1
|
Sabri N, Cuneo MJ, Marzahn MR, Lee J, Bouchard JJ, Güllülü Ö, Vaithiyalingam S, Borgia MB, Schmit J, Mittag T. Reduction of oligomer size modulates the competition between cluster formation and phase separation of the tumor suppressor SPOP. J Biol Chem 2023; 299:105427. [PMID: 37926283 PMCID: PMC10696467 DOI: 10.1016/j.jbc.2023.105427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 05/09/2023] [Revised: 09/26/2023] [Accepted: 10/17/2023] [Indexed: 11/07/2023] Open
Abstract
Phase separation compartmentalizes many cellular pathways. Given that the same interactions that drive phase separation mediate the formation of soluble complexes below the saturation concentration, the contribution of condensates versus complexes to function is sometimes unclear. Here, we characterized several new cancer-associated mutations of the tumor suppressor speckle-type POZ protein (SPOP), a substrate recognition subunit of the Cullin3-RING ubiquitin ligase. This pointed to a strategy for generating separation-of-function mutations. SPOP self-associates into linear oligomers and interacts with multivalent substrates, and this mediates the formation of condensates. These condensates bear the hallmarks of enzymatic ubiquitination activity. We characterized the effect of mutations in the dimerization domains of SPOP on its linear oligomerization, binding to its substrate DAXX, and phase separation with DAXX. We showed that the mutations reduce SPOP oligomerization and shift the size distribution of SPOP oligomers to smaller sizes. The mutations therefore reduce the binding affinity to DAXX but unexpectedly enhance the poly-ubiquitination activity of SPOP toward DAXX. Enhanced activity may be explained by enhanced phase separation of DAXX with the SPOP mutants. Our results provide a comparative assessment of the functional role of complexes versus condensates and support a model in which phase separation is an important factor in SPOP function. Our findings also suggest that tuning of linear SPOP self-association could be used by the cell to modulate activity and provide insights into the mechanisms underlying hypermorphic SPOP mutations. The characteristics of cancer-associated SPOP mutations suggest a route for designing separation-of-function mutations in other phase-separating systems.
Collapse
Affiliation(s)
- Nafiseh Sabri
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Matthew J Cuneo
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Melissa R Marzahn
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jihun Lee
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jill J Bouchard
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ömer Güllülü
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Sivaraja Vaithiyalingam
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Madeleine B Borgia
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jeremy Schmit
- Department of Physics, Kansas State University, Manhattan, Kansas, USA
| | - Tanja Mittag
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA.
| |
Collapse
|
2
|
Sabri N, Cuneo MJ, Marzahn MR, Lee J, Bouchard JJ, Vaithiyalingam S, Borgia MB, Schmit J, Mittag T. Reduction of oligomer size modulates the competition between cluster formation and phase separation of the tumor suppressor SPOP. bioRxiv 2023:2023.02.11.528154. [PMID: 36993550 PMCID: PMC10054981 DOI: 10.1101/2023.02.11.528154] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Phase separation is a ubiquitous process that compartmentalizes many cellular pathways. Given that the same interactions that drive phase separation mediate the formation of complexes below the saturation concentration, the contribution of condensates vs complexes to function is not always clear. Here, we characterized several new cancer-associated mutations of the tumor suppressor Speckle-type POZ protein (SPOP), a substrate recognition subunit of the Cullin3-RING ubiquitin ligase (CRL3), which pointed to a strategy for generating separation-of-function mutations. SPOP self-associates into linear oligomers and interacts with multivalent substrates, and this mediates the formation of condensates. These condensates bear the hallmarks of enzymatic ubiquitination activity. We characterized the effect of mutations in the dimerization domains of SPOP on its linear oligomerization, binding to the substrate DAXX, and phase separation with DAXX. We showed that the mutations reduce SPOP oligomerization and shift the size distribution of SPOP oligomers to smaller sizes. The mutations therefore reduce the binding affinity to DAXX, but enhance the poly-ubiquitination activity of SPOP towards DAXX. This unexpectedly enhanced activity may be explained by enhanced phase separation of DAXX with the SPOP mutants. Our results provide a comparative assessment of the functional role of clusters versus condensates and support a model in which phase separation is an important factor in SPOP function. Our findings also suggest that tuning of linear SPOP self-association could be used by the cell to modulate its activity, and provide insights into the mechanisms underlying hypermorphic SPOP mutations. The characteristics of these cancer-associated SPOP mutations suggest a route for designing separation-of-function mutations in other phase-separating systems.
Collapse
Affiliation(s)
- Nafiseh Sabri
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38103, USA
| | - Matthew J. Cuneo
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38103, USA
| | - Melissa R. Marzahn
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38103, USA
- Current address: Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Jihun Lee
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38103, USA
- Current address: Celltrion, South Korea
| | - Jill J. Bouchard
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38103, USA
- Current address: Dewpoint Therapeutics, Boston, MA 02210, USA
| | - Sivaraja Vaithiyalingam
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38103, USA
| | - Madeleine B. Borgia
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38103, USA
| | - Jeremy Schmit
- Department of Physics, Kansas State University, Manhattan, Kansas 66506, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38103, USA
| |
Collapse
|
3
|
Cuneo MJ, O'Flynn BG, Lo YH, Sabri N, Mittag T. Higher-order SPOP assembly reveals a basis for cancer mutant dysregulation. Mol Cell 2023; 83:731-745.e4. [PMID: 36693379 PMCID: PMC9992347 DOI: 10.1016/j.molcel.2022.12.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 08/05/2022] [Revised: 11/19/2022] [Accepted: 12/30/2022] [Indexed: 01/24/2023]
Abstract
The speckle-type POZ protein (SPOP) functions in the Cullin3-RING ubiquitin ligase (CRL3) as a receptor for the recognition of substrates involved in cell growth, survival, and signaling. SPOP mutations have been attributed to the development of many types of cancers, including prostate and endometrial cancers. Prostate cancer mutations localize in the substrate-binding site of the substrate recognition (MATH) domain and reduce or prevent binding. However, most endometrial cancer mutations are dispersed in seemingly inconspicuous solvent-exposed regions of SPOP, offering no clear basis for their cancer-causing and peculiar gain-of-function properties. Herein, we present the first structure of SPOP in its oligomeric form, uncovering several new interfaces important for SPOP self-assembly and normal function. Given that many previously unaccounted-for cancer mutations are localized in these newly identified interfaces, we uncover molecular mechanisms underlying dysregulation of SPOP function, with effects ranging from gross structural changes to enhanced self-association, and heightened stability and activity.
Collapse
Affiliation(s)
- Matthew J Cuneo
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38103, USA
| | - Brian G O'Flynn
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38103, USA
| | - Yu-Hua Lo
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38103, USA
| | - Nafiseh Sabri
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38103, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38103, USA.
| |
Collapse
|
4
|
Thomasen FE, Cuneo MJ, Mittag T, Lindorff-Larsen K. Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations. eLife 2023; 12:e84147. [PMID: 36856266 PMCID: PMC9998093 DOI: 10.7554/elife.84147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 10/12/2022] [Accepted: 02/20/2023] [Indexed: 03/02/2023] Open
Abstract
Speckle-type POZ protein (SPOP) is a substrate adaptor in the ubiquitin proteasome system, and plays important roles in cell-cycle control, development, and cancer pathogenesis. SPOP forms linear higher-order oligomers following an isodesmic self-association model. Oligomerization is essential for SPOP's multivalent interactions with substrates, which facilitate phase separation and localization to biomolecular condensates. Structural characterization of SPOP in its oligomeric state and in solution is, however, challenging due to the inherent conformational and compositional heterogeneity of the oligomeric species. Here, we develop an approach to simultaneously and self-consistently characterize the conformational ensemble and the distribution of oligomeric states of SPOP by combining small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. We build initial conformational ensembles of SPOP oligomers using coarse-grained molecular dynamics simulations, and use a Bayesian/maximum entropy approach to refine the ensembles, along with the distribution of oligomeric states, against a concentration series of SAXS experiments. Our results suggest that SPOP oligomers behave as rigid, helical structures in solution, and that a flexible linker region allows SPOP's substrate-binding domains to extend away from the core of the oligomers. Additionally, our results are in good agreement with previous characterization of the isodesmic self-association of SPOP. In the future, the approach presented here can be extended to other systems to simultaneously characterize structural heterogeneity and self-assembly.
Collapse
Affiliation(s)
- F Emil Thomasen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of CopenhagenCopenhagenDenmark
| | - Matthew J Cuneo
- Department of Structural Biology, St. Jude Children’s Research HospitalMemphisUnited States
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children’s Research HospitalMemphisUnited States
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of CopenhagenCopenhagenDenmark
| |
Collapse
|
5
|
Abstract
A spectrum of cancers arises from chromosomal translocations that fuse receptor tyrosine kinase domains to oligomerization domains from unrelated proteins. Tulpule et al. (2021) demonstrate that fusion proteins with the ability to assemble higher-order cytoplasmic protein granules can activate RAS signaling in a lipid membrane-independent manner.
