
| | - Helaina J Lehrer
- Departments of Chemistry and Biochemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University , Waltham, Massachusetts 02454-9110, United States
| | - Dagmar Ringe
- Departments of Chemistry and Biochemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University , Waltham, Massachusetts 02454-9110, United States
| | - Neil L Kelleher
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, and Center for Molecular Innovation and Drug Discovery, Northwestern University , Evanston, Illinois 60208, United States
| | - Richard B Silverman
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, and Center for Molecular Innovation and Drug Discovery, Northwestern University , Evanston, Illinois 60208, United States
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago , Chicago, Illinois 60660, United States
| |
Collapse
|
8
|
Abstract
Acireductone dioxygenase (ARD) from the methionine salvage pathway (MSP) is a unique enzyme that exhibits dual chemistry determined solely by the identity of the divalent transition-metal ion (Fe2+ or Ni2+) in the active site. The Fe2+-containing isozyme catalyzes the on-pathway reaction using substrates 1,2-dihydroxy-3-keto-5-methylthiopent-1-ene (acireductone) and dioxygen to generate formate and the ketoacid precursor of methionine, 2-keto-4-methylthiobutyrate, whereas the Ni2+-containing isozyme catalyzes an off-pathway shunt with the same substrates, generating methylthiopropionate, carbon monoxide, and formate. The dual chemistry of ARD was originally discovered in the bacterium Klebsiella oxytoca, but it has recently been shown that mammalian ARD enzymes (mouse and human) are also capable of catalyzing metal-dependent dual chemistry in vitro. This is particularly interesting, since carbon monoxide, one of the products of off-pathway reaction, has been identified as an antiapoptotic molecule in mammals. In addition, several biochemical and genetic studies have indicated an inhibitory role of human ARD in cancer. This comprehensive review describes the biochemical and structural characterization of the ARD family, the proposed experimental and theoretical approaches to establishing mechanisms for the dual chemistry, insights into the mechanism based on comparison with structurally and functionally similar enzymes, and the applications of this research to the field of artificial metalloenzymes and synthetic biology.
Collapse
Affiliation(s)
- Aditi R Deshpande
- Departments of Biochemistry and ‡Chemistry and §the Rosenstiel Institute for Basic Biomedical Research, Brandeis University , Waltham, Massachusetts 02454, United States
| | - Thomas C Pochapsky
- Departments of Biochemistry and ‡Chemistry and §the Rosenstiel Institute for Basic Biomedical Research, Brandeis University , Waltham, Massachusetts 02454, United States
| | - Dagmar Ringe
- Departments of Biochemistry and ‡Chemistry and §the Rosenstiel Institute for Basic Biomedical Research, Brandeis University , Waltham, Massachusetts 02454, United States
| |
Collapse
|
9
|
Deshpande AR, Pochapsky TC, Petsko GA, Ringe D. Dual chemistry catalyzed by human acireductone dioxygenase. Protein Eng Des Sel 2017; 30:197-204. [PMID: 28062648 DOI: 10.1093/protein/gzw078] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/15/2016] [Indexed: 11/14/2022] Open
Abstract
Acireductone dioxygenase (ARD) from the methionine salvage pathway of Klebsiella oxytoca is the only known naturally occurring metalloenzyme that catalyzes different reactions in vivo based solely on the identity of the divalent transition metal ion (Fe2+ or Ni2+) bound in the active site. The iron-containing isozyme catalyzes the cleavage of substrate 1,2-dihydroxy-3-keto-5-(thiomethyl)pent-1-ene (acireductone) by O2 to formate and the ketoacid precursor of methionine, whereas the nickel-containing isozyme uses the same substrates to catalyze an off-pathway shunt to form methylthiopropionate, carbon monoxide and formate. This dual chemistry was recently demonstrated in vitro by ARD from Mus musculus (MmARD), providing the first example of a mammalian ARD exhibiting metal-dependent catalysis. We now show that human ARD (HsARD) is also capable of metal-dependent dual chemistry. Recombinant HsARD was expressed and purified to obtain a homogeneous enzyme with a single transition metal ion bound. As with MmARD, the Fe2+-bound HsARD shows the highest activity and catalyzes on-pathway chemistry, whereas Ni2+, Co2+ or Mn2+ forms catalyze off-pathway chemistry. The thermal stability of the HsARD isozymes is a function of the metal ion identity, with Ni2+-bound HsARD being the most stable followed by Co2+ and Fe2+, and Mn2+-bound HsARD being the least stable. As with the bacterial ARD, solution NMR data suggest that HsARD isozymes can have significant structural differences depending upon the metal ion bound.
Collapse
Affiliation(s)
- Aditi R Deshpande
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Thomas C Pochapsky
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA.,Department of Chemistry, Brandeis University, Waltham, MA 02454, USA.,Rosenstiel Institute for Basic Biomedical Research, Brandeis University, Waltham, MA 02454, USA
| | - Gregory A Petsko
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA.,Department of Chemistry, Brandeis University, Waltham, MA 02454, USA.,Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medical College, New York, NY 10065, USA
| | - Dagmar Ringe
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA.,Department of Chemistry, Brandeis University, Waltham, MA 02454, USA.,Rosenstiel Institute for Basic Biomedical Research, Brandeis University, Waltham, MA 02454, USA
| |
Collapse
|
10
|
Zahniser MPD, Prasad S, Kneen MM, Kreinbring CA, Petsko GA, Ringe D, McLeish MJ. Structure and mechanism of benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633, a member of the Class 3 aldehyde dehydrogenase superfamily. Protein Eng Des Sel 2017; 30:271-278. [PMID: 28338942 DOI: 10.1093/protein/gzx015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 02/23/2017] [Indexed: 11/14/2022] Open
Abstract
Benzaldehyde dehydrogenase from Pseudomonas putida (PpBADH) belongs to the Class 3 aldehyde dehydrogenase (ALDH) family. The Class 3 ALDHs are unusual in that they are generally dimeric (rather than tetrameric), relatively non-specific and utilize both NAD+ and NADP+. To date, X-ray structures of three Class 3 ALDHs have been determined, of which only two have cofactor bound, both in the NAD+ form. Here we report the crystal structure of PpBADH in complex with NADP+ and a thioacyl intermediate adduct. The overall architecture of PpBADH resembles that of most other members of the ALDH superfamily, and the cofactor binding residues are well conserved. Conversely, the pattern of cofactor binding for the rat Class 3 ALDH differs from that of PpBADH and other ALDHs. This has been interpreted in terms of a different mechanism for the rat enzyme. Comparison with the PpBADH structure, as well as multiple sequence alignments, suggest that one of two conserved glutamates, at positions 215 (209 in rat) and 337 (333 in rat), would act as the general base necessary to hydrolyze the thioacyl intermediate. While the latter is the general base in the rat Class 3 ALDH, site-specific mutagenesis indicates that Glu215 is the likely candidate for PpBADH, a result more typical of the Class 1 and 2 ALDH families. Finally, this study shows that hydride transfer is not rate limiting, lending further credence to the suggestion that PpBADH is more similar to the Class 1 and 2 ALDHs than it is to other Class 3 ALDHs.
Collapse
Affiliation(s)
- Megan P D Zahniser
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454,USA
| | - Shreenath Prasad
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N. Blackford Street, Indianapolis, IN 46202,USA
| | - Malea M Kneen
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N. Blackford Street, Indianapolis, IN 46202,USA
| | - Cheryl A Kreinbring
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA.,Rosenstiel Basic Medical Sciences Research Center, MS029, 415 South Street, Waltham, MA 02454, USA
| | - Gregory A Petsko
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA.,Rosenstiel Basic Medical Sciences Research Center, MS029, 415 South Street, Waltham, MA 02454, USA
| | - Dagmar Ringe
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA.,Rosenstiel Basic Medical Sciences Research Center, MS029, 415 South Street, Waltham, MA 02454, USA.,Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Michael J McLeish
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N. Blackford Street, Indianapolis, IN 46202,USA
| |
Collapse
|
11
|
Wierenga RK, Ringe D. The EMBO biocatalysis conference “The biochemistry and chemistry of biocatalysis: from understanding to design”. Protein Eng Des Sel 2017. [DOI: 10.1093/protein/gzx020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
12
|
Abstract
The two acireductone dioxygenase (ARD) isozymes from the methionine salvage pathway of Klebsiella oxytoca are the only known pair of naturally occurring metalloenzymes with distinct chemical and physical properties determined solely by the identity of the divalent transition metal ion (Fe(2+) or Ni(2+)) in the active site. We now show that this dual chemistry can also occur in mammals. ARD from Mus musculus (MmARD) was studied to relate the metal ion identity and three-dimensional structure to enzyme function. The iron-containing isozyme catalyzes the cleavage of 1,2-dihydroxy-3-keto-5-(thiomethyl)pent-1-ene (acireductone) by O2 to formate and the ketoacid precursor of methionine, which is the penultimate step in methionine salvage. The nickel-bound form of ARD catalyzes an off-pathway reaction resulting in formate, carbon monoxide (CO), and 3-(thiomethyl) propionate. Recombinant MmARD was expressed and purified to obtain a homogeneous enzyme with a single transition metal ion bound. The Fe(2+)-bound protein, which shows about 10-fold higher activity than that of others, catalyzes on-pathway chemistry, whereas the Ni(2+), Co(2+), or Mn(2+) forms exhibit off-pathway chemistry, as has been seen with ARD from Klebsiella. Thermal stability of the isozymes is strongly affected by the metal ion identity, with Ni(2+)-bound MmARD being the most stable, followed by Co(2+) and Fe(2+), and Mn(2+)-bound ARD being the least stable. Ni(2+)- and Co(2+)-bound MmARD were crystallized, and the structures of the two proteins found to be similar. Enzyme-ligand complexes provide insight into substrate binding, metal coordination, and the catalytic mechanism.