Collapse
Affiliation(s)
- Matthew J Cuneo
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| |
Collapse
|
6
|
Martin EW, Thomasen FE, Milkovic NM, Cuneo MJ, Grace C, Nourse A, Lindorff-Larsen K, Mittag T. Interplay of folded domains and the disordered low-complexity domain in mediating hnRNPA1 phase separation. Nucleic Acids Res 2021; 49:2931-2945. [PMID: 33577679 PMCID: PMC7969017 DOI: 10.1093/nar/gkab063] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [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: 05/14/2020] [Revised: 12/29/2020] [Accepted: 01/29/2021] [Indexed: 01/24/2023] Open
Abstract
Liquid-liquid phase separation underlies the membrane-less compartmentalization of cells. Intrinsically disordered low-complexity domains (LCDs) often mediate phase separation, but how their phase behavior is modulated by folded domains is incompletely understood. Here, we interrogate the interplay between folded and disordered domains of the RNA-binding protein hnRNPA1. The LCD of hnRNPA1 is sufficient for mediating phase separation in vitro. However, we show that the folded RRM domains and a folded solubility-tag modify the phase behavior, even in the absence of RNA. Notably, the presence of the folded domains reverses the salt dependence of the driving force for phase separation relative to the LCD alone. Small-angle X-ray scattering experiments and coarse-grained MD simulations show that the LCD interacts transiently with the RRMs and/or the solubility-tag in a salt-sensitive manner, providing a mechanistic explanation for the observed salt-dependent phase separation. These data point to two effects from the folded domains: (i) electrostatically-mediated interactions that compact hnRNPA1 and contribute to phase separation and (ii) increased solubility at higher ionic strengths mediated by the folded domains. The interplay between disordered and folded domains can modify the dependence of phase behavior on solution conditions and can obscure signatures of physicochemical interactions underlying phase separation.
Collapse
Affiliation(s)
- Erik W Martin
- Department of Structural Biology, St. Jude Children's Research Hospital, TN 38105, USA
| | - F Emil Thomasen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, 2200, Denmark
| | - Nicole M Milkovic
- Department of Structural Biology, St. Jude Children's Research Hospital, TN 38105, USA
| | - Matthew J Cuneo
- Department of Structural Biology, St. Jude Children's Research Hospital, TN 38105, USA
| | - Christy R Grace
- Department of Structural Biology, St. Jude Children's Research Hospital, TN 38105, USA
| | - Amanda Nourse
- Protein Technologies Center, Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, 2200, Denmark
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, TN 38105, USA
| |
Collapse
|
7
|
Abstract
Few other elements play a more central role in biology than hydrogen. The interactions, bonding and movement of hydrogen atoms are central to biological catalysis, structure and function. Yet owing to the elusive nature of a single hydrogen atom few experimental and computational techniques can precisely determine its location. This is exemplified in short hydrogen bonds (SHBs) where the location of the hydrogen atom is indicative of the underlying strength of the bonds, which can vary from 1-5 kcal/mol in canonical hydrogen bonds, to an almost covalent nature in single-well hydrogen bonds. Owing to the often-times inferred position of hydrogen, the role of SHBs in biology has remained highly contested and debated. This has also led to discrepancies in computational, biochemical and structural studies of proteins thought to use SHBs in performing chemistry and stabilizing interactions. Herein, we discuss in detail two distinct examples, namely the conserved catalytic triad and the photoreceptor, photoactive yellow protein, where studies of these SHB-containing systems have permitted contextualization of the role these unique hydrogen bonds play in biology.
Collapse
Affiliation(s)
- Prashasti Kumar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pratul K Agarwal
- Arium BioLabs LLC, Knoxville, TN, 37932, USA
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, OK 74078, USA
| | - Matthew J Cuneo
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38103, USA
| |
Collapse
|
8
|
López de Los Santos Y, Bernard DN, Egesborg P, Létourneau M, Lafortune C, Cuneo MJ, Urvoas A, Chatenet D, Mahy JP, St-Pierre Y, Ricoux R, Doucet N. Binding of a Soluble meso-Tetraarylporphyrin to Human Galectin-7 Induces Oligomerization and Modulates Its Pro-Apoptotic Activity. Biochemistry 2020; 59:4591-4600. [PMID: 33231438 DOI: 10.1021/acs.biochem.0c00736] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The selective targeting of protein-protein interactions remains a significant determinant for the proper modulation and regulation of cell apoptosis. Prototypic galectins such as human galectin-7 (GAL-7) are characterized by their ability to form homodimers that control the molecular fate of a cell by mediating subtle yet critical glycan-dependent interactions between pro- and anti-apoptotic molecular partners. Altering the structural architecture of GAL-7 can therefore result in resistance to apoptosis in various human cancer cells, further illustrating its importance in cell survival. In this study, we used a combination of biophysical and cellular assays to illustrate that binding of a water-soluble meso-tetraarylporphyrin molecule to GAL-7 induces protein oligomerization and modulation of GAL-7-induced apoptosis in human Jurkat T cells. Our results suggest that the integrity of the GAL-7 homodimer architecture is essential for its molecular function, in addition to providing an interesting porphyrin binding modulator for controlling apoptosis in mammalian cells.
Collapse
Affiliation(s)
- Yossef López de Los Santos
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, Laval, QC H7V 1B7, Canada
| | - David N Bernard
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, Laval, QC H7V 1B7, Canada
| | - Philippe Egesborg
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, Laval, QC H7V 1B7, Canada
| | - Myriam Létourneau
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, Laval, QC H7V 1B7, Canada
| | - Clara Lafortune
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, Laval, QC H7V 1B7, Canada
| | - Matthew J Cuneo
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Agathe Urvoas
- Institut de biologie intégrative de la cellule (I2BC), CNRS, Université Paris-Saclay, 91190 Orsay, France
| | - David Chatenet
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, Laval, QC H7V 1B7, Canada
| | - Jean-Pierre Mahy
- Laboratoire de chimie bioorganique et bioinorganique, Institut de chimie moléculaire et des matériaux d'Orsay (ICMMO), CNRS, Université Paris-Saclay, 91190 Orsay, France
| | - Yves St-Pierre
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, Laval, QC H7V 1B7, Canada
| | - Rémy Ricoux
- Laboratoire de chimie bioorganique et bioinorganique, Institut de chimie moléculaire et des matériaux d'Orsay (ICMMO), CNRS, Université Paris-Saclay, 91190 Orsay, France
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS), Université du Québec, Laval, QC H7V 1B7, Canada.,PROTEO, the Quebec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Quebec City, QC G1V 0A6, Canada
| |
Collapse
|
9
|
Abstract
Nucleotidyl transfer is an archetypal enzyme reaction central to DNA replication and repair. Here we describe a variation of the nucleotidylation reaction termed "catch and release" that is used by an antibiotic modifying enzyme. The aminoglycoside nucleotidyl transferase 4' (ANT4') inactivates antibiotics such as kanamycin and neomycin through nucleotidylation within an active site that shares significant structural, and inferred underlying catalytic similarity, with human DNA polymerase beta. Here we follow the entire nucleotidyl transfer reaction coordinate of ANT4' covalently inactivating neomycin using X-ray crystallography. These studies show that although the underlying reaction mechanism is conserved with polymerases, a short 2.35 A hydrogen bond is initially formed to facilitate tight binding of the aminoglycoside substrate and is subsequently disrupted by the assembly of the catalytically active ternary complex. This enables the release of products post catalysis due to a lower free energy of the product state compared to the starting substrate complex. We propose that this "catch and release" mechanism of antibiotic turnover observed in ANT4' is a variation of nucleotidyl transfer that has been adapted for the inactivation of antibiotics.
Collapse
Affiliation(s)
- Brinda Selvaraj
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Seda Kocaman
- The Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, 1311 Cumberland Ave, Knoxville, Tennessee 37916, United States
| | - Maria Trifas
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Engin H. Serpersu
- The Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, 1311 Cumberland Ave, Knoxville, Tennessee 37916, United States
- National Science Foundation, 2415 Eisenhower Avenue, Alexandria, Virginia 22314, United States
| | - Matthew J. Cuneo
- Department of Structural Biology, 262 Danny Thomas Pl, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| |
Collapse
|
10
|
Saxena R, Stanley CB, Kumar P, Cuneo MJ, Patil D, Jha J, Weiss KL, Chattoraj DK, Crooke E. A nucleotide-dependent oligomerization of the Escherichia coli replication initiator DnaA requires residue His136 for remodeling of the chromosomal origin. Nucleic Acids Res 2020; 48:200-211. [PMID: 31665475 PMCID: PMC7145717 DOI: 10.1093/nar/gkz939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/30/2019] [Accepted: 10/08/2019] [Indexed: 12/03/2022] Open
Abstract
Escherichia coli replication initiator protein DnaA binds ATP with high affinity but the amount of ATP required to initiate replication greatly exceeds the amount required for binding. Previously, we showed that ATP-DnaA, not ADP-DnaA, undergoes a conformational change at the higher nucleotide concentration, which allows DnaA oligomerization at the replication origin but the association state remains unclear. Here, we used Small Angle X-ray Scattering (SAXS) to investigate oligomerization of DnaA in solution. Whereas ADP-DnaA was predominantly monomeric, AMP–PNP–DnaA (a non-hydrolysable ATP-analog bound-DnaA) was oligomeric, primarily dimeric. Functional studies using DnaA mutants revealed that DnaA(H136Q) is defective in initiating replication in vivo. The mutant retains high-affinity ATP binding, but was defective in producing replication-competent initiation complexes. Docking of ATP on a structure of E. coli DnaA, modeled upon the crystallographic structure of Aquifex aeolicus DnaA, predicts a hydrogen bond between ATP and imidazole ring of His136, which is disrupted when Gln is present at position 136. SAXS performed on AMP–PNP–DnaA (H136Q) indicates that the protein has lost its ability to form oligomers. These results show the importance of high ATP in DnaA oligomerization and its dependence on the His136 residue.