Collapse
Affiliation(s)
| | | | - Thomas C. Pochapsky
- Department of Biochemistry, Brandeis University, Waltham, MA 02454,Department of Chemistry, Brandeis University, Waltham, MA 02454,Rosenstiel Institute for Basic Biomedical Research, Brandeis University, Waltham, MA 02454
| | - Gregory A. Petsko
- Department of Biochemistry, Brandeis University, Waltham, MA 02454,Department of Chemistry, Brandeis University, Waltham, MA 02454,Helen and Robert Appel Alzheimer’s Disease Research Institute, Weill Cornell Medical College, New York, NY 10065
| | - Dagmar Ringe
- Department of Biochemistry, Brandeis University, Waltham, MA 02454,Department of Chemistry, Brandeis University, Waltham, MA 02454,Rosenstiel Institute for Basic Biomedical Research, Brandeis University, Waltham, MA 02454,Corresponding Author. To whom correspondence should be addressed. . Phone: 781-736-4902
| |
Collapse
|
13
|
Brodkin HR, DeLateur NA, Somarowthu S, Mills CL, Novak WR, Beuning PJ, Ringe D, Ondrechen MJ. Prediction of distal residue participation in enzyme catalysis. Protein Sci 2015; 24:762-78. [PMID: 25627867 PMCID: PMC4420525 DOI: 10.1002/pro.2648] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 01/10/2015] [Accepted: 01/26/2015] [Indexed: 11/09/2022]
Abstract
A scoring method for the prediction of catalytically important residues in enzyme structures is presented and used to examine the participation of distal residues in enzyme catalysis. Scores are based on the Partial Order Optimum Likelihood (POOL) machine learning method, using computed electrostatic properties, surface geometric features, and information obtained from the phylogenetic tree as input features. Predictions of distal residue participation in catalysis are compared with experimental kinetics data from the literature on variants of the featured enzymes; some additional kinetics measurements are reported for variants of Pseudomonas putida nitrile hydratase (ppNH) and for Escherichia coli alkaline phosphatase (AP). The multilayer active sites of P. putida nitrile hydratase and of human phosphoglucose isomerase are predicted by the POOL log ZP scores, as is the single-layer active site of P. putida ketosteroid isomerase. The log ZP score cutoff utilized here results in over-prediction of distal residue involvement in E. coli alkaline phosphatase. While fewer experimental data points are available for P. putida mandelate racemase and for human carbonic anhydrase II, the POOL log ZP scores properly predict the previously reported participation of distal residues.
Collapse
Affiliation(s)
- Heather R Brodkin
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
| | - Nicholas A DeLateur
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Srinivas Somarowthu
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Caitlyn L Mills
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Walter R Novak
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Dagmar Ringe
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
| | - Mary Jo Ondrechen
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| |
Collapse
|
14
|
Auclair J, Ringe D, Petsko G, Agar J. Cysteinylation of the ALS‐Associated Protein SOD1 Confers Resistance to Oxidation. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.717.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jared Auclair
- BiochemistryBrandeis UniversityWalthamMAUnited States
- ChemistryNortheastern UniversityBostonMAUnited States
| | - Dagmar Ringe
- BiochemistryBrandeis UniversityWalthamMAUnited States
| | | | - Jeffrey Agar
- ChemistryNortheastern UniversityBostonMAUnited States
| |
Collapse
|
15
|
Berman DE, Ringe D, Petsko GA, Small SA. The use of pharmacological retromer chaperones in Alzheimer's disease and other endosomal-related disorders. Neurotherapeutics 2015; 12:12-8. [PMID: 25472693 PMCID: PMC4322078 DOI: 10.1007/s13311-014-0321-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The retromer is an evolutionary conserved multiprotein complex involved in the sorting and retrograde trafficking of cargo from endosomal compartments to the Golgi network and to the cell surface. The neuronal retromer traffics the amyloid precursor protein away from the endosomes, a site where amyloid precursor protein is enzymatically cleaved into pathogenic fragments in Alzheimer's disease. In recent years, deficiencies in retromer-mediated transport have been implicated in several neurological and non-neurological diseases, including Parkinson's disease, suggesting that improving the efficacy of the retromer trafficking pathway would result in decreased pathology. We recently identified a new family of small molecules that appear to stabilize the interaction between members of the retromer complex and enhance its function in neurons: the retromer pharmacological chaperones. Here we discuss the role of these molecules in the improvement of retromer trafficking and endosomal dysfunction, as well as their potential as therapeutics for neurological and non-neurological disorders.
Collapse
Affiliation(s)
- Diego E Berman
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, and Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY, 10032, USA,
| | | | | | | |
Collapse
|
16
|
Jackson KL, Dayton RD, Orchard EA, Ju S, Ringe D, Petsko GA, Maquat LE, Klein RL. Preservation of forelimb function by UPF1 gene therapy in a rat model of TDP-43-induced motor paralysis. Gene Ther 2014; 22:20-8. [PMID: 25354681 DOI: 10.1038/gt.2014.101] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 09/04/2014] [Accepted: 10/07/2014] [Indexed: 12/13/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is an RNA surveillance mechanism that requires upframeshift protein 1 (UPF1). This study demonstrates that human UPF1 exerts protective effects in a rat paralysis model based on the amyotrophic lateral sclerosis (ALS)-associated protein, TDP-43 (transactive response DNA-binding protein 43 kDa). An adeno-associated virus vector (AAV9) was used to express TDP-43 throughout the spinal cord of rats, inducing reproducible limb paralysis, to recapitulate the paralysis in ALS. We selected UPF1 for therapeutic testing based on a genetic screen in yeast. The expression of human TDP-43 or human UPF1 in the spinal cord was titrated to less than twofold over the respective endogenous level. AAV9 human mycUPF1 clearly improved overall motor scores in rats also expressing TDP-43. The gene therapy effect of mycUPF1 was specific and reproducible compared with groups receiving either empty vector or green fluorescent protein vector controls. The gene therapy maintained forelimb motor function in rats that would otherwise become quadriplegic. This work helps validate UPF1 as a novel therapeutic for ALS and other TDP-43-related diseases and may implicate UPF1 and NMD involvement in the underlying disease mechanisms.
Collapse
Affiliation(s)
- K L Jackson
- Department of Pharmacology, Toxicology and Neuroscience, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, USA
| | - R D Dayton
- Department of Pharmacology, Toxicology and Neuroscience, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, USA
| | - E A Orchard
- Department of Animal Resources, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - S Ju
- Department of Biological Sciences, Wright State University, Dayton, OH, USA
| | - D Ringe
- Department of Biochemistry and Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, USA
| | - G A Petsko
- 1] Department of Biochemistry and Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, USA [2] Department of Neurology and Neuroscience, Helen and Robert Appel Alzheimer's Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY, USA
| | - L E Maquat
- 1] Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA [2] Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - R L Klein
- Department of Pharmacology, Toxicology and Neuroscience, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, USA
| |
Collapse
|
17
|
Keedy DA, van den Bedem H, Sivak DA, Petsko GA, Ringe D, Wilson MA, Fraser JS. Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR. Structure 2014; 22:899-910. [PMID: 24882744 DOI: 10.1016/j.str.2014.04.016] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 04/26/2014] [Accepted: 04/29/2014] [Indexed: 11/28/2022]
Abstract
Most macromolecular X-ray structures are determined from cryocooled crystals, but it is unclear whether cryocooling distorts functionally relevant flexibility. Here we compare independently acquired pairs of high-resolution data sets of a model Michaelis complex of dihydrofolate reductase (DHFR), collected by separate groups at both room and cryogenic temperatures. These data sets allow us to isolate the differences between experimental procedures and between temperatures. Our analyses of multiconformer models and time-averaged ensembles suggest that cryocooling suppresses and otherwise modifies side-chain and main-chain conformational heterogeneity, quenching dynamic contact networks. Despite some idiosyncratic differences, most changes from room temperature to cryogenic temperature are conserved and likely reflect temperature-dependent solvent remodeling. Both cryogenic data sets point to additional conformations not evident in the corresponding room temperature data sets, suggesting that cryocooling does not merely trap preexisting conformational heterogeneity. Our results demonstrate that crystal cryocooling consistently distorts the energy landscape of DHFR, a paragon for understanding functional protein dynamics.
Collapse
Affiliation(s)
- Daniel A Keedy
- Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Henry van den Bedem
- Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, Stanford, CA 94025, USA
| | - David A Sivak
- Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Gregory A Petsko
- Department of Biochemistry and Chemistry, Brandeis University, Waltham, MA 02454, USA; Department of Neurology and Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02139, USA
| | - Dagmar Ringe
- Department of Neurology and Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02139, USA
| | - Mark A Wilson
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA.
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
18
|
Naffin-Olivos JL, Georgieva M, Goldfarb N, Madan-Lala R, Dong L, Bizzell E, Valinetz E, Brandt GS, Yu S, Shabashvili DE, Ringe D, Dunn BM, Petsko GA, Rengarajan J. Mycobacterium tuberculosis Hip1 modulates macrophage responses through proteolysis of GroEL2. PLoS Pathog 2014; 10:e1004132. [PMID: 24830429 PMCID: PMC4022732 DOI: 10.1371/journal.ppat.1004132] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 04/03/2014] [Indexed: 11/29/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) employs multiple strategies to evade host immune responses and persist within macrophages. We have previously shown that the cell envelope-associated Mtb serine hydrolase, Hip1, prevents robust macrophage activation and dampens host pro-inflammatory responses, allowing Mtb to delay immune detection and accelerate disease progression. We now provide key mechanistic insights into the molecular and biochemical basis of Hip1 function. We establish that Hip1 is a serine protease with activity against protein and peptide substrates. Further, we show that the Mtb GroEL2 protein is a direct substrate of Hip1 protease activity. Cleavage of GroEL2 is specifically inhibited by serine protease inhibitors. We mapped the cleavage site within the N-terminus of GroEL2 and confirmed that this site is required for proteolysis of GroEL2 during Mtb growth. Interestingly, we discovered that Hip1-mediated cleavage of GroEL2 converts the protein from a multimeric to a monomeric form. Moreover, ectopic expression of cleaved GroEL2 monomers into the hip1 mutant complemented the hyperinflammatory phenotype of the hip1 mutant and restored wild type levels of cytokine responses in infected macrophages. Our studies point to Hip1-dependent proteolysis as a novel regulatory mechanism that helps Mtb respond rapidly to changing host immune environments during infection. These findings position Hip1 as an attractive target for inhibition for developing immunomodulatory therapeutics against Mtb.
Collapse
Affiliation(s)
- Jacqueline L. Naffin-Olivos
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Maria Georgieva
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Nathan Goldfarb
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, United States of America
| | - Ranjna Madan-Lala
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Lauren Dong
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Erica Bizzell
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Ethan Valinetz
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Gabriel S. Brandt
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
- Franklin and Marshall College, Lancaster, Pennsylvania, United States of America
| | - Sarah Yu
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, United States of America
| | - Daniil E. Shabashvili
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, United States of America
| | - Dagmar Ringe
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Ben M. Dunn
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, United States of America
| | - Gregory A. Petsko
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Jyothi Rengarajan
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, United States of America
| |
Collapse
|
19
|
Auclair JR, Salisbury JP, Johnson JL, Petsko GA, Ringe D, Bosco DA, Agar NYR, Santagata S, Durham HD, Agar JN. Artifacts to avoid while taking advantage of top-down mass spectrometry based detection of protein S-thiolation. Proteomics 2014; 14:1152-7. [PMID: 24634066 DOI: 10.1002/pmic.201300450] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 02/14/2014] [Accepted: 03/07/2014] [Indexed: 11/12/2022]
Abstract
Bottom-up MS studies typically employ a reduction and alkylation step that eliminates a class of PTM, S-thiolation. Given that molecular oxygen can mediate S-thiolation from reduced thiols, which are abundant in the reducing intracellular milieu, we investigated the possibility that some S-thiolation modifications are artifacts of protein preparation. Cu/Zn-superoxide dismutase (SOD1) was chosen for this case study as it has a reactive surface cysteine residue, which is readily cysteinylated in vitro. The ability of oxygen to generate S-thiolation artifacts was tested by comparing purification of SOD1 from postmortem human cerebral cortex under aerobic and anaerobic conditions. S-thiolation was ∼50% higher in aerobically processed preparations, consistent with oxygen-dependent artifactual S-thiolation. The ability of endogenous small molecule disulfides (e.g. cystine) to participate in artifactual S-thiolation was tested by blocking reactive protein cysteine residues during anaerobic homogenization. A 50-fold reduction in S-thiolation occurred indicating that the majority of S-thiolation observed aerobically was artifact. Tissue-specific artifacts were explored by comparing brain- and blood-derived protein, with remarkably more artifacts observed in brain-derived SOD1. Given the potential for such artifacts, rules of thumb for sample preparation are provided. This study demonstrates that without taking extraordinary precaution, artifactual S-thiolation of highly reactive, surface-exposed, cysteine residues can result.
Collapse
Affiliation(s)
- Jared R Auclair
- Department of Chemistry and Chemical Biology, Barnett Institute, Northeastern University, Boston, MA, USA; Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA; Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, USA; Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Auclair JR, Brodkin HR, D'Aquino JA, Petsko GA, Ringe D, Agar JN. Structural consequences of cysteinylation of Cu/Zn-superoxide dismutase. Biochemistry 2013; 52:6145-50. [PMID: 23919400 DOI: 10.1021/bi400613h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The metalloenzyme Cu/Zn-superoxide dismutase (SOD1) catalyzes the reduction of superoxide anions into molecular oxygen and hydrogen peroxide. Hydrogen peroxide can oxidize SOD1, resulting in aberrant protein conformational changes, disruption of SOD1 function, and DNA damage. Cells may have evolved mechanisms of regulation that prevent such oxidation. We observed that cysteinylation of cysteine 111 (Cys111) of SOD1 prevents oxidation by peroxide (DOI 10.1021/bi4006122 ). In this article, we characterize cysteinylated SOD1 using differential scanning fluorometry and X-ray crystallography. The stoichiometry of binding was one cysteine per SOD1 dimer, and there does not appear to be free volume for a second cysteine without disrupting the dimer interface. Much of the three-dimensional structure of SOD1 is unaffected by cysteinylation. However, local conformational changes are observed in the cysteinylated monomer that include changes in conformation of the electrostatic loop (loop VII; residues 133-144) and the dimer interface (loop VI; residues 102-115). In addition, our data shows how cysteinylation precludes oxidation of cysteine 111 and suggests possible cross-talk between the dimer interface and the electrostatic loop.
Collapse
Affiliation(s)
- Jared R Auclair
- Departments of Biochemistry and Chemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University , Waltham, Massachusetts 02454, United States
| | | | | | | | | | | |
Collapse
|
21
|
Auclair JR, Johnson JL, Liu Q, Salisbury JP, Rotunno MS, Petsko GA, Ringe D, Brown RH, Bosco DA, Agar JN. Post-translational modification by cysteine protects Cu/Zn-superoxide dismutase from oxidative damage. Biochemistry 2013; 52:6137-44. [PMID: 23927036 DOI: 10.1021/bi4006122] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Reactive oxygen species (ROS) are cytotoxic. To remove ROS, cells have developed ROS-specific defense mechanisms, including the enzyme Cu/Zn superoxide dismutase (SOD1), which catalyzes the disproportionation of superoxide anions into molecular oxygen and hydrogen peroxide. Although hydrogen peroxide is less reactive than superoxide, it is still capable of oxidizing, unfolding, and inactivating SOD1, at least in vitro. To explore the relevance of post-translational modification (PTM) of SOD1, including peroxide-related modifications, SOD1 was purified from postmortem human nervous tissue. As much as half of all purified SOD1 protein contained non-native post-translational modifications (PTMs), the most prevalent modifications being cysteinylation and peroxide-related oxidations. Many PTMs targeted a single reactive SOD1 cysteine, Cys111. An intriguing observation was that unlike native SOD1, cysteinylated SOD1 was not oxidized. To further characterize how cysteinylation may protect SOD1 from oxidation, cysteine-modified SOD1 was prepared in vitro and exposed to peroxide. Cysteinylation conferred nearly complete protection from peroxide-induced oxidation of SOD1. Moreover, SOD1 that has been cysteinylated and peroxide oxidized in vitro comprised a set of PTMs that bear a striking resemblance to the myriad of PTMs observed in SOD1 purified from human tissue.
Collapse
Affiliation(s)
- Jared R Auclair
- Departments of Biochemistry and Chemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University , Waltham, Massachusetts 02454, United States
| | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Bharadwaj PR, Verdile G, Barr RK, Gupta V, Steele JW, Lachenmayer ML, Yue Z, Ehrlich ME, Petsko G, Ju S, Ringe D, Sankovich SE, Caine JM, Macreadie IG, Gandy S, Martins RN. Latrepirdine (dimebon) enhances autophagy and reduces intracellular GFP-Aβ42 levels in yeast. J Alzheimers Dis 2013; 32:949-67. [PMID: 22903131 DOI: 10.3233/jad-2012-120178] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Latrepirdine (Dimebon), an anti-histamine, has shown some benefits in trials of neurodegenerative diseases characterized by accumulation of aggregated or misfolded protein such as Alzheimer's disease (AD) and has been shown to promote the removal of α-synuclein protein aggregates in vivo. An important pathway for removal of aggregated or misfolded proteins is the autophagy-lysosomal pathway, which has been implicated in AD pathogenesis, and enhancing this pathway has been shown to have therapeutic potential in AD and other proteinopathies. Here we use a yeast model, Saccharomyces cerevisiae, to investigate whether latrepirdine can enhance autophagy and reduce levels of amyloid-β (Aβ)42 aggregates. Latrepirdine was shown to upregulate yeast vacuolar (lysosomal) activity and promote transport of the autophagic marker (Atg8) to the vacuole. Using an in vitro green fluorescent protein (GFP) tagged Aβ yeast expression system, we investigated whether latrepirdine-enhanced autophagy was associated with a reduction in levels of intracellular GFP-Aβ42. GFP-Aβ42 was localized into punctate patterns compared to the diffuse cytosolic pattern of GFP and the GFP-Aβ42 (19:34), which does not aggregate. In the autophagy deficient mutant (Atg8Δ), GFP-Aβ42 showed a more diffuse cytosolic localization, reflecting the inability of this mutant to sequester GFP-Aβ42. Similar to rapamycin, we observed that latrepirdine significantly reduced GFP-Aβ42 in wild-type compared to the Atg8Δ mutant. Further, latrepirdine treatment attenuated Aβ42-induced toxicity in wild-type cells but not in the Atg8Δ mutant. Together, our findings provide evidence for a novel mechanism of action for latrepirdine in inducing autophagy and reducing intracellular levels of GFP-Aβ42.
Collapse
Affiliation(s)
- Prashant R Bharadwaj
- Centre of Excellence for Alzheimer's Disease Research and Care, School of Medical Sciences, Edith Cowan University, WA, Australia
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Steele JW, Ju S, Lachenmayer ML, Liken J, Stock A, Kim SH, Delgado LM, Alfaro IE, Bernales S, Verdile G, Bharadwaj P, Gupta V, Barr R, Friss A, Dolios G, Wang R, Ringe D, Protter AA, Martins RN, Ehrlich ME, Yue Z, Petsko GA, Gandy S. Latrepirdine stimulates autophagy and reduces accumulation of α-synuclein in cells and in mouse brain. Mol Psychiatry 2013; 18:882-8. [PMID: 22869031 PMCID: PMC3523214 DOI: 10.1038/mp.2012.115] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 06/04/2012] [Accepted: 06/12/2012] [Indexed: 11/29/2022]
Abstract
Latrepirdine (Dimebon; dimebolin) is a neuroactive compound that was associated with enhanced cognition, neuroprotection and neurogenesis in laboratory animals, and has entered phase II clinical trials for both Alzheimer's disease and Huntington's disease (HD). Based on recent indications that latrepirdine protects cells against cytotoxicity associated with expression of aggregatable neurodegeneration-related proteins, including Aβ42 and γ-synuclein, we sought to determine whether latrepirdine offers protection to Saccharomyces cerevisiae. We utilized separate and parallel expression in yeast of several neurodegeneration-related proteins, including α-synuclein (α-syn), the amyotrophic lateral sclerosis-associated genes TDP43 and FUS, and the HD-associated protein huntingtin with a 103 copy-polyglutamine expansion (HTT gene; htt-103Q). Latrepirdine effects on α-syn clearance and toxicity were also measured following treatment of SH-SY5Y cells or chronic treatment of wild-type mice. Latrepirdine only protected yeast against the cytotoxicity associated with α-syn, and this appeared to occur via induction of autophagy. We further report that latrepirdine stimulated the degradation of α-syn in differentiated SH-SY5Y neurons, and in mouse brain following chronic administration, in parallel with elevation of the levels of markers of autophagic activity. Ongoing experiments will determine the utility of latrepirdine to abrogate α-syn accumulation in transgenic mouse models of α-syn neuropathology. We propose that latrepirdine may represent a novel scaffold for discovery of robust pro-autophagic/anti-neurodegeneration compounds, which might yield clinical benefit for synucleinopathies including Parkinson's disease, Lewy body dementia, rapid eye movement (REM) sleep disorder and/or multiple system atrophy, following optimization of its pro-autophagic and pro-neurogenic activities.