Collapse
Affiliation(s)
- Rahul Saxena
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Christopher B Stanley
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Pankaj Kumar
- Department of Biochemistry, Jamia Hamdard University, Delhi 110062, India
| | - Matthew J Cuneo
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Digvijay Patil
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Jyoti Jha
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Dhruba K Chattoraj
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Elliott Crooke
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA.,Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA
| |
Collapse
|
11
|
Park J, Selvaraj B, McShan AC, Boyken SE, Wei KY, Oberdorfer G, DeGrado W, Sgourakis NG, Cuneo MJ, Myles DAA, Baker D. De novo design of a homo-trimeric amantadine-binding protein. eLife 2019; 8:e47839. [PMID: 31854299 PMCID: PMC6922598 DOI: 10.7554/elife.47839] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 12/03/2019] [Indexed: 12/25/2022] Open
Abstract
The computational design of a symmetric protein homo-oligomer that binds a symmetry-matched small molecule larger than a metal ion has not yet been achieved. We used de novo protein design to create a homo-trimeric protein that binds the C3 symmetric small molecule drug amantadine with each protein monomer making identical interactions with each face of the small molecule. Solution NMR data show that the protein has regular three-fold symmetry and undergoes localized structural changes upon ligand binding. A high-resolution X-ray structure reveals a close overall match to the design model with the exception of water molecules in the amantadine binding site not included in the Rosetta design calculations, and a neutron structure provides experimental validation of the computationally designed hydrogen-bond networks. Exploration of approaches to generate a small molecule inducible homo-trimerization system based on the design highlight challenges that must be overcome to computationally design such systems.
Collapse
Affiliation(s)
- Jooyoung Park
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
- Institute for Protein DesignUniversity of WashingtonSeattleUnited States
| | - Brinda Selvaraj
- Neutron Sciences DirectorateOak Ridge National LaboratoryOak RidgeUnited States
| | - Andrew C McShan
- Department of Chemistry and BiochemistryUniversity of California, Santa CruzSanta CruzUnited States
| | - Scott E Boyken
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
- Institute for Protein DesignUniversity of WashingtonSeattleUnited States
| | - Kathy Y Wei
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
- Institute for Protein DesignUniversity of WashingtonSeattleUnited States
- Department of BioengineeringUniversity of California, BerkeleyBerkeleyUnited States
| | | | - William DeGrado
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoUnited States
| | - Nikolaos G Sgourakis
- Department of Chemistry and BiochemistryUniversity of California, Santa CruzSanta CruzUnited States
| | - Matthew J Cuneo
- Neutron Sciences DirectorateOak Ridge National LaboratoryOak RidgeUnited States
- Department of Structural BiologySt. Jude Children’s Research HospitalMemphisUnited States
| | - Dean AA Myles
- Neutron Sciences DirectorateOak Ridge National LaboratoryOak RidgeUnited States
| | - David Baker
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
- Institute for Protein DesignUniversity of WashingtonSeattleUnited States
| |
Collapse
|
12
|
Kumar P, Agarwal PK, Waddell MB, Mittag T, Serpersu EH, Cuneo MJ. Low‐Barrier and Canonical Hydrogen Bonds Modulate Activity and Specificity of a Catalytic Triad. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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)
- Prashasti Kumar
- Graduate School of Genome Science and Technology University of Tennessee Knoxville TN 37996 USA
- Present address: Department of Pharmacological Sciences Icahn School of Medicine at Mount Sinai New York NY 10029 USA
| | - Pratul K. Agarwal
- Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville TN 37996 USA
| | - M. Brett Waddell
- Molecular Interaction Analysis Shared Resource St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Tanja Mittag
- Department of Structural Biology St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Engin H. Serpersu
- Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville TN 37996 USA
- National Science Foundation Alexandria VA 22314 USA
| | - Matthew J. Cuneo
- Department of Structural Biology St. Jude Children's Research Hospital Memphis TN 38105 USA
- Oak Ridge National Laboratory Oak Ridge TN 37830 USA
| |
Collapse
|
13
|
Kumar P, Agarwal PK, Waddell MB, Mittag T, Serpersu EH, Cuneo MJ. Low-Barrier and Canonical Hydrogen Bonds Modulate Activity and Specificity of a Catalytic Triad. Angew Chem Int Ed Engl 2019; 58:16260-16266. [PMID: 31515870 DOI: 10.1002/anie.201908535] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 07/09/2019] [Revised: 09/11/2019] [Indexed: 01/14/2023]
Abstract
The position, bonding and dynamics of hydrogen atoms in the catalytic centers of proteins are essential for catalysis. The role of short hydrogen bonds in catalysis has remained highly debated and led to establishment of several distinctive geometrical arrangements of hydrogen atoms vis-à-vis the heavier donor and acceptor counterparts, that is, low-barrier, single-well or short canonical hydrogen bonds. Here we demonstrate how the position of a hydrogen atom in the catalytic triad of an aminoglycoside inactivating enzyme leads to a thirty-fold increase in catalytic turnover. A low-barrier hydrogen bond is present in the enzyme active site for the substrates that are turned over the best, whereas a canonical hydrogen bond is found with the least preferred substrate. This is the first comparison of these hydrogen bonds involving an identical catalytic network, while directly demonstrating how active site electrostatics adapt to the electronic nature of substrates to tune catalysis.
Collapse
Affiliation(s)
- Prashasti Kumar
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.,Present address: Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pratul K Agarwal
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - M Brett Waddell
- Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Engin H Serpersu
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.,National Science Foundation, Alexandria, VA, 22314, USA
| | - Matthew J Cuneo
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.,Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| |
Collapse
|
14
|
Abstract
The dysregulation of ubiquitin-mediated proteasomal degradation has emerged as an important mechanism of pathogenesis in several cancers. The speckle-type POZ protein (SPOP) functions as a substrate adaptor for the cullin3-RING ubiquitin ligase and controls the cellular persistence of a diverse array of protein substrates in hormone signalling, epigenetic control and cell cycle regulation, to name a few. Mutations in SPOP and the resulting dysregulation of this proteostatic pathway play causative roles in the pathogenesis of prostate and endometrial cancers, whereas overexpression and mislocalization are associated with kidney cancer. Understanding the molecular mechanism of the normal function of SPOP as well as the cause of SPOP-mediated oncogenesis is thus critical for eventual therapeutic targeting of SPOP and other related pathways. Here, we will review SPOP structure, function and the molecular mechanism of how this function is achieved. We will then review how mutations and protein mislocalization contribute to cancer pathogenesis and will provide a perspective on how SPOP may be targeted therapeutically.
Collapse
Affiliation(s)
- Matthew J Cuneo
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| |
Collapse
|
15
|
Lu X, Selvaraj B, Ghimire-Rijal S, Orf GS, Meilleur F, Blankenship RE, Cuneo MJ, Myles DAA. Neutron and X-ray analysis of the Fenna-Matthews-Olson photosynthetic antenna complex from Prosthecochloris aestuarii. Acta Crystallogr F Struct Biol Commun 2019; 75:171-175. [PMID: 30839291 DOI: 10.1107/s2053230x19000724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/16/2019] [Indexed: 11/10/2022]
Abstract
The Fenna-Matthews-Olson protein from Prosthecochloris aestuarii (PaFMO) has been crystallized in a new form that is amenable to high-resolution X-ray and neutron analysis. The crystals belonged to space group H3, with unit-cell parameters a = b = 83.64, c = 294.78 Å, and diffracted X-rays to ∼1.7 Å resolution at room temperature. Large PaFMO crystals grown to volumes of 0.3-0.5 mm3 diffracted neutrons to 2.2 Å resolution on the MaNDi neutron diffractometer at the Spallation Neutron Source. The resolution of the neutron data will allow direct determination of the positions of H atoms in the structure, which are believed to be fundamentally important in tuning the individual excitation energies of bacteriochlorophylls in this archetypal photosynthetic antenna complex. This is one of the largest unit-cell systems yet studied using neutron diffraction, and will allow the first high-resolution neutron analysis of a photosynthetic antenna complex.
Collapse
Affiliation(s)
- Xun Lu
- Neutron Science Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Brinda Selvaraj
- Neutron Science Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Sudipa Ghimire-Rijal
- Neutron Science Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gregory S Orf
- Departments of Biology and Chemistry, Washington University in St Louis, St Louis, MO 63130, USA
| | - Flora Meilleur
- Neutron Science Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Robert E Blankenship
- Departments of Biology and Chemistry, Washington University in St Louis, St Louis, MO 63130, USA
| | - Matthew J Cuneo
- Neutron Science Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Dean A A Myles
- Neutron Science Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| |
Collapse
|
16
|
Kumar P, Cuneo MJ, Selvaraj B, Serpersu EH. Molecular Basis of Ligand Selectivity in Aminoglycoside Acetyltransferases. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.298] [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: 11/25/2022] Open
|
17
|
Abstract
Aminoglycoside antibiotics are a large family of antibiotics that can be divided into two distinct classes on the basis of the substitution pattern of the central deoxystreptamine ring. Although aminoglycosides are chemically, structurally, and topologically diverse, some aminoglycoside-modifying enzymes (AGMEs) are able to inactivate as many as 15 aminoglycosides from the two main classes, the kanamycin- and neomycin-based antibiotics. Here, we present the crystal structure of a promiscuous AGME, aminoglycoside- N3-acetyltransferase-IIIb (AAC-IIIb), in the apo form, in binary drug (sisomicin, neomycin, and paromomycin) and coenzyme A (CoASH) complexes, and in the ternary neomycin-CoASH complex. These data provide a structural framework for interpretation of the thermodynamics of enzyme-ligand interactions and the role of solvent in the recognition of ligands. In combination with the recent structure of an AGME that does not have broad substrate specificity, these structures allow for the direct determination of how antibiotic promiscuity is encoded in some AGMEs.
Collapse
Affiliation(s)
- Prashasti Kumar
- Graduate School of Genome Science and Technology , The University of Tennessee and Oak Ridge National Laboratory , 1414 West Cumberland Avenue , Knoxville , Tennessee 37996 , United States
| | - Brinda Selvaraj
- Neutron Sciences Directorate , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
| | - Engin H Serpersu
- Graduate School of Genome Science and Technology , The University of Tennessee and Oak Ridge National Laboratory , 1414 West Cumberland Avenue , Knoxville , Tennessee 37996 , United States.,National Science Foundation , 2415 Eisenhower Avenue , Alexandria , Virginia 22314 , United States.,Department of Biochemistry and Cellular and Molecular Biology , The University of Tennessee , 1414 West Cumberland Avenue , Knoxville , Tennessee 37996 , United States
| | - Matthew J Cuneo
- Department of Structural Biology , St. Jude Children's Research Hospital , 262 Danny Thomas Place , Memphis , Tennessee 38105 , United States
| |
Collapse
|
18
|
Shukla S, Bafna K, Gullett C, Myles DAA, Agarwal PK, Cuneo MJ. Differential Substrate Recognition by Maltose Binding Proteins Influenced by Structure and Dynamics. Biochemistry 2018; 57:5864-5876. [PMID: 30204415 PMCID: PMC6189639 DOI: 10.1021/acs.biochem.8b00783] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 01/25/2023]
Abstract
The genome of the hyperthermophile Thermotoga maritima contains three isoforms of maltose binding protein (MBP) that are high-affinity receptors for di-, tri-, and tetrasaccharides. Two of these proteins (tmMBP1 and tmMBP2) share significant sequence identity, approximately 90%, while the third (tmMBP3) shares less than 40% identity. MBP from Escherichia coli (ecMBP) shares 35% sequence identity with the tmMBPs. This subset of MBP isoforms offers an interesting opportunity to investigate the mechanisms underlying the evolution of substrate specificity and affinity profiles in a genome where redundant MBP genes are present. In this study, the X-ray crystal structures of tmMBP1, tmMBP2, and tmMBP3 are reported in the absence and presence of oligosaccharides. tmMBP1 and tmMBP2 have binding pockets that are larger than that of tmMBP3, enabling them to bind to larger substrates, while tmMBP1 and tmMBP2 also undergo substrate-induced hinge bending motions (∼52°) that are larger than that of tmMBP3 (∼35°). Small-angle X-ray scattering was used to compare protein behavior in solution, and computer simulations provided insights into dynamics of these proteins. Comparing quantitative protein-substrate interactions and dynamical properties of tmMBPs with those of the promiscuous ecMBP and disaccharide selective Thermococcus litoralis MBP provides insights into the features that enable selective binding. Collectively, the results provide insights into how the structure and dynamics of tmMBP homologues enable them to differentiate between a myriad of chemical entities while maintaining their common fold.
Collapse
Affiliation(s)
- Shantanu Shukla
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Khushboo Bafna
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee
| | - Caeley Gullett
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Dean A. A. Myles
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Pratul K. Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee
| | - Matthew J. Cuneo
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
- Deparment of Structural Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| |
Collapse
|
19
|
Duff MR, Borreguero JM, Cuneo MJ, Ramanathan A, He J, Kamath G, Chennubhotla SC, Meilleur F, Howell EE, Herwig KW, Myles DAA, Agarwal PK. Modulating Enzyme Activity by Altering Protein Dynamics with Solvent. Biochemistry 2018; 57:4263-4275. [PMID: 29901984 DOI: 10.1021/acs.biochem.8b00424] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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
Optimal enzyme activity depends on a number of factors, including structure and dynamics. The role of enzyme structure is well recognized; however, the linkage between protein dynamics and enzyme activity has given rise to a contentious debate. We have developed an approach that uses an aqueous mixture of organic solvent to control the functionally relevant enzyme dynamics (without changing the structure), which in turn modulates the enzyme activity. Using this approach, we predicted that the hydride transfer reaction catalyzed by the enzyme dihydrofolate reductase (DHFR) from Escherichia coli in aqueous mixtures of isopropanol (IPA) with water will decrease by ∼3 fold at 20% (v/v) IPA concentration. Stopped-flow kinetic measurements find that the pH-independent khydride rate decreases by 2.2 fold. X-ray crystallographic enzyme structures show no noticeable differences, while computational studies indicate that the transition state and electrostatic effects were identical for water and mixed solvent conditions; quasi-elastic neutron scattering studies show that the dynamical enzyme motions are suppressed. Our approach provides a unique avenue to modulating enzyme activity through changes in enzyme dynamics. Further it provides vital insights that show the altered motions of DHFR cause significant changes in the enzyme's ability to access its functionally relevant conformational substates, explaining the decreased khydride rate. This approach has important implications for obtaining fundamental insights into the role of rate-limiting dynamics in catalysis and as well as for enzyme engineering.
Collapse
Affiliation(s)
- Michael R Duff
- Biochemistry & Cellular and Molecular Biology Department , University of Tennessee , Knoxville , Tennessee , United States
| | - Jose M Borreguero
- Neutron Data Analysis and Visualization Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| | - Matthew J Cuneo
- Biology and Soft Matter Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| | - Arvind Ramanathan
- Computer Science and Engineering Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| | - Junhong He
- Neutron Technologies Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| | - Ganesh Kamath
- Computer Science and Engineering Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| | - S Chakra Chennubhotla
- Department of Computational and Systems Biology , University of Pittsburgh , Pittsburgh , Pennsylvania , United States
| | - Flora Meilleur
- Biology and Soft Matter Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States.,Molecular and Structural Biochemistry Department , North Carolina State University , Raleigh , North Carolina , United States
| | - Elizabeth E Howell
- Biochemistry & Cellular and Molecular Biology Department , University of Tennessee , Knoxville , Tennessee , United States
| | - Kenneth W Herwig
- Neutron Technologies Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| | - Dean A A Myles
- Biology and Soft Matter Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| | - Pratul K Agarwal
- Biochemistry & Cellular and Molecular Biology Department , University of Tennessee , Knoxville , Tennessee , United States.,Computer Science and Engineering Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee , United States
| |
Collapse
|
20
|
Kumar P, Serpersu EH, Cuneo MJ. A low-barrier hydrogen bond mediates antibiotic resistance in a noncanonical catalytic triad. Sci Adv 2018; 4:eaas8667. [PMID: 29632894 PMCID: PMC5884680 DOI: 10.1126/sciadv.aas8667] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 02/20/2018] [Indexed: 05/16/2023]
Abstract
One group of enzymes that confer resistance to aminoglycoside antibiotics through covalent modification belongs to the GCN5-related N-acetyltransferase (GNAT) superfamily. We show how a unique GNAT subfamily member uses a previously unidentified noncanonical catalytic triad, consisting of a glutamic acid, a histidine, and the antibiotic substrate itself, which acts as a nucleophile and attacks the acetyl donor molecule. Neutron diffraction studies allow for unambiguous identification of a low-barrier hydrogen bond, predicted in canonical catalytic triads to increase basicity of the histidine. This work highlights the role of this unique catalytic triad in mediating antibiotic resistance while providing new insights into the design of the next generation of aminoglycosides.
Collapse
Affiliation(s)
- Prashasti Kumar
- University of Tennessee–Oak Ridge National Laboratory Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA
| | - Engin H. Serpersu
- University of Tennessee–Oak Ridge National Laboratory Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA
- National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA 22314, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
- Corresponding author. (E.H.S.); (M.J.C.)
| | - Matthew J. Cuneo
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Corresponding author. (E.H.S.); (M.J.C.)
| |
Collapse
|
21
|
Kovalevsky A, Aggarwal M, Velazquez H, Cuneo MJ, Blakeley MP, Weiss KL, Smith JC, Fisher SZ, McKenna R. "To Be or Not to Be" Protonated: Atomic Details of Human Carbonic Anhydrase-Clinical Drug Complexes by Neutron Crystallography and Simulation. Structure 2018; 26:383-390.e3. [PMID: 29429876 DOI: 10.1016/j.str.2018.01.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [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: 10/23/2017] [Revised: 12/15/2017] [Accepted: 01/10/2018] [Indexed: 10/18/2022]
Abstract
Human carbonic anhydrases (hCAs) play various roles in cells, and have been drug targets for decades. Sequence similarities of hCA isoforms necessitate designing specific inhibitors, which requires detailed structural information for hCA-inhibitor complexes. We present room temperature neutron structures of hCA II in complex with three clinical drugs that provide in-depth analysis of drug binding, including protonation states of the inhibitors, hydration water structure, and direct visualization of hydrogen-bonding networks in the enzyme's active site. All sulfonamide inhibitors studied bind to the Zn metal center in the deprotonated, anionic, form. Other chemical groups of the drugs can remain neutral or be protonated when bound to hCA II. MD simulations have shown that flexible functional groups of the inhibitors may alter their conformations at room temperature and occupy different sub-sites. This study offers insights into the design of specific drugs to target cancer-related hCA isoform IX.