Collapse
Affiliation(s)
- John W. Steele
- Department of Neurology, Mount Sinai School of Medicine, New York NY 10029,Department of Psychiatry and Mount Sinai Alzheimer’s Disease Research Center, Mount Sinai School of Medicine, New York NY 10029,Laboratory of Molecular and Cellular Neuroscience, Rockefeller University, New York NY 10065
| | - Shulin Ju
- Department of Biochemistry and Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham MA 02453
| | - M. Lenard Lachenmayer
- Department of Neurology, Mount Sinai School of Medicine, New York NY 10029,Department of Neurology, University of Bonn, Bonn, Germany
| | - Jessica Liken
- Department of Biochemistry and Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham MA 02453
| | - Aryeh Stock
- Department of Neurology, Mount Sinai School of Medicine, New York NY 10029,Department of Psychiatry and Mount Sinai Alzheimer’s Disease Research Center, Mount Sinai School of Medicine, New York NY 10029
| | - Soong Ho Kim
- Department of Neurology, Mount Sinai School of Medicine, New York NY 10029,Department of Psychiatry and Mount Sinai Alzheimer’s Disease Research Center, Mount Sinai School of Medicine, New York NY 10029
| | | | | | - Sebastian Bernales
- Fundación Ciencia Para La Vida, Santiago, Chile,Medivation, Inc., San Francisco, CA 94105 USA
| | - Giuseppe Verdile
- Centre of Excellence for Alzheimer’s Disease Research & Care, School of Medical Sciences, Edith Cowan University, Western Australia, Australia, 6027
| | - Prashant Bharadwaj
- Centre of Excellence for Alzheimer’s Disease Research & Care, School of Medical Sciences, Edith Cowan University, Western Australia, Australia, 6027
| | - Veer Gupta
- Centre of Excellence for Alzheimer’s Disease Research & Care, School of Medical Sciences, Edith Cowan University, Western Australia, Australia, 6027
| | - Renae Barr
- Centre of Excellence for Alzheimer’s Disease Research & Care, School of Medical Sciences, Edith Cowan University, Western Australia, Australia, 6027
| | - Amy Friss
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York NY 10029
| | - Georgia Dolios
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York NY 10029
| | - Rong Wang
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York NY 10029
| | - Dagmar Ringe
- Department of Biochemistry and Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham MA 02453
| | | | - Ralph N. Martins
- Centre of Excellence for Alzheimer’s Disease Research & Care, School of Medical Sciences, Edith Cowan University, Western Australia, Australia, 6027,School of Psychiatry and Clinical Neurosciences, University of Western Australia, Crawley, WA, Australia,Sir James McCusker Alzheimer’s Disease Research Unit, Hollywood Private Hospital, Nedlands, WA, Australia
| | - Michelle E. Ehrlich
- Department of Neurology, Mount Sinai School of Medicine, New York NY 10029,Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York NY 10029,Department of Pediatrics, Mount Sinai School of Medicine, New York NY 10029
| | - Zhenyu Yue
- Department of Neurology, Mount Sinai School of Medicine, New York NY 10029,Department of Neuroscience, Mount Sinai School of Medicine, New York NY 10029
| | - Gregory A. Petsko
- Department of Biochemistry and Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham MA 02453
| | - Sam Gandy
- Department of Neurology, Mount Sinai School of Medicine, New York NY 10029,Department of Psychiatry and Mount Sinai Alzheimer’s Disease Research Center, Mount Sinai School of Medicine, New York NY 10029,James J Peters VA Medical Center, Bronx NY 10468,To whom correspondence should be addressed: Sam Gandy, M.D., Ph.D., Departments of Neurology and Psychiatry, Mount Sinai School of Medicine, One Gustave L. Levy Place, Box 1137, New York, NY 10029 USA or
| |
Collapse
|
24
|
Steele JW, Lachenmayer ML, Ju S, Stock A, Liken J, Kim SH, Delgado LM, Alfaro IE, Bernales S, Verdile G, Bharadwaj P, Gupta V, Barr R, Friss A, Dolios G, Wang R, Ringe D, Fraser P, Westaway D, St George-Hyslop PH, Szabo P, Relkin NR, Buxbaum JD, Glabe CG, Protter AA, Martins RN, Ehrlich ME, Petsko GA, Yue Z, Gandy S. Latrepirdine improves cognition and arrests progression of neuropathology in an Alzheimer's mouse model. Mol Psychiatry 2013; 18:889-97. [PMID: 22850627 PMCID: PMC3625697 DOI: 10.1038/mp.2012.106] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 05/31/2012] [Indexed: 01/25/2023]
Abstract
Latrepirdine (Dimebon) is a pro-neurogenic, antihistaminic compound that has yielded mixed results in clinical trials of mild to moderate Alzheimer's disease, with a dramatically positive outcome in a Russian clinical trial that was unconfirmed in a replication trial in the United States. We sought to determine whether latrepirdine (LAT)-stimulated amyloid precursor protein (APP) catabolism is at least partially attributable to regulation of macroautophagy, a highly conserved protein catabolism pathway that is known to be impaired in brains of patients with Alzheimer's disease (AD). We utilized several mammalian cellular models to determine whether LAT regulates mammalian target of rapamycin (mTOR) and Atg5-dependent autophagy. Male TgCRND8 mice were chronically administered LAT prior to behavior analysis in the cued and contextual fear conditioning paradigm, as well as immunohistological and biochemical analysis of AD-related neuropathology. Treatment of cultured mammalian cells with LAT led to enhanced mTOR- and Atg5-dependent autophagy. Latrepirdine treatment of TgCRND8 transgenic mice was associated with improved learning behavior and with a reduction in accumulation of Aβ42 and α-synuclein. We conclude that LAT possesses pro-autophagic properties in addition to the previously reported pro-neurogenic properties, both of which are potentially relevant to the treatment and/or prevention of neurodegenerative diseases. We suggest that elucidation of the molecular mechanism(s) underlying LAT effects on neurogenesis, autophagy and behavior might warranty the further study of LAT as a potentially viable lead compound that might yield more consistent clinical benefit following the optimization of its pro-neurogenic, pro-autophagic and/or pro-cognitive activities.
Collapse
Affiliation(s)
- John W. Steele
- Department of Neurology, Mount Sinai School of Medicine, New York NY 10029
,Department of Psychiatry and The Mount Sinai Alzheimer’s Disease Research Center, Mount Sinai School of Medicine, New York NY 10029
,Laboratory of Molecular and Cellular Neuroscience, Rockefeller University, New York NY 10065
| | - M. Lenard Lachenmayer
- Department of Neurology, Mount Sinai School of Medicine, New York NY 10029
,Department of Neurology, University of Bonn, Bonn, Germany
| | - Shulin Ju
- Departments of Biochemistry and Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham MA 02453
| | - Aryeh Stock
- Department of Neurology, Mount Sinai School of Medicine, New York NY 10029
| | - Jessica Liken
- Departments of Biochemistry and Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham MA 02453
| | - Soong Ho Kim
- Department of Neurology, Mount Sinai School of Medicine, New York NY 10029
,Department of Psychiatry and The Mount Sinai Alzheimer’s Disease Research Center, Mount Sinai School of Medicine, New York NY 10029
| | - Luz M. Delgado
- Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | | | - Sebastian Bernales
- Fundación Ciencia & Vida, Santiago, Chile
,Medivation, Inc., San Francisco, CA 94105 USA
| | - Giuseppe Verdile
- Centre of Excellence for Alzheimer’s Disease Research & Care, School of Medical Sciences, Edith Cowan University, Western Australia, Australia, 6027.
| | - Prashant Bharadwaj
- Centre of Excellence for Alzheimer’s Disease Research & Care, School of Medical Sciences, Edith Cowan University, Western Australia, Australia, 6027.
| | - Veer Gupta
- Centre of Excellence for Alzheimer’s Disease Research & Care, School of Medical Sciences, Edith Cowan University, Western Australia, Australia, 6027.
| | - Renae Barr
- Centre of Excellence for Alzheimer’s Disease Research & Care, School of Medical Sciences, Edith Cowan University, Western Australia, Australia, 6027.
| | - Amy Friss
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York NY 10029
| | - Georgia Dolios
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York NY 10029
| | - Rong Wang
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York NY 10029
| | - Dagmar Ringe
- Departments of Biochemistry and Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham MA 02453
| | - Paul Fraser
- Tanz Centre for Research in Neurodegenerative Diseases and Department of Medical Biophysics, University of Toronto, Toronto ON M5S 3H2 Canada
| | - David Westaway
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB, T5J 4P6, Canada
| | - Peter H. St George-Hyslop
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB, T5J 4P6, Canada
| | - Paul Szabo
- Department of Neurology and Neurosciences, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Norman R. Relkin
- Department of Neurology and Neurosciences, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Joseph D. Buxbaum
- Department of Psychiatry and The Mount Sinai Alzheimer’s Disease Research Center, Mount Sinai School of Medicine, New York NY 10029
,Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York NY 10029
,Department of Psychiatry, Seaver Autism Center for Research and Treatment, and The Friedman Brain Institute, Mount Sinai School of Medicine, New York NY 10029
| | - Charles G. Glabe
- Department of Neurology, University of California Irvine School of Medicine, Irvine, CA 92697, USA
| | | | - Ralph N. Martins
- Centre of Excellence for Alzheimer’s Disease Research & Care, School of Medical Sciences, Edith Cowan University, Western Australia, Australia, 6027.
,School of Psychiatry and Clinical Neurosciences, University of Western Australia, Crawley, WA, Australia.
,Sir James McCusker Alzheimer’s Disease Research Unit, Hollywood Private Hospital, Nedlands, WA, Australia.
| | - Michelle E. Ehrlich
- Department of Neurology, Mount Sinai School of Medicine, New York NY 10029
,Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York NY 10029
,Department of Pediatrics, Mount Sinai School of Medicine, New York NY 10029
| | - Gregory A. Petsko
- Departments of Biochemistry and Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham MA 02453
,Department of Neurology and Neurosciences, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Zhenyu Yue
- Department of Neurology, Mount Sinai School of Medicine, New York NY 10029
,Department of Neuroscience, Mount Sinai School of Medicine, New York NY 10029
| | - Sam Gandy
- Department of Neurology, Mount Sinai School of Medicine, New York NY 10029
,Department of Psychiatry and The Mount Sinai Alzheimer’s Disease Research Center, Mount Sinai School of Medicine, New York NY 10029
,James J Peters VA Medical Center, Bronx NY 10468
,To whom correspondence should be addressed: Departments of Neurology and Psychiatry, Mount Sinai School of Medicine, One Gustave L. Levy Place, Box 1137, New York, NY 10029 USA or .
| |
Collapse
|
25
|
Liu CF, Liu D, Momb J, Thomas PW, Lajoie A, Petsko GA, Fast W, Ringe D. A phenylalanine clamp controls substrate specificity in the quorum-quenching metallo-γ-lactonase from Bacillus thuringiensis. Biochemistry 2013; 52:1603-10. [PMID: 23387521 DOI: 10.1021/bi400050j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Autoinducer inactivator A (AiiA) is a metal-dependent N-acyl homoserine lactone hydrolase that displays broad substrate specificity but shows a preference for substrates with long N-acyl substitutions. Previously, crystal structures of AiiA in complex with the ring-opened product N-hexanoyl-l-homoserine revealed binding interactions near the metal center but did not identify a binding pocket for the N-acyl chains of longer substrates. Here we report the crystal structure of an AiiA mutant, F107W, determined in the presence and absence of N-decanoyl-l-homoserine. F107 is located in a hydrophobic cavity adjacent to the previously identified ligand binding pocket, and the F107W mutation results in the formation of an unexpected interaction with the ring-opened product. Notably, the structure reveals a previously unidentified hydrophobic binding pocket for the substrate's N-acyl chain. Two aromatic residues, F64 and F68, form a hydrophobic clamp, centered around the seventh carbon in the product-bound structure's decanoyl chain, making an interaction that would also be available for longer substrates, but not for shorter substrates. Steady-state kinetics using substrates of various lengths with AiiA bearing mutations at the hydrophobic clamp, including insertion of a redox-sensitive cysteine pair, confirms the importance of this hydrophobic feature for substrate preference. Identifying the specificity determinants of AiiA will aid the development of more selective quorum-quenching enzymes as tools and as potential therapeutics.
Collapse
Affiliation(s)
- Ce Feng Liu
- Department of Chemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Abstract
This year, the Albert Lasker Basic Medical Research Award will be shared by Michael Sheetz, James Spudich, and Ronald Vale for discoveries concerning the biophysical actions of cytoskeletal motor-protein machines that move cargo within cells, contract muscles, and enable cell motility.
Collapse
Affiliation(s)
- Dagmar Ringe
- Departments of Biochemistry and Chemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA.
| | | |
Collapse
|
27
|
Auclair JR, Somasundaran M, Green KM, Evans JE, Schiffer CA, Ringe D, Petsko GA, Agar JN. Mass spectrometry tools for analysis of intermolecular interactions. Methods Mol Biol 2012; 896:387-98. [PMID: 22821539 DOI: 10.1007/978-1-4614-3704-8_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
The small quantities of protein required for mass spectrometry (MS) make it a powerful tool to detect binding (protein-protein, protein-small molecule, etc.) of proteins that are difficult to express in large quantities, as is the case for many intrinsically disordered proteins. Chemical cross-linking, proteolysis, and MS analysis, combined, are a powerful tool for the identification of binding domains. Here, we present a traditional approach to determine protein-protein interaction binding sites using heavy water ((18)O) as a label. This technique is relatively inexpensive and can be performed on any mass spectrometer without specialized software.
Collapse
Affiliation(s)
- Jared R Auclair
- Department of Biochemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, USA.
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Somarowthu S, Brodkin HR, D’Aquino JA, Ringe D, Ondrechen MJ, Beuning PJ. A Tale of Two Isomerases: Compact versus Extended Active Sites in Ketosteroid Isomerase and Phosphoglucose Isomerase. Biochemistry 2011; 50:9283-95. [DOI: 10.1021/bi201089v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Srinivas Somarowthu
- Department of Chemistry and
Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Heather R. Brodkin
- Departments of Biochemistry
and Chemistry and Rosenstiel Basic Medical Sciences Center, Brandeis University, Waltham, Massachusetts 02454-9110,
United States
| | - J. Alejandro D’Aquino
- Departments of Biochemistry
and Chemistry and Rosenstiel Basic Medical Sciences Center, Brandeis University, Waltham, Massachusetts 02454-9110,
United States
| | - Dagmar Ringe
- Departments of Biochemistry
and Chemistry and Rosenstiel Basic Medical Sciences Center, Brandeis University, Waltham, Massachusetts 02454-9110,
United States
| | - Mary Jo Ondrechen
- Department of Chemistry and
Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
- Center for
Interdisciplinary Research
on Complex Systems, Northeastern University, Boston, Massachusetts 02115, United States
| | - Penny J. Beuning
- Department of Chemistry and
Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
- Center for
Interdisciplinary Research
on Complex Systems, Northeastern University, Boston, Massachusetts 02115, United States
| |
Collapse
|
29
|
Bosco DA, LaVoie MJ, Petsko GA, Ringe D. Proteostasis and movement disorders: Parkinson's disease and amyotrophic lateral sclerosis. Cold Spring Harb Perspect Biol 2011; 3:a007500. [PMID: 21844169 DOI: 10.1101/cshperspect.a007500] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Parkinson's disease (PD) is a movement disorder that afflicts over one million in the U.S.; amyotrophic lateral sclerosis (ALS or Lou Gehrig's disease) is less prevalent but also has a high incidence. The two disorders sometimes present together, making a comparative study of interest. Both ALS and PD are neurodegenerative diseases, and are characterized by the presence of intraneuronal inclusions; however, different classes of neurons are affected and the primary protein in the inclusions differs between the diseases, and in some cases is different in distinct forms of the same disease. These observations might suggest that the more general approach of proteostasis pathway alteration would be a powerful one in treating these disorders. Examining results from human genetics and studies in model organisms, as well as from biochemical and biophysical characterization of the proteins involved in both diseases, we find that most instances of PD can be considered as arising from the misfolding, and self-association to a toxic species, of the small neuronal protein α-synuclein, and that proteostasis strategies are likely to be of value for this disorder. For ALS, the situation is much more complex and less clear-cut; the available data are most consistent with a view that ALS may actually be a family of disorders, presenting similarly but arising from distinct and nonoverlapping causes, including mislocalization of some properly folded proteins and derangement of RNA quality control pathways. Applying proteostasis approaches to this disease may require rethinking or broadening the concept of what proteostasis means.
Collapse
Affiliation(s)
- Daryl A Bosco
- Department of Neurology, University of Massachusetts Medical Center, Worcester, Massachusetts 01655, USA
| | | | | | | |
Collapse
|
30
|
Brodkin HR, Novak WRP, Milne AC, D'Aquino JA, Karabacak NM, Goldberg IG, Agar JN, Payne MS, Petsko GA, Ondrechen MJ, Ringe D. Evidence of the participation of remote residues in the catalytic activity of Co-type nitrile hydratase from Pseudomonas putida. Biochemistry 2011; 50:4923-35. [PMID: 21473592 DOI: 10.1021/bi101761e] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Active sites may be regarded as layers of residues, whereby the residues that interact directly with substrate also interact with residues in a second shell and these in turn interact with residues in a third shell. These residues in the second and third layers may have distinct roles in maintaining the essential chemical properties of the first-shell catalytic residues, particularly their spatial arrangement relative to the substrate binding pocket, and their electrostatic and dynamic properties. The extent to which these remote residues participate in catalysis and precisely how they affect first-shell residues remains unexplored. To improve our understanding of the roles of second- and third-shell residues in catalysis, we used THEMATICS to identify residues in the second and third shells of the Co-type nitrile hydratase from Pseudomonas putida (ppNHase) that may be important for catalysis. Five of these predicted residues, and three additional, conserved residues that were not predicted, have been conservatively mutated, and their effects have been studied both kinetically and structurally. The eight residues have no direct contact with the active site metal ion or bound substrate. These results demonstrate that three of the predicted second-shell residues (α-Asp164, β-Glu56, and β-His147) and one predicted third-shell residue (β-His71) have significant effects on the catalytic efficiency of the enzyme. One of the predicted residues (α-Glu168) and the three residues not predicted (α-Arg170, α-Tyr171, and β-Tyr215) do not have any significant effects on the catalytic efficiency of the enzyme.
Collapse
Affiliation(s)
- Heather R Brodkin
- Department of Chemistry and Chemical Biology and Institute for Complex Scientific Software, Northeastern University, Boston, Massachusetts 02115, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Lazar LM, Fisher SZ, Moulin AG, Kovalevsky A, Novak WRP, Langan P, Petsko GA, Ringe D. Time-of-flight neutron diffraction study of bovine γ-chymotrypsin at the Protein Crystallography Station. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:587-90. [PMID: 21543868 DOI: 10.1107/s1744309111009341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 03/11/2011] [Indexed: 11/11/2022]
Abstract
The overarching goal of this research project is to determine, for a subset of proteins, exact hydrogen positions using neutron diffraction, thereby improving H-atom placement in proteins so that they may be better used in various computational methods that are critically dependent upon said placement. In order to be considered applicable for neutron diffraction studies, the protein of choice must be amenable to ultrahigh-resolution X-ray crystallography, be able to form large crystals (1 mm(3) or greater) and have a modestly sized unit cell (no dimension longer than 100 Å). As such, γ-chymotrypsin is a perfect candidate for neutron diffraction. To understand and probe the role of specific active-site residues and hydrogen-bonding patterns in γ-chymotrypsin, neutron diffraction studies were initiated at the Protein Crystallography Station (PCS) at Los Alamos Neutron Science Center (LANSCE). A large single crystal was subjected to H/D exchange prior to data collection. Time-of-flight neutron diffraction data were collected to 2.0 Å resolution at the PCS with ~85% completeness. Here, the first time-of-flight neutron data collection from γ-chymotrypsin is reported.
Collapse
Affiliation(s)
- Louis M Lazar
- Department of Biochemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Ju S, Tardiff DF, Han H, Divya K, Zhong Q, Maquat LE, Bosco DA, Hayward LJ, Brown RH, Lindquist S, Ringe D, Petsko GA. A yeast model of FUS/TLS-dependent cytotoxicity. PLoS Biol 2011; 9:e1001052. [PMID: 21541368 PMCID: PMC3082520 DOI: 10.1371/journal.pbio.1001052] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 03/17/2011] [Indexed: 12/12/2022] Open
Abstract
FUS/TLS is a nucleic acid binding protein that, when mutated, can cause a subset
of familial amyotrophic lateral sclerosis (fALS). Although FUS/TLS is normally
located predominantly in the nucleus, the pathogenic mutant forms of FUS/TLS
traffic to, and form inclusions in, the cytoplasm of affected spinal motor
neurons or glia. Here we report a yeast model of human FUS/TLS expression that
recapitulates multiple salient features of the pathology of the disease-causing
mutant proteins, including nuclear to cytoplasmic translocation, inclusion
formation, and cytotoxicity. Protein domain analysis indicates that the
carboxyl-terminus of FUS/TLS, where most of the ALS-associated mutations are
clustered, is required but not sufficient for the toxicity of the protein. A
genome-wide genetic screen using a yeast over-expression library identified five
yeast DNA/RNA binding proteins, encoded by the yeast genes
ECM32, NAM8, SBP1,
SKO1, and VHR1, that rescue the toxicity
of human FUS/TLS without changing its expression level, cytoplasmic
translocation, or inclusion formation. Furthermore, hUPF1, a
human homologue of ECM32, also rescues the toxicity of FUS/TLS
in this model, validating the yeast model and implicating a possible
insufficiency in RNA processing or the RNA quality control machinery in the
mechanism of FUS/TLS mediated toxicity. Examination of the effect of FUS/TLS
expression on the decay of selected mRNAs in yeast indicates that the
nonsense-mediated decay pathway is probably not the major determinant of either
toxicity or suppression. Of all the thousand natural shocks that flesh is heir to, one of the most
devastating is amyotrophic lateral sclerosis (ALS), commonly known as Lou
Gehrig's Disease. This disorder, which comes in both inherited and random
forms, is characterized by degeneration of spinal motor neurons, leading to
paralysis and death. The cause of the sporadic form is unknown, but new insight
has come from studying the genetic variations that lead to the rarer familial
forms. One such gene, accounting for 5%–10% of inherited
ALS, is FUS/TLS, which encodes a protein that normally lives in the nucleus of
the cell and is involved in the life-cycle of messenger RNA (mRNA).