Collapse
Affiliation(s)
- Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
| | - Mayank Aggarwal
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Hector Velazquez
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Biochemistry and Cellular Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Matthew J Cuneo
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Matthew P Blakeley
- Large Scale Structures Group, Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Kevin L Weiss
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jeremy C Smith
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Biochemistry and Cellular Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - S Zoë Fisher
- Scientific Activities Division, Science Directorate, European Spallation Source ERIC, 22100 Lund, Sweden; Department of Biology, Lund University, 35 Sölvegatan, 22362 Lund, Sweden
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
| |
Collapse
|
22
|
Rodriguez Y, Howard MJ, Cuneo MJ, Prasad R, Wilson SH. Unencumbered Pol β lyase activity in nucleosome core particles. Nucleic Acids Res 2017; 45:8901-8915. [PMID: 28911106 PMCID: PMC5587807 DOI: 10.1093/nar/gkx593] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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] [Received: 03/28/2017] [Accepted: 06/30/2017] [Indexed: 12/11/2022] Open
Abstract
Packaging of DNA into the nucleosome core particle (NCP) is considered to exert constraints to all DNA-templated processes, including base excision repair where Pol β catalyzes two key enzymatic steps: 5′-dRP lyase gap trimming and template-directed DNA synthesis. Despite its biological significance, knowledge of Pol β activities on NCPs is still limited. Here, we show that removal of the 5′-dRP block by Pol β is unaffected by NCP constraints at all sites tested and is even enhanced near the DNA ends. In contrast, strong inhibition of DNA synthesis is observed. These results indicate 5′-dRP gap trimming proceeds unperturbed within the NCP; whereas, gap filling is strongly limited. In the absence of additional factors, base excision repair in NCPs will stall at the gap-filling step.
Collapse
Affiliation(s)
- Yesenia Rodriguez
- Laboratory of Genome Integrity and Structural Biology, NIEHS-NIH, Research Triangle Park, NC 27709, USA
| | - Michael J Howard
- Laboratory of Genome Integrity and Structural Biology, NIEHS-NIH, Research Triangle Park, NC 27709, USA
| | | | - Rajendra Prasad
- Laboratory of Genome Integrity and Structural Biology, NIEHS-NIH, Research Triangle Park, NC 27709, USA
| | - Samuel H Wilson
- Laboratory of Genome Integrity and Structural Biology, NIEHS-NIH, Research Triangle Park, NC 27709, USA
| |
Collapse
|
23
|
Li L, Ghimire-Rijal S, Lucas SL, Stanley CB, Wright E, Agarwal PK, Myles DA, Cuneo MJ. Periplasmic Binding Protein Dimer Has a Second Allosteric Event Tied to Ligand Binding. Biochemistry 2017; 56:5328-5337. [PMID: 28876049 DOI: 10.1021/acs.biochem.7b00657] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The ligand-induced conformational changes of periplasmic binding proteins (PBP) play a key role in the acquisition of metabolites in ATP binding cassette (ABC) transport systems. This conformational change allows for differential recognition of the ligand occupancy of the PBP by the ABC transporter. This minimizes futile ATP hydrolysis in the transporter, a phenomenon in which ATP hydrolysis is not coupled to metabolite transport. In many systems, the PBP conformational change is insufficient at eliminating futile ATP hydrolysis. Here we identify an additional state of the PBP that is also allosterically regulated by the ligand. Ligand binding to the homodimeric apo PBP leads to a tightening of the interface α-helices so that the hydrogen bonding pattern shifts to that of a 310 helix, in-turn altering the contacts and the dynamics of the protein interface so that the monomer exists in the presence of ligand.
Collapse
Affiliation(s)
| | | | - Sarah L Lucas
- Department of Biomedical Engineering, North Carolina State University , Raleigh North Carolina 27607, United States
| | | | - Edward Wright
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Pratul K Agarwal
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | | | | |
Collapse
|
24
|
Hayes DG, Ye R, Dunlap RN, Cuneo MJ, Pingali SV, O'Neill HM, Urban VS. Protein extraction into the bicontinuous microemulsion phase of a Water/SDS/pentanol/dodecane winsor-III system: Effect on nanostructure and protein conformation. Colloids Surf B Biointerfaces 2017; 160:144-153. [PMID: 28922633 DOI: 10.1016/j.colsurfb.2017.09.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [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: 06/24/2017] [Revised: 08/22/2017] [Accepted: 09/04/2017] [Indexed: 02/04/2023]
Abstract
Bicontinuous microemulsions (BμEs), consisting of water and oil nanodomains separated by surfactant monolayers of near-zero curvature, are potentially valuable systems for purification and delivery of biomolecules, for hosting multiphasic biochemical reactions, and as templating media for preparing nanomaterials. We formed Winsor-III systems by mixing aqueous protein and sodium dodecyl sulfate (SDS) solutions with dodecane and 1-pentanol (cosurfactant) to efficiently extract proteins into the middle (BμE) phase. Bovine serum albumin (BSA) and cytochrome c partitioned to the BμE phase at 64% and 81% efficiency, respectively, producing highly concentrated protein solutions (32 and 44gL-1, respectively), through release of water and oil from the BμEs. Circular dichroism spectroscopic analysis demonstrated that BSA underwent minor secondary structural changes upon incorporation into BμEs, while the secondary structure of cytochrome c and pepsin underwent major changes. Small-angle x-ray scattering (SAXS) results show that proteins promoted an increase of the interfacial fluidity and surface area per volume for the BμE surfactant monolayers, and that each protein uniquely altered self-assembly in the Winsor-III systems. Cytochrome c partitioned via electrostatic attractions between SDS and the protein's positively-charged groups, residing near the surfactant head groups of BμE monolayers, where it decreased surfactant packing efficiency. BSA partitioned through formation of SDS-BSA complexes via hydrophobic and electrostatic attractive interactions. As the BSA-SDS ratio increased, complexes' partitioning favored BμEs over the oil excess phase due to the increased hydrophilicity of the complexes. This study demonstrates the potential utility of BμEs to purify proteins and prepare nanostructured fluids possessing high protein concentration.
Collapse
Affiliation(s)
- Douglas G Hayes
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN 37996-4531 USA.
| | - Ran Ye
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN 37996-4531 USA
| | - Rachel N Dunlap
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN 37996-4531 USA; Biology & Soft Matter Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831-6475, USA
| | - Matthew J Cuneo
- Biology & Soft Matter Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831-6475, USA
| | - Sai Venkatesh Pingali
- Biology & Soft Matter Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831-6475, USA
| | - Hugh M O'Neill
- Biology & Soft Matter Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831-6475, USA
| | - Volker S Urban
- Biology & Soft Matter Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831-6475, USA
| |
Collapse
|
25
|
Li L, Shukla S, Meilleur F, Standaert RF, Pierce J, Myles DAA, Cuneo MJ. Neutron crystallographic studies of T4 lysozyme at cryogenic temperature. Protein Sci 2017; 26:2098-2104. [PMID: 28707382 DOI: 10.1002/pro.3231] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 05/11/2017] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 11/10/2022]
Abstract
Bacteriophage T4 lysozyme (T4L) has been used as a paradigm for seminal biophysical studies on protein structure, dynamics, and stability. Approximately 700 mutants of this protein and their respective complexes have been characterized by X-ray crystallography; however, despite the high resolution diffraction limits attained in several studies, no hydrogen atoms were reported being visualized in the electron density maps. To address this, a 2.2 Å-resolution neutron data set was collected at 80 K from a crystal of perdeuterated T4L pseudo-wild type. We describe a near complete atomic structure of T4L, which includes the positions of 1737 hydrogen atoms determined by neutron crystallography. The cryogenic neutron model reveals explicit detail of the hydrogen bonding interactions in the protein, in addition to the protonation states of several important residues.
Collapse
Affiliation(s)
- Le Li
- Oak Ridge National Laboratory, Neutron Sciences Directorate, Oak Ridge, Tennessee, 37831
| | - Shantanu Shukla
- Oak Ridge National Laboratory, Neutron Sciences Directorate, Oak Ridge, Tennessee, 37831.,Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Flora Meilleur
- Oak Ridge National Laboratory, Neutron Sciences Directorate, Oak Ridge, Tennessee, 37831.,Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, 27695
| | - Robert F Standaert
- Energy and Environmental Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831
| | - Josh Pierce
- Oak Ridge National Laboratory, Neutron Sciences Directorate, Oak Ridge, Tennessee, 37831
| | - Dean A A Myles
- Oak Ridge National Laboratory, Neutron Sciences Directorate, Oak Ridge, Tennessee, 37831.,Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Matthew J Cuneo
- Oak Ridge National Laboratory, Neutron Sciences Directorate, Oak Ridge, Tennessee, 37831
| |
Collapse
|
26
|
Selvaraj B, Lu X, Cuneo MJ, Myles DAA. Investigation of the bacteriochlorin rings and its environment in Fenna–Matthews–Olsen antenna complex revealed by neutron and ultra-high resolution X-ray crystallography. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s0108767317096520] [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
|
27
|
Bacik JP, Mekasha S, Forsberg Z, Kovalevsky AY, Vaaje-Kolstad G, Eijsink VGH, Nix JC, Coates L, Cuneo MJ, Unkefer CJ, Chen JCH. Neutron and Atomic Resolution X-ray Structures of a Lytic Polysaccharide Monooxygenase Reveal Copper-Mediated Dioxygen Binding and Evidence for N-Terminal Deprotonation. Biochemistry 2017; 56:2529-2532. [DOI: 10.1021/acs.biochem.7b00019] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- John-Paul Bacik
- Protein
Crystallography Station, Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Sophanit Mekasha
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1430 Ås, Norway
| | - Zarah Forsberg
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1430 Ås, Norway
| | - Andrey Y. Kovalevsky
- Biology
and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel
Valley Road, P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | - Gustav Vaaje-Kolstad
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1430 Ås, Norway
| | - Vincent G. H. Eijsink
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), PO Box 5003, 1430 Ås, Norway
| | - Jay C. Nix
- Advanced
Light Source, Lawrence Berkeley Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Leighton Coates
- Biology
and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel
Valley Road, P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | - Matthew J. Cuneo
- Biology
and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel
Valley Road, P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | - Clifford J. Unkefer
- Protein
Crystallography Station, Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Julian C.-H. Chen
- Protein
Crystallography Station, Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| |
Collapse
|
28
|
Moon AF, Krahn JM, Lu X, Cuneo MJ, Pedersen LC. Structural characterization of the virulence factor Sda1 nuclease from Streptococcus pyogenes. Nucleic Acids Res 2016; 44:3946-57. [PMID: 26969731 PMCID: PMC4856990 DOI: 10.1093/nar/gkw143] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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] [Received: 12/21/2015] [Accepted: 02/25/2016] [Indexed: 11/22/2022] Open
Abstract
Infection by Group A Streptococcus pyogenes (GAS) is a leading cause of severe invasive disease in humans, including streptococcal toxic shock syndrome and necrotizing fasciitis. GAS infections lead to nearly 163,000 annual deaths worldwide. Hypervirulent strains of S. pyogenes have evolved a plethora of virulence factors that aid in disease—by promoting bacterial adhesion to host cells, subsequent invasion of deeper tissues and blocking the immune system's attempts to eradicate the infection. Expression and secretion of the extracellular nuclease Sda1 is advantageous for promoting bacterial dissemination throughout the host organism, and evasion of the host's innate immune response. Here we present two crystal structures of Sda1, as well as biochemical studies to address key structural features and surface residues involved in DNA binding and catalysis. In the active site, Asn211 is observed to directly chelate a hydrated divalent metal ion and Arg124, on the putative substrate binding loop, likely stabilizes the transition state during phosphodiester bond cleavage. These structures provide a foundation for rational drug design of small molecule inhibitors to be used in prevention of invasive streptococcal disease.
Collapse
Affiliation(s)
- Andrea F Moon
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Juno M Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Xun Lu
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Matthew J Cuneo
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Lars C Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| |
Collapse
|
29
|
Bacik JP, Mekasha S, Forsberg Z, Kovalevsky A, Nix JC, Cuneo MJ, Coates L, Vaaje-Kolstad G, Chen JCH, Eijsink VGH, Unkefer CJ. Neutron and high-resolution room-temperature X-ray data collection from crystallized lytic polysaccharide monooxygenase. Acta Crystallogr F Struct Biol Commun 2015; 71:1448-52. [PMID: 26527275 PMCID: PMC4631597 DOI: 10.1107/s2053230x15019743] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [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] [Received: 08/07/2015] [Accepted: 10/19/2015] [Indexed: 11/10/2022] Open
Abstract
Bacteria and fungi express lytic polysaccharide monooxgyenase (LPMO) enzymes that act in conjunction with canonical hydrolytic sugar-processing enzymes to rapidly convert polysaccharides such as chitin, cellulose and starch to single monosaccharide products. In order to gain a better understanding of the structure and oxidative mechanism of these enzymes, large crystals (1-3 mm(3)) of a chitin-processing LPMO from the Gram-positive soil bacterium Jonesia denitrificans were grown and screened for their ability to diffract neutrons. In addition to the collection of neutron diffraction data, which were processed to 2.1 Å resolution, a high-resolution room-temperature X-ray diffraction data set was collected and processed to 1.1 Å resolution in space group P212121. To our knowledge, this work marks the first successful neutron crystallographic experiment on an LPMO. Joint X-ray/neutron refinement of the resulting data will reveal new details of the structure and mechanism of this recently discovered class of enzymes.
Collapse
Affiliation(s)
- John-Paul Bacik
- Protein Crystallography Station, Bioscience Division, Los Alamos National Laboratory, TA-03, Bldg 4200, MS T007, Los Alamos, NM 87545, USA
| | - Sophanit Mekasha
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1430 Ås, Norway
| | - Zarah Forsberg
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1430 Ås, Norway
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, PO Box 2008, Oak Ridge, NM 37831, USA
| | - Jay C. Nix
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Matthew J. Cuneo
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, PO Box 2008, Oak Ridge, NM 37831, USA
| | - Leighton Coates
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, PO Box 2008, Oak Ridge, NM 37831, USA
| | - Gustav Vaaje-Kolstad
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1430 Ås, Norway
| | - Julian C.-H. Chen
- Protein Crystallography Station, Bioscience Division, Los Alamos National Laboratory, TA-03, Bldg 4200, MS T007, Los Alamos, NM 87545, USA
| | - Vincent G. H. Eijsink
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1430 Ås, Norway
| | - Clifford J. Unkefer
- Protein Crystallography Station, Bioscience Division, Los Alamos National Laboratory, TA-03, Bldg 4200, MS T007, Los Alamos, NM 87545, USA
| |
Collapse
|
30
|
Jiang J, Zhang H, Lu X, Lu Y, Cuneo MJ, O'Neill HM, Urban V, Lo CS, Blankenship RE. Oligomerization state and pigment binding strength of the peridinin-Chl a-protein. FEBS Lett 2015; 589:2713-9. [PMID: 26241331 DOI: 10.1016/j.febslet.2015.07.039] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 07/13/2015] [Accepted: 07/20/2015] [Indexed: 11/28/2022]
Abstract
The peridinin-chlorophyll a-protein (PCP) is one of the major light harvesting complexes (LHCs) in photosynthetic dinoflagellates. We analyzed the oligomeric state of PCP isolated from the dinoflagellate Symbiodinium, which has received increasing attention in recent years because of its role in coral bleaching. Size-exclusion chromatography (SEC) and small angle neutron scattering (SANS) analysis indicated PCP exists as monomers. Native mass spectrometry (native MS) demonstrated two oligomeric states of PCP, with the monomeric PCP being dominant. The trimerization may not be necessary for PCP to function as a light-harvesting complex.
Collapse
Affiliation(s)
- Jing Jiang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Xun Lu
- Center for Structural Molecular Biology, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yue Lu
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Matthew J Cuneo
- Center for Structural Molecular Biology, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Hugh M O'Neill
- Center for Structural Molecular Biology, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Volker Urban
- Center for Structural Molecular Biology, Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Cynthia S Lo
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Robert E Blankenship
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
| |
Collapse
|
31
|
Coates L, Cuneo MJ, Frost MJ, He J, Weiss KL, Tomanicek SJ, McFeeters H, Vandavasi VG, Langan P, Iverson EB. The Macromolecular Neutron Diffractometer MaNDi at the Spallation Neutron Source. J Appl Crystallogr 2015. [DOI: 10.1107/s1600576715011243] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The Macromolecular Neutron Diffractometer (MaNDi) is located on beamline 11B of the Spallation Neutron Source at Oak Ridge National Laboratory. The instrument is a neutron time-of-flight wavelength-resolved Laue diffractometer optimized to collect diffraction data from single crystals. The instrument has been designed to provide flexibility in several instrumental parameters, such as beam divergence and wavelength bandwidth, to allow data collection from a range of macromolecular systems.
Collapse
|
32
|
Gabel SA, Smith CE, Cuneo MJ, Mueller GA, Kirby TW, DeRose EF, Krahn JM, London RE. Characterization of the redox transition of the XRCC1 N-terminal domain. Structure 2014; 22:1754-1763. [PMID: 25456813 DOI: 10.1016/j.str.2014.09.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/11/2014] [Accepted: 09/05/2014] [Indexed: 10/24/2022]
Abstract
XRCC1, a scaffold protein involved in DNA repair, contains an N-terminal domain (X1NTD) that interacts specifically with DNA polymerase β. It was recently discovered that X1NTD contains a disulfide switch that allows it to adopt either of two metamorphic structures. In the present study, we demonstrate that formation of an N-terminal proline carbimate adduct resulting from the nonenzymatic reaction of Pro2 with CO2 is essential for stabilizing the oxidized structure, X1NTDox. The kinetic response of X1NTDred to H2O2, monitored by NMR, was determined to be very slow, consistent with involvement of the buried, kinetically trapped Cys12 residue, but was significantly accelerated by addition of protein disulfide isomerase or by Cu(2+). NMR analysis of a sample containing the pol β polymerase domain, and both the reduced and oxidized forms of X1NTD, indicates that the oxidized form binds to the enzyme 25-fold more tightly than the reduced form.