ALS-associated mutations in FUS/TLS cause the protein to mislocalize outside the
nucleus into stress granules. Understanding the basis for the toxicity of
mislocalized FUS/TLS could lead to new approaches to the treatment of ALS. We
have made a yeast model for FUS/TLS cellular toxicity that recapitulates the
mislocalization, granular accumulation, and cell death. We have exploited the
yeast model to obtain information about what part of the protein is required for
proper localization and what part is essential for toxicity. We have also
identified several human genes that, when over-expressed in yeast, are able to
rescue the cell from the toxicity of mislocalized FUS/TLS. These genes all have
functions in mRNA quality control, implicating changes in this pathway in the
pathology of ALS.
Collapse
Affiliation(s)
- Shulin Ju
- Department of Biochemistry and Chemistry, Rosenstiel Basic Medical
Sciences Research Center, Brandeis University, Waltham, Massachusetts, United
States of America
- Department of Neurology and Center for Neurologic Diseases, Harvard
Medical School and Brigham & Women's Hospital, Cambridge,
Massachusetts, United States of America
| | - Daniel F. Tardiff
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts,
United States of America
- Howard Hughes Medical Institute, Department of Biology, Massachusetts
Institute of Technology, Cambridge, Massachusetts, United States of
America
| | - Haesun Han
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts,
United States of America
- Howard Hughes Medical Institute, Department of Biology, Massachusetts
Institute of Technology, Cambridge, Massachusetts, United States of
America
| | - Kanneganti Divya
- Department of Biochemistry and Chemistry, Rosenstiel Basic Medical
Sciences Research Center, Brandeis University, Waltham, Massachusetts, United
States of America
| | - Quan Zhong
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston,
Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts,
United States of America
| | - Lynne E. Maquat
- Department of Biochemistry and Biophysics and Center for RNA Biology,
School of Medicine and Dentistry, University of Rochester, Rochester, New York,
United States of America
| | - Daryl A. Bosco
- Department of Neurology, University of Massachusetts Medical School,
Worcester, Massachusetts, United States of America
| | - Lawrence J. Hayward
- Department of Neurology, University of Massachusetts Medical School,
Worcester, Massachusetts, United States of America
| | - Robert H. Brown
- Department of Neurology, University of Massachusetts Medical School,
Worcester, Massachusetts, United States of America
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts,
United States of America
- Howard Hughes Medical Institute, Department of Biology, Massachusetts
Institute of Technology, Cambridge, Massachusetts, United States of
America
| | - Dagmar Ringe
- Department of Biochemistry and Chemistry, Rosenstiel Basic Medical
Sciences Research Center, Brandeis University, Waltham, Massachusetts, United
States of America
- Department of Neurology and Center for Neurologic Diseases, Harvard
Medical School and Brigham & Women's Hospital, Cambridge,
Massachusetts, United States of America
- * E-mail: (DR); (GAP)
| | - Gregory A. Petsko
- Department of Biochemistry and Chemistry, Rosenstiel Basic Medical
Sciences Research Center, Brandeis University, Waltham, Massachusetts, United
States of America
- Department of Neurology and Center for Neurologic Diseases, Harvard
Medical School and Brigham & Women's Hospital, Cambridge,
Massachusetts, United States of America
- * E-mail: (DR); (GAP)
| |
Collapse
|
33
|
Liu D, Pozharski E, Fu M, Silverman RB, Ringe D. Mechanism of inactivation of Escherichia coli aspartate aminotransferase by (S)-4-amino-4,5-dihydro-2-furancarboxylic acid . Biochemistry 2010; 49:10507-15. [PMID: 21033689 PMCID: PMC3013228 DOI: 10.1021/bi101325z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As a potential drug to treat neurological diseases, the mechanism-based inhibitor (S)-4-amino-4,5-dihydro-2-furancarboxylic acid (S-ADFA) has been found to inhibit the γ-aminobutyric acid aminotransferase (GABA-AT) reaction. To circumvent the difficulties in structural studies of a S-ADFA-enzyme complex using GABA-AT, l-aspartate aminotransferase (l-AspAT) from Escherichia coli was used as a model PLP-dependent enzyme. Crystal structures of the E. coli aspartate aminotransferase with S-ADFA bound to the active site were obtained via cocrystallization at pH 7.5 and 8. The complex structures suggest that S-ADFA inhibits the transamination reaction by forming adducts with the catalytic lysine 246 via a covalent bond while producing 1 equiv of pyridoxamine 5'-phosphate (PMP). Based on the structures, formation of the K246-S-ADFA adducts requires a specific initial binding configuration of S-ADFA in the l-AspAT active site, as well as deprotonation of the ε-amino group of lysine 246 after the formation of the quinonoid and/or ketimine intermediate in the overall inactivation reaction.
Collapse
Affiliation(s)
- Dali Liu
- Departments of Biochemistry and Chemistry, and Rosenstiel Basic Sciences Research Center MS029, Brandeis University, Waltham, Massachusetts 02454-9110
| | - Edwin Pozharski
- Departments of Biochemistry and Chemistry, and Rosenstiel Basic Sciences Research Center MS029, Brandeis University, Waltham, Massachusetts 02454-9110
| | - Mengmeng Fu
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, the Center for Molecular Innovation and Drug Discovery and Chemistry of Life Processes Institute, Northwestern University, and Evanston, Illinois 60208-3113
| | - Richard B. Silverman
- Department of Chemistry, Department of Biochemistry, Molecular Biology, and Cell Biology, the Center for Molecular Innovation and Drug Discovery and Chemistry of Life Processes Institute, Northwestern University, and Evanston, Illinois 60208-3113
| | - Dagmar Ringe
- Departments of Biochemistry and Chemistry, and Rosenstiel Basic Sciences Research Center MS029, Brandeis University, Waltham, Massachusetts 02454-9110
| |
Collapse
|
34
|
Lepore BW, Liu D, Peng Y, Fu M, Yasuda C, Manning JM, Silverman RB, Ringe D. Chiral discrimination among aminotransferases: inactivation by 4-amino-4,5-dihydrothiophenecarboxylic acid. Biochemistry 2010; 49:3138-47. [PMID: 20192272 DOI: 10.1021/bi902052x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mechanism-based inhibitors such as cycloserine and gabaculine can inactivate aminotransferases via reactions of the compounds with the pyridoxal phosphate cofactor forming an irreversible adduct. The reaction is chirally specific in that any one enzyme usually only recognizes one enantiomer of the inactivator. For instance, l-aspartate aminotransferase (l-AspAT) is inactivated by 4-amino-4,5-dihydro-2-thiophenecarboxylic acid (ADTA), however, only by the S-isomer. We have now shown that d-amino acid aminotransferase (d-a-AT) is irreversibly inactivated by the R-isomer of the same compound. The X-ray crystal structure (PDB code: 3LQS ) of the inactivated enzyme shows that in the product the enzyme no longer makes a Schiff base linkage to the pyridoxal 5'-phosphate (PLP) cofactor, and instead the compound has formed a derivative of the cofactor. The adduct is similar to that formed between d-cycloserine and d-a-AT or alanine racemase (Ala-Rac) in that the thiophene ring of R-ADTA is intact and seems to be aromatic. The plane of the ring is rotated by nearly 90 degrees with respect to the plane of the pyridine ring of the cofactor, in comparison with the enzyme inactivated by cycloserine. Based on the structure of the product, the mechanism of inactivation most probably involves a transamination followed by aromatization to form an aromatic thiophene ring.
Collapse
Affiliation(s)
- Bryan W Lepore
- Graduate Program in Bioorganic Chemistry, Graduate Program in Biophysics and Biochemistry, Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454-9110, USA
| | | | | | | | | | | | | | | |
Collapse
|
35
|
Brandt GS, Kneen MM, Petsko GA, Ringe D, McLeish MJ. Active-Site Engineering of Benzaldehyde Lyase Shows That a Point Mutation Can Confer Both New Reactivity and Susceptibility to Mechanism-Based Inhibition. J Am Chem Soc 2009; 132:438-9. [DOI: 10.1021/ja907064w] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gabriel S. Brandt
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, and Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202
| | - Malea M. Kneen
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, and Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202
| | - Gregory A. Petsko
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, and Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202
| | - Dagmar Ringe
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, and Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202
| | - Michael J. McLeish
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, and Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202
| |
Collapse
|
36
|
Affiliation(s)
- Dagmar Ringe
- Departments of Biochemistry and Chemistry and the Rosenstiel Center, Brandeis University, 415 South Street, Waltham, MA 02454, USA.
| | | |
Collapse
|
37
|
Abstract
Hydrogen bond networks are key elements of biological structure and function. Nevertheless, their structural properties are challenging to assess within complex macromolecules. Hydrogen-bonded protons are not observed in the vast majority of protein X-ray structures, and static crystallographic models provide limited information regarding the dynamical coupling within hydrogen bond networks. We have brought together 1.1-1.3 A resolution X-ray crystallography, (1)H NMR, site-directed mutagenesis, and deuterium isotope effects on the geometry and chemical shifts of hydrogen-bonded protons to probe the conformational coupling of hydrogen bonds donated by Y16 and D103 in the oxyanion hole of bacterial ketosteroid isomerase. Our results suggest a robust physical coupling of the equilibrium structures of these two hydrogen bonds such that a lengthening of one hydrogen bond by as little as 0.01 A results in a shortening of the neighbor by a similar magnitude. Furthermore, the structural rearrangements detected by NMR in response to mutations within the active site hydrogen bond network can be explained on the basis of the observed coupling. The results herein elucidate fundamental structural properties of hydrogen bonds within the idiosyncratic environment of an enzyme active site and provide a foundation for future experimental and computational explorations of the role of coupled motions within hydrogen bond networks.
Collapse
Affiliation(s)
- Paul A Sigala
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
| | | | | | | | | |
Collapse
|
38
|
Landon MR, Lieberman RL, Hoang QQ, Ju S, Caaveiro JMM, Orwig SD, Kozakov D, Brenke R, Chuang GY, Beglov D, Vajda S, Petsko GA, Ringe D. Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase. J Comput Aided Mol Des 2009; 23:491-500. [PMID: 19521672 PMCID: PMC2889209 DOI: 10.1007/s10822-009-9283-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Accepted: 05/13/2009] [Indexed: 12/28/2022]
Abstract
The identification of hot spots, i.e., binding regions that contribute substantially to the free energy of ligand binding, is a critical step for structure-based drug design. Here we present the application of two fragment-based methods to the detection of hot spots for DJ-1 and glucocerebrosidase (GCase), targets for the development of therapeutics for Parkinson's and Gaucher's diseases, respectively. While the structures of these two proteins are known, binding information is lacking. In this study we employ the experimental multiple solvent crystal structures (MSCS) method and computational fragment mapping (FTMap) to identify regions suitable for the development of pharmacological chaperones for DJ-1 and GCase. Comparison of data derived via MSCS and FTMap also shows that FTMap, a computational method for the identification of fragment binding hot spots, is an accurate and robust alternative to the performance of expensive and difficult crystallographic experiments.