Collapse
Affiliation(s)
- Scott A Gabel
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Cassandra E Smith
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Matthew J Cuneo
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Geoffrey A Mueller
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Thomas W Kirby
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Eugene F DeRose
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Juno M Krahn
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Robert E London
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA.
| |
Collapse
|
33
|
Ghimire-Rijal S, Lu X, Myles DA, Cuneo MJ. Duplication of genes in an ATP-binding cassette transport system increases dynamic range while maintaining ligand specificity. J Biol Chem 2014; 289:30090-100. [PMID: 25210043 DOI: 10.1074/jbc.m114.590992] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many bacteria exist in a state of feast or famine where high nutrient availability leads to periods of growth followed by nutrient scarcity and growth stagnation. To adapt to the constantly changing nutrient flux, metabolite acquisition systems must be able to function over a broad range. This, however, creates difficulties as nutrient concentrations vary over many orders of magnitude, requiring metabolite acquisition systems to simultaneously balance ligand specificity and the dynamic range in which a response to a metabolite is elicited. Here we present how a gene duplication of a periplasmic binding protein in a mannose ATP-binding cassette transport system potentially resolves this dilemma through gene functionalization. Determination of ligand binding affinities and specificities of the gene duplicates with fluorescence and circular dichroism demonstrates that although the binding specificity is maintained the Kd values for the same ligand differ over three orders of magnitude. These results suggest that this metabolite acquisition system can transport ligand at both low and high environmental concentrations while preventing saturation with related and less preferentially metabolized compounds. The x-ray crystal structures of the β-mannose-bound proteins help clarify the structural basis of gene functionalization and reveal that affinity and specificity are potentially encoded in different regions of the binding site. These studies suggest a possible functional role and adaptive advantage for the presence of two periplasmic-binding proteins in ATP-binding cassette transport systems and a way bacteria can adapt to varying nutrient flux through functionalization of gene duplicates.
Collapse
Affiliation(s)
- Sudipa Ghimire-Rijal
- From the Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Xun Lu
- From the Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Dean A Myles
- From the Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Matthew J Cuneo
- From the Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| |
Collapse
|
34
|
Bodenheimer AM, Cuneo MJ, Swartz PD, He J, O’Neill HM, Myles DAA, Evans BR, Meilleur F. Crystallization and preliminary X-ray diffraction analysis of Hypocrea jecorina Cel7A in two new crystal forms. Acta Crystallogr F Struct Biol Commun 2014; 70:773-6. [PMID: 24915091 PMCID: PMC4051535 DOI: 10.1107/s2053230x14008851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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] [Received: 03/25/2014] [Accepted: 04/17/2014] [Indexed: 11/10/2022] Open
Abstract
Cel7A (previously known as cellobiohydrolase I) from Hypocrea jecorina was crystallized in two crystalline forms, neither of which have been previously reported. Both forms co-crystallize under the same crystallization conditions. The first crystal form belonged to space group C2, with unit-cell parameters a=152.5, b=44.9, c=57.6 Å, β=101.2°, and diffracted X-rays to 1.5 Å resolution. The second crystal form belonged to space group P6₃22, with unit-cell parameters a=b≃155, c≃138 Å, and diffracted X-rays to 2.5 Å resolution. The crystals were obtained using full-length Cel7A, which consists of a large 434-residue N-terminal catalytic domain capable of cleaving cellulose, a 27-residue flexible linker and a small 36-residue C-terminal carbohydrate-binding module (CBM). However, a preliminary analysis of the electron-density maps suggests that the linker and CBM are disordered in both crystal forms. Complete refinement and structure analysis are currently in progress.
Collapse
Affiliation(s)
- Annette M. Bodenheimer
- Molecular and Structural Biochemistry Department, North Carolina State University, Raleigh, North Carolina, USA
| | - Matthew J. Cuneo
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Paul D. Swartz
- Molecular and Structural Biochemistry Department, North Carolina State University, Raleigh, North Carolina, USA
| | - Junhong He
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Hugh M. O’Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Dean A. A. Myles
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Barbara R. Evans
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Flora Meilleur
- Molecular and Structural Biochemistry Department, North Carolina State University, Raleigh, North Carolina, USA
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| |
Collapse
|
35
|
Zheng X, Pedersen LC, Gabel SA, Mueller GA, Cuneo MJ, DeRose EF, Krahn JM, London RE. Selective unfolding of one Ribonuclease H domain of HIV reverse transcriptase is linked to homodimer formation. Nucleic Acids Res 2014; 42:5361-77. [PMID: 24574528 PMCID: PMC4005681 DOI: 10.1093/nar/gku143] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [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: 11/14/2022] Open
Abstract
HIV-1 reverse transcriptase (RT), a critical enzyme of the HIV life cycle and an important drug target, undergoes complex and largely uncharacterized conformational rearrangements that underlie its asymmetric folding, dimerization and subunit-selective ribonuclease H domain (RH) proteolysis. In the present article we have used a combination of NMR spectroscopy, small angle X-ray scattering and X-ray crystallography to characterize the p51 and p66 monomers and the conformational maturation of the p66/p66′ homodimer. The p66 monomer exists as a loosely structured molecule in which the fingers/palm/connection, thumb and RH substructures are connected by flexible (disordered) linking segments. The initially observed homodimer is asymmetric and includes two fully folded RH domains, while exhibiting other conformational features similar to that of the RT heterodimer. The RH′ domain of the p66′ subunit undergoes selective unfolding with time constant ∼6.5 h, consistent with destabilization due to residue transfer to the polymerase′ domain on the p66′ subunit. A simultaneous increase in the intensity of resonances near the random coil positions is characterized by a similar time constant. Consistent with the residue transfer hypothesis, a construct of the isolated RH domain lacking the two N-terminal residues is shown to exhibit reduced stability. These results demonstrate that RH′ unfolding is coupled to homodimer formation.
Collapse
Affiliation(s)
- Xunhai Zheng
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Munshi P, Stanley CB, Ghimire-Rijal S, Lu X, Myles DA, Cuneo MJ. Molecular details of ligand selectivity determinants in a promiscuous β-glucan periplasmic binding protein. BMC Struct Biol 2013; 13:18. [PMID: 24090243 PMCID: PMC3850815 DOI: 10.1186/1472-6807-13-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 09/27/2013] [Indexed: 01/07/2023]
Abstract
BACKGROUND Members of the periplasmic binding protein (PBP) superfamily utilize a highly conserved inter-domain ligand binding site that adapts to specifically bind a chemically diverse range of ligands. This paradigm of PBP ligand binding specificity was recently altered when the structure of the Thermotoga maritima cellobiose-binding protein (tmCBP) was solved. The tmCBP binding site is bipartite, comprising a canonical solvent-excluded region (subsite one), adjacent to a solvent-filled cavity (subsite two) where specific and semi-specific ligand recognition occur, respectively. RESULTS A molecular level understanding of binding pocket adaptation mechanisms that simultaneously allow both ligand specificity at subsite one and promiscuity at subsite two has potentially important implications in ligand binding and drug design studies. We sought to investigate the determinants of ligand binding selectivity in tmCBP through biophysical characterization of tmCBP in the presence of varying β-glucan oligosaccharides. Crystal structures show that whilst the amino acids that comprise both the tmCBP subsite one and subsite two binding sites remain fixed in conformation regardless of which ligands are present, the rich hydrogen bonding potential of water molecules may facilitate the ordering and the plasticity of this unique PBP binding site. CONCLUSIONS The identification of the roles these water molecules play in ligand recognition suggests potential mechanisms that can be utilized to adapt a single ligand binding site to recognize multiple distinct ligands.
Collapse
Affiliation(s)
- Parthapratim Munshi
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA,Department of Chemistry, Middle Tennessee State University, Murfreesboro, TN 37132, USA,Current address. Shiv Nadar University, Department of Chemistry, Oak Ridge National Laboratory, Uttar Pradesh, India
| | - Christopher B Stanley
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Sudipa Ghimire-Rijal
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xun Lu
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Dean A Myles
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Matthew J Cuneo
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| |
Collapse
|
37
|
Horton JK, Stefanick DF, Gassman NR, Williams JG, Gabel SA, Cuneo MJ, Prasad R, Kedar PS, Derose EF, Hou EW, London RE, Wilson SH. Preventing oxidation of cellular XRCC1 affects PARP-mediated DNA damage responses. DNA Repair (Amst) 2013; 12:774-85. [PMID: 23871146 DOI: 10.1016/j.dnarep.2013.06.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [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: 01/11/2013] [Revised: 06/04/2013] [Accepted: 06/18/2013] [Indexed: 01/12/2023]
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) binds intermediates of base excision repair (BER) and becomes activated for poly(ADP-ribose) (PAR) synthesis. PAR mediates recruitment and functions of the key BER factors XRCC1 and DNA polymerase β (pol β) that in turn regulate PAR. Yet, the molecular mechanism and implications of coordination between XRCC1 and pol β in regulating the level of PAR are poorly understood. A complex of PARP-1, XRCC1 and pol β is found in vivo, and it is known that pol β and XRCC1 interact through a redox-sensitive binding interface in the N-terminal domain of XRCC1. We confirmed here that both oxidized and reduced forms of XRCC1 are present in mouse fibroblasts. To further understand the importance of the C12-C20 oxidized form of XRCC1 and the interaction with pol β, we characterized cell lines representing stable transfectants in Xrcc1(-/-) mouse fibroblasts of wild-type XRCC1 and two mutants of XRCC1, a novel reduced form with the C12-C20 disulfide bond blocked (C12A) and a reference mutant that is unable to bind pol β (V88R). XRCC1-deficient mouse fibroblasts are extremely hypersensitive to methyl methanesulfonate (MMS), and transfected wild-type and C12A mutant XRCC1 proteins similarly reversed MMS hypersensitivity. However, after MMS exposure the cellular PAR level was found to increase to a much greater extent in cells expressing the C12A mutant than in cells expressing wild-type XRCC1. PARP inhibition resulted in very strong MMS sensitization in cells expressing wild-type XRCC1, but this sensitization was much less in cells expressing the C12A mutant. The results suggest a role for the oxidized form of XRCC1 in the interaction with pol β in (1) controlling the PAR level after MMS exposure and (2) enabling the extreme cytotoxicity of PARP inhibition during the MMS DNA damage response.