Collapse
Affiliation(s)
- Melissa R Landon
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Center, Brandeis University, 415 South Street MS 029, Waltham, MA 02454, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Lieberman RL, D'aquino JA, Ringe D, Petsko GA. Effects of pH and iminosugar pharmacological chaperones on lysosomal glycosidase structure and stability. Biochemistry 2009; 48:4816-27. [PMID: 19374450 DOI: 10.1021/bi9002265] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Human lysosomal enzymes acid-beta-glucosidase (GCase) and acid-alpha-galactosidase (alpha-Gal A) hydrolyze the sphingolipids glucosyl- and globotriaosylceramide, respectively, and mutations in these enzymes lead to the lipid metabolism disorders Gaucher and Fabry disease, respectively. We have investigated the structure and stability of GCase and alpha-Gal A in a neutral-pH environment reflective of the endoplasmic reticulum and an acidic-pH environment reflective of the lysosome. These details are important for the development of pharmacological chaperone therapy for Gaucher and Fabry disease, in which small molecules bind mutant enzymes in the ER to enable the mutant enzyme to meet quality control requirements for lysosomal trafficking. We report crystal structures of apo GCase at pH 4.5, at pH 5.5, and in complex with the pharmacological chaperone isofagomine (IFG) at pH 7.5. We also present thermostability analysis of GCase at pH 7.4 and 5.2 using differential scanning calorimetry. We compare our results with analogous experiments using alpha-Gal A and the chaperone 1-deoxygalactonijirimycin (DGJ), including the first structure of alpha-Gal A with DGJ. Both GCase and alpha-Gal A are more stable at lysosomal pH with and without their respective iminosugars bound, and notably, the stability of the GCase-IFG complex is pH sensitive. We show that the conformations of the active site loops in GCase are sensitive to ligand binding but not pH, whereas analogous galactose- or DGJ-dependent conformational changes in alpha-Gal A are not seen. Thermodynamic parameters obtained from alpha-Gal A unfolding indicate two-state, van't Hoff unfolding in the absence of the iminosugar at neutral and lysosomal pH, and non-two-state unfolding in the presence of DGJ. Taken together, these results provide insight into how GCase and alpha-Gal A are thermodynamically stabilized by iminosugars and suggest strategies for the development of new pharmacological chaperones for lysosomal storage disorders.
Collapse
Affiliation(s)
- Raquel L Lieberman
- Structural Neurology Lab at the Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA.
| | | | | | | |
Collapse
|
40
|
Brandt GS, Kneen MM, Chakraborty S, Baykal AT, Nemeria N, Yep A, Ruby DI, Petsko GA, Kenyon GL, McLeish MJ, Jordan F, Ringe D. Snapshot of a reaction intermediate: analysis of benzoylformate decarboxylase in complex with a benzoylphosphonate inhibitor. Biochemistry 2009; 48:3247-57. [PMID: 19320438 DOI: 10.1021/bi801950k] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Benzoylformate decarboxylase (BFDC) is a thiamin diphosphate- (ThDP-) dependent enzyme acting on aromatic substrates. In addition to its metabolic role in the mandelate pathway, BFDC shows broad substrate specificity coupled with tight stereo control in the carbon-carbon bond-forming reverse reaction, making it a useful biocatalyst for the production of chiral alpha-hydroxy ketones. The reaction of methyl benzoylphosphonate (MBP), an analogue of the natural substrate benzoylformate, with BFDC results in the formation of a stable analogue (C2alpha-phosphonomandelyl-ThDP) of the covalent ThDP-substrate adduct C2alpha-mandelyl-ThDP. Formation of the stable adduct is confirmed both by formation of a circular dichroism band characteristic of the 1',4'-iminopyrimidine tautomeric form of ThDP (commonly observed when ThDP forms tetrahedral complexes with its substrates) and by high-resolution mass spectrometry of the reaction mixture. In addition, the structure of BFDC with the MBP inhibitor was solved by X-ray crystallography to a spatial resolution of 1.37 A (PDB ID 3FSJ). The electron density clearly shows formation of a tetrahedral adduct between the C2 atom of ThDP and the carbonyl carbon atom of the MBP. This adduct resembles the intermediate from the penultimate step of the carboligation reaction between benzaldehyde and acetaldehyde. The combination of real-time kinetic information via stopped-flow circular dichroism with steady-state data from equilibrium circular dichroism measurements and X-ray crystallography reveals details of the first step of the reaction catalyzed by BFDC. The MBP-ThDP adduct on BFDC is compared to the recently solved structure of the same adduct on benzaldehyde lyase, another ThDP-dependent enzyme capable of catalyzing aldehyde condensation with high stereospecificity.
Collapse
Affiliation(s)
- Gabriel S Brandt
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
D'Aquino JA, Denninger AR, Moulin AG, D'Aquino KE, Ringe D. Decreased sensitivity to changes in the concentration of metal ions as the basis for the hyperactivity of DtxR(E175K). J Mol Biol 2009; 390:112-23. [PMID: 19433095 DOI: 10.1016/j.jmb.2009.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Revised: 04/29/2009] [Accepted: 05/06/2009] [Indexed: 11/25/2022]
Abstract
The metal-ion-activated diphtheria toxin repressor (DtxR) is responsible for the regulation of virulence and other genes in Corynebacterium diphtheriae. A single point mutation in DtxR, DtxR(E175K), causes this mutant repressor to have a hyperactive phenotype. Mice infected with Mycobacterium tuberculosis transformed with plasmids carrying this mutant gene show reduced signs of the tuberculosis infection. Corynebacterial DtxR is able to complement mycobacterial IdeR and vice versa. To date, an explanation for the hyperactivity of DtxR(E175K) has remained elusive. In an attempt to address this issue, we have solved the first crystal structure of DtxR(E175K) and characterized this mutant using circular dichroism, isothermal titration calorimetry, and other biochemical techniques. The results show that although DtxR(E175K) and the wild type have similar secondary structures, DtxR(E175K) gains additional thermostability upon activation with metal ions, which may lead to this mutant requiring a lower concentration of metal ions to reach the same levels of thermostability as the wild-type protein. The E175K mutation causes binding site 1 to retain metal ion bound at all times, which can only be removed by incubation with an ion chelator. The crystal structure of DtxR(E175K) shows an empty binding site 2 without evidence of oxidation of Cys102. The association constant for this low-affinity binding site of DtxR(E175K) obtained from calorimetric titration with Ni(II) is K(a)=7.6+/-0.5x10(4), which is very similar to the reported value for the wild-type repressor, K(a)=6.3x10(4). Both the wild type and DtxR(E175K) require the same amount of metal ion to produce a shift in the electrophoretic mobility shift assay, but unlike the wild type, DtxR(E175K) binding to its cognate DNA [tox promoter-operator (toxPO)] does not require metal-ion supplementation in the running buffer. In the timescale of these experiments, the Mn(II)-DtxR(E175K)-toxPO complex is insensitive to changes in the environmental cation concentrations. In addition to Mn(II), Ni(II), Co(II), Cd(II), and Zn(II) are able to sustain the hyperactive phenotype. These results demonstrate a prominent role of binding site 1 in the activation of DtxR and support the hypothesis that DtxR(E175K) attenuates the expression of virulence due to the decreased ability of the Me(II)-DtxR(E175K)-toxPO complex to dissociate at low concentrations of metal ions.
Collapse
Affiliation(s)
- J Alejandro D'Aquino
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA
| | | | | | | | | |
Collapse
|
42
|
Chakraborty S, Nemeria NS, Balakrishnan A, Brandt GS, Kneen MM, Yep A, McLeish MJ, Kenyon GL, Petsko GA, Ringe D, Jordan F. Detection and time course of formation of major thiamin diphosphate-bound covalent intermediates derived from a chromophoric substrate analogue on benzoylformate decarboxylase. Biochemistry 2009; 48:981-94. [PMID: 19140682 DOI: 10.1021/bi801810h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism of the enzyme benzoylformate decarboxylase (BFDC), which carries out a typical thiamin diphosphate (ThDP)-dependent nonoxidative decarboxylation reaction, was studied with the chromophoric alternate substrate (E)-2-oxo-4(pyridin-3-yl)-3-butenoic acid (3-PKB). Addition of 3-PKB resulted in the appearance of two transient intermediates formed consecutively, the first one to be formed a predecarboxylation ThDP-bound intermediate with lambda(max) at 477 nm, and the second one corresponding to the first postdecarboxylation intermediate the enamine with lambda(max) at 437 nm. The time course of formation/depletion of the PKB-ThDP covalent complex and of the enamine showed that decarboxylation was slower than formation of the PKB-ThDP covalent adduct. When the product of decarboxylation 3-(pyridin-3-yl)acrylaldehyde (PAA) was added to BFDC, again an absorbance with lambda(max) at 473 nm was formed, corresponding to the tetrahedral adduct of PAA with ThDP. Addition of well-formed crystals of BFDC to a solution of PAA resulted in a high resolution (1.34 A) structure of the BFDC-bound adduct of ThDP with PAA confirming the tetrahedral nature at the C2alpha atom, rather than of the enamine, and supporting the assignment of the lambda(max) at 473 nm to the PAA-ThDP adduct. The structure of the PAA-ThDP covalent complex is the first example of a product-ThDP adduct on BFDC. Similar studies with 3-PKB indicated that decarboxylation had taken place. Evidence was also obtained for the slow formation of the enamine intermediate when BFDC was incubated with benzaldehyde, the product of the decarboxylation reaction thus confirming its presence on the reaction pathway.
Collapse
Affiliation(s)
- Sumit Chakraborty
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Novak WRP, Moulin AG, Blakeley MP, Schlichting I, Petsko GA, Ringe D. A preliminary neutron diffraction study of gamma-chymotrypsin. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:317-320. [PMID: 19255494 PMCID: PMC2650460 DOI: 10.1107/s1744309109006630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Accepted: 02/23/2009] [Indexed: 05/27/2023]
Abstract
The crystal preparation and preliminary neutron diffraction analysis of gamma-chymotrypsin are presented. Large hydrogenated crystals of gamma-chymotrypsin were exchanged into deuterated buffer via vapor diffusion in a capillary and neutron Laue diffraction data were collected from the resulting crystal to 2.0 A resolution on the LADI-III diffractometer at the Institut Laue-Langevin (ILL) at room temperature. The neutron structure of a well studied protein such as gamma-chymotrypsin, which is also amenable to ultrahigh-resolution X-ray crystallography, represents the first step in developing a model system for the study of H atoms in protein crystals.
Collapse
Affiliation(s)
- Walter R. P. Novak
- Departments of Chemistry and Biochemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454-9110, USA
| | - Aaron G. Moulin
- Departments of Chemistry and Biochemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454-9110, USA
| | | | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Gregory A. Petsko
- Departments of Chemistry and Biochemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454-9110, USA
| | - Dagmar Ringe
- Departments of Chemistry and Biochemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454-9110, USA
| |
Collapse
|
44
|
Sigala PA, Kraut DA, Caaveiro JMM, Pybus B, Ruben EA, Ringe D, Petsko GA, Herschlag D. Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole. J Am Chem Soc 2008; 130:13696-708. [PMID: 18808119 DOI: 10.1021/ja803928m] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymes are classically proposed to accelerate reactions by binding substrates within active-site environments that are structurally preorganized to optimize binding interactions with reaction transition states rather than ground states. This is a remarkably formidable task considering the limited 0.1-1 A scale of most substrate rearrangements. The flexibility of active-site functional groups along the coordinate of substrate rearrangement, the distance scale on which enzymes can distinguish structural rearrangement, and the energetic significance of discrimination on that scale remain open questions that are fundamental to a basic physical understanding of enzyme active sites and catalysis. We bring together 1.2-1.5 A resolution X-ray crystallography, (1)H and (19)F NMR spectroscopy, quantum mechanical calculations, and transition-state analogue binding measurements to test the distance scale on which noncovalent forces can constrain the structural relaxation or translation of side chains and ligands along a specific coordinate and the energetic consequences of such geometric constraints within the active site of bacterial ketosteroid isomerase (KSI). Our results strongly suggest that packing and binding interactions within the KSI active site can constrain local side-chain reorientation and prevent hydrogen bond shortening by 0.1 A or less. Further, this constraint has substantial energetic effects on ligand binding and stabilization of negative charge within the oxyanion hole. These results provide evidence that subtle geometric effects, indistinguishable in most X-ray crystallographic structures, can have significant energetic consequences and highlight the importance of using synergistic experimental approaches to dissect enzyme function.
Collapse
Affiliation(s)
- Paul A Sigala
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
| | | | | | | | | | | | | | | |
Collapse
|
45
|
Momb J, Wang C, Liu D, Thomas PW, Petsko GA, Guo H, Ringe D, Fast W. Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 2. Substrate modeling and active site mutations. Biochemistry 2008; 47:7715-25. [PMID: 18627130 PMCID: PMC2646874 DOI: 10.1021/bi8003704] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The N-acyl-l-homoserine lactone hydrolases (AHL lactonases) have attracted considerable attention because of their ability to quench AHL-mediated quorum-sensing pathways in Gram-negative bacteria and because of their relation to other enzymes in the metallo-β-lactamase superfamily. To elucidate the detailed catalytic mechanism of AHL lactonase, mutations are made on residues that presumably contribute to substrate binding and catalysis. Steady-state kinetic studies are carried out on both the wild-type and mutant enzymes using a spectrum of substrates. Two mutations, Y194F and D108N, present significant effects on the overall catalysis. On the basis of a high-resolution structural model of the enzyme−product complex, a hybrid quantum mechanical/molecular mechanical method is used to model the substrate binding orientation and to probe the effect of the Y194F mutation. Combining all experimental and computational results, we propose a detailed mechanism for the ring-opening hydrolysis of AHL substrates as catalyzed by the AHL lactonase from Bacillus thuringiensis. Several features of the mechanism that are also found in related enzymes are discussed and may help to define an evolutionary thread that connects the hydrolytic enzymes of this mechanistically diverse superfamily.
Collapse
Affiliation(s)
- Jessica Momb
- Graduate Program in Biochemistry, The University of Texas, Austin, Texas 78712, USA
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Abstract
The predictability of catalytic and binding sites from apo structures is addressed for proteins that undergo significant conformational change upon binding. Theoretical microscopic titration curves (THEMATICS), an electrostatics-based method for the prediction of functional sites, is performed on a test set of 24 proteins with both apo and holo structures available. For 23 of these 24 proteins (96%), THEMATICS predicts the correct catalytic or binding site for both the apo and holo forms. For only one of the 24 proteins, THEMATICS makes the correct prediction for the holo structure but fails for the apo structure. The metrics used by THEMATICS to identify functional residues generally are larger in absolute value for the functional residues in the holo forms compared to the corresponding residues in the apo forms. However, even in the apo forms, these identifying metrics are still statistically significantly larger for functional residues than for residues not involved in catalysis or binding. This indicates that some of the unusual electrostatic properties of functional residues are preserved in the apo conformation. Evidence is presented that certain residues immediately surrounding the active catalytic and binding residues impart functionally important chemical and electrostatic properties to the active residues. At least parts of these microenvironments exist in the unbound conformations, such that THEMATICS is able to distinguish the functional residues even in the apo structures.
Collapse
Affiliation(s)
- Leonel F Murga
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454-9110, USA
| | | | | |
Collapse
|
47
|
Liu D, Momb J, Thomas PW, Moulin A, Petsko GA, Fast W, Ringe D. Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 1. Product-bound structures. Biochemistry 2008; 47:7706-14. [PMID: 18627129 PMCID: PMC2646676 DOI: 10.1021/bi800368y] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Revised: 05/15/2008] [Indexed: 11/28/2022]
Abstract
Enzymes capable of hydrolyzing N-acyl- l-homoserine lactones (AHLs) used in some bacterial quorum-sensing pathways are of considerable interest for their ability to block undesirable phenotypes. Most known AHL hydrolases that catalyze ring opening (AHL lactonases) are members of the metallo-beta-lactamase enzyme superfamily and rely on a dinuclear zinc site for catalysis and stability. Here we report the three-dimensional structures of three product complexes formed with the AHL lactonase from Bacillus thuringiensis. Structures of the lactonase bound with two different concentrations of the ring-opened product of N-hexanoyl- l-homoserine lactone are determined at 0.95 and 1.4 A resolution and exhibit different product configurations. A structure of the ring-opened product of the non-natural N-hexanoyl- l-homocysteine thiolactone at 1.3 A resolution is also determined. On the basis of these product-bound structures, a substrate-binding model is presented that differs from previous proposals. Additionally, the proximity of the product to active-site residues and observed changes in protein conformation and metal coordination provide insight into the catalytic mechanism of this quorum-quenching metalloenzyme.
Collapse
Affiliation(s)
| | | | | | | | | | - Walter Fast
- To whom correspondence should be addressed. D.R.: Departments of Chemistry and Biochemistry and Rosenstiel Basic Medical Sciences Research Center, MS029, Brandeis University, Waltham, MA 02454-9110; e-mail, . W.F.: The University of Texas, College of Pharmacy, PHAR-MED CHEM, 1 University Station, A1935, Austin, TX 78712; phone, (512) 232-4000; fax, (512) 232-2606; e-mail,
| | - Dagmar Ringe
- To whom correspondence should be addressed. D.R.: Departments of Chemistry and Biochemistry and Rosenstiel Basic Medical Sciences Research Center, MS029, Brandeis University, Waltham, MA 02454-9110; e-mail, . W.F.: The University of Texas, College of Pharmacy, PHAR-MED CHEM, 1 University Station, A1935, Austin, TX 78712; phone, (512) 232-4000; fax, (512) 232-2606; e-mail,
| |
Collapse
|
48
|
Ataie NJ, Hoang QQ, Zahniser MPD, Tu Y, Milne A, Petsko GA, Ringe D. Zinc coordination geometry and ligand binding affinity: the structural and kinetic analysis of the second-shell serine 228 residue and the methionine 180 residue of the aminopeptidase from Vibrio proteolyticus. Biochemistry 2008; 47:7673-83. [PMID: 18576673 DOI: 10.1021/bi702188e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The chemical properties of zinc make it an ideal metal to study the role of coordination strain in enzymatic rate enhancement. The zinc ion and the protein residues that are bound directly to the zinc ion represent a functional charge/dipole complex, and polarization of this complex, which translates to coordination distortion, may tune electrophilicity, and hence, reactivity. Conserved protein residues outside of the charge/dipole complex, such as second-shell residues, may play a role in supporting the electronic strain produced as a consequence of functional polarization. To test the correlation between charge/dipole polarity and ligand binding affinity, structure-function studies were carried out on the dizinc aminopeptidase from Vibrio proteolyticus. Alanine substitutions of S228 and M180 resulted in catalytically diminished enzymes whose crystal structures show very little change in the positions of the metal ions and the protein residues. However, more detailed inspections of the crystal structures show small positional changes that account for differences in the zinc ion coordination geometry. Measurements of the binding affinity of leucine phosphonic acid, a transition state analogue, and leucine, a product, show a correlation between coordination geometry and ligand binding affinity. These results suggest that the coordination number and polarity may tune the electrophilicity of zinc. This may have provided the evolving enzyme with the ability to discriminate between reaction coordinate species.
Collapse
Affiliation(s)
- Niloufar J Ataie
- Rosenstiel Basic Medical Sciences Research Center and Department of Biochemistry, Program in Biochemistry and Biophysics, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, USA
| | | | | | | | | | | | | |
Collapse
|
49
|
Brandt GS, Nemeria N, Chakraborty S, McLeish MJ, Yep A, Kenyon GL, Petsko GA, Jordan F, Ringe D. Probing the active center of benzaldehyde lyase with substitutions and the pseudosubstrate analogue benzoylphosphonic acid methyl ester. Biochemistry 2008; 47:7734-43. [PMID: 18570438 DOI: 10.1021/bi8004413] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Benzaldehyde lyase (BAL) catalyzes the reversible cleavage of ( R)-benzoin to benzaldehyde utilizing thiamin diphosphate and Mg (2+) as cofactors. The enzyme is important for the chemoenzymatic synthesis of a wide range of compounds via its carboligation reaction mechanism. In addition to its principal functions, BAL can slowly decarboxylate aromatic amino acids such as benzoylformic acid. It is also intriguing mechanistically due to the paucity of acid-base residues at the active center that can participate in proton transfer steps thought to be necessary for these types of reactions. Here methyl benzoylphosphonate, an excellent electrostatic analogue of benzoylformic acid, is used to probe the mechanism of benzaldehyde lyase. The structure of benzaldehyde lyase in its covalent complex with methyl benzoylphosphonate was determined to 2.49 A (Protein Data Bank entry 3D7K ) and represents the first structure of this enzyme with a compound bound in the active site. No large structural reorganization was detected compared to the complex of the enzyme with thiamin diphosphate. The configuration of the predecarboxylation thiamin-bound intermediate was clarified by the structure. Both spectroscopic and X-ray structural studies are consistent with inhibition resulting from the binding of MBP to the thiamin diphosphate in the active centers. We also delineated the role of His29 (the sole potential acid-base catalyst in the active site other than the highly conserved Glu50) and Trp163 in cofactor activation and catalysis by benzaldehyde lyase.
Collapse
Affiliation(s)
- Gabriel S Brandt
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Affiliation(s)
- Dagmar Ringe
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA.
| | | |
Collapse
|