Collapse
Affiliation(s)
- Julie K Horton
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, NC 29909-2233, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Loeffler PA, Cuneo MJ, Mueller GA, DeRose EF, Gabel SA, London RE. Structural studies of the PARP-1 BRCT domain. BMC Struct Biol 2011; 11:37. [PMID: 21967661 PMCID: PMC3195086 DOI: 10.1186/1472-6807-11-37] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2011] [Accepted: 10/03/2011] [Indexed: 01/19/2023]
Abstract
Background Poly(ADP-ribose) polymerase-1 (PARP-1) is one of the first proteins localized to foci of DNA damage. Upon activation by encountering nicked DNA, the PARP-1 mediated trans-poly(ADP-ribosyl)ation of DNA binding proteins occurs, facilitating access and accumulation of DNA repair factors. PARP-1 also auto-(ADP-ribosyl)ates its central BRCT-containing domain forming part of an interaction site for the DNA repair scaffolding protein X-ray cross complementing group 1 protein (XRCC1). The co-localization of XRCC1, as well as bound DNA repair factors, to sites of DNA damage is important for cell survival and genomic integrity. Results Here we present the solution structure and biophysical characterization of the BRCT domain of rat PARP-1. The PARP-1 BRCT domain has the globular α/β fold characteristic of BRCT domains and has a thermal melting transition of 43.0°C. In contrast to a previous characterization of this domain, we demonstrate that it is monomeric in solution using both gel-filtration chromatography and small-angle X-ray scattering. Additionally, we report that the first BRCT domain of XRCC1 does not interact significantly with the PARP-1 BRCT domain in the absence of ADP-ribosylation. Moreover, none of the interactions with other longer PARP-1 constructs which previously had been demonstrated in a pull-down assay of mammalian cell extracts were detected. Conclusions The PARP-1 BRCT domain has the conserved BRCT fold that is known to be an important protein:protein interaction module in DNA repair and cell signalling pathways. Data indicating no significant protein:protein interactions between PARP-1 and XRCC1 likely results from the absence of poly(ADP-ribose) in one or both binding partners, and further implicates a poly(ADP-ribose)-dependent mechanism for localization of XRCC1 to sites of DNA damage.
Collapse
Affiliation(s)
- Paul A Loeffler
- Department of Chemistry, Sam Houston State University, Huntsville, Texas 77340, USA
| | | | | | | | | | | |
Collapse
|
39
|
Cuneo MJ, Gabel SA, Krahn JM, Ricker MA, London RE. The structural basis for partitioning of the XRCC1/DNA ligase III-α BRCT-mediated dimer complexes. Nucleic Acids Res 2011; 39:7816-27. [PMID: 21652643 PMCID: PMC3177190 DOI: 10.1093/nar/gkr419] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [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: 02/03/2023] Open
Abstract
The ultimate step common to almost all DNA repair pathways is the ligation of the nicked intermediate to form contiguous double-stranded DNA. In the mammalian nucleotide and base excision repair pathways, the ligation step is carried out by ligase III-α. For efficient ligation, ligase III-α is constitutively bound to the scaffolding protein XRCC1 through interactions between the C-terminal BRCT domains of each protein. Although structural data for the individual domains has been available, no structure of the complex has been determined and several alternative proposals for this interaction have been advanced. Interpretation of the models is complicated by the formation of homodimers that, depending on the model, may either contribute to, or compete with heterodimer formation. We report here the structures of both homodimer complexes as well as the heterodimer complex. Structural characterization of the heterodimer formed from a longer XRCC1 BRCT domain construct, including residues comprising the interdomain linker region, revealed an expanded heterodimer interface with the ligase III-α BRCT domain. This enhanced linker-mediated binding interface plays a significant role in the determination of heterodimer/homodimer selectivity. These data provide fundamental insights into the structural basis of BRCT-mediated dimerization, and resolve questions related to the organization of this important repair complex.
Collapse
Affiliation(s)
- Matthew J Cuneo
- National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC, USA
| | | | | | | | | |
Collapse
|
40
|
Antunes MS, Morey KJ, Smith JJ, Albrecht KD, Bowen TA, Zdunek JK, Troupe JF, Cuneo MJ, Webb CT, Hellinga HW, Medford JI. Programmable ligand detection system in plants through a synthetic signal transduction pathway. PLoS One 2011; 6:e16292. [PMID: 21283542 PMCID: PMC3026823 DOI: 10.1371/journal.pone.0016292] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 12/23/2010] [Indexed: 11/18/2022] Open
Abstract
Background There is an unmet need to monitor human and natural environments for substances that are intentionally or unintentionally introduced. A long-sought goal is to adapt plants to sense and respond to specific substances for use as environmental monitors. Computationally re-designed periplasmic binding proteins (PBPs) provide a means to design highly sensitive and specific ligand sensing capabilities in receptors. Input from these proteins can be linked to gene expression through histidine kinase (HK) mediated signaling. Components of HK signaling systems are evolutionarily conserved between bacteria and plants. We previously reported that in response to cytokinin-mediated HK activation in plants, the bacterial response regulator PhoB translocates to the nucleus and activates transcription. Also, we previously described a plant visual response system, the de-greening circuit, a threshold sensitive reporter system that produces a visual response which is remotely detectable and quantifiable. Methodology/Principal Findings We describe assembly and function of a complete synthetic signal transduction pathway in plants that links input from computationally re-designed PBPs to a visual response. To sense extracellular ligands, we targeted the computational re-designed PBPs to the apoplast. PBPs bind the ligand and develop affinity for the extracellular domain of a chemotactic protein, Trg. We experimentally developed Trg fusions proteins, which bind the ligand-PBP complex, and activate intracellular PhoR, the HK cognate of PhoB. We then adapted Trg-PhoR fusions for function in plants showing that in the presence of an external ligand PhoB translocates to the nucleus and activates transcription. We linked this input to the de-greening circuit creating a detector plant. Conclusions/Significance Our system is modular and PBPs can theoretically be designed to bind most small molecules. Hence our system, with improvements, may allow plants to serve as a simple and inexpensive means to monitor human surroundings for substances such as pollutants, explosives, or chemical agents.
Collapse
Affiliation(s)
- Mauricio S. Antunes
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Kevin J. Morey
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - J. Jeff Smith
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Kirk D. Albrecht
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Tessa A. Bowen
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jeffrey K. Zdunek
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jared F. Troupe
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Matthew J. Cuneo
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Colleen T. Webb
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Homme W. Hellinga
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
| | - June I. Medford
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
| |
Collapse
|
41
|
Midon M, Schäfer P, Pingoud A, Ghosh M, Moon AF, Cuneo MJ, London RE, Meiss G. Mutational and biochemical analysis of the DNA-entry nuclease EndA from Streptococcus pneumoniae. Nucleic Acids Res 2010; 39:623-34. [PMID: 20846957 PMCID: PMC3025545 DOI: 10.1093/nar/gkq802] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [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: 01/05/2023] Open
Abstract
EndA is a membrane-attached surface-exposed DNA-entry nuclease previously known to be required for genetic transformation of Streptococcus pneumoniae. More recent studies have shown that the enzyme also plays an important role during the establishment of invasive infections by degrading extracellular chromatin in the form of neutrophil extracellular traps (NETs), enabling streptococci to overcome the innate immune system in mammals. As a virulence factor, EndA has become an interesting target for future drug design. Here we present the first mutational and biochemical analysis of recombinant forms of EndA produced either in a cell-free expression system or in Escherichia coli. We identify His160 and Asn191 to be essential for catalysis and Asn182 to be required for stability of EndA. The role of His160 as the putative general base in the catalytic mechanism is supported by chemical rescue of the H160A variant of EndA with imidazole added in excess. Our study paves the way for the identification and development of protein or low-molecular-weight inhibitors for EndA in future high-throughput screening assays.
Collapse
Affiliation(s)
- Marika Midon
- Institute of Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Mueller GA, Gosavi RA, Krahn JM, Edwards LL, Cuneo MJ, Glesner J, Pomés A, Chapman MD, London RE, Pedersen LC. Der p 5 crystal structure provides insight into the group 5 dust mite allergens. J Biol Chem 2010; 285:25394-401. [PMID: 20534590 DOI: 10.1074/jbc.m110.128306] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Group 5 allergens from house dust mites elicit strong IgE antibody binding in mite-allergic patients. The structure of Der p 5 was determined by x-ray crystallography to better understand the IgE epitopes, to investigate the biologic function in mites, and to compare with the conflicting published Blo t 5 structures, designated 2JMH and 2JRK in the Protein Data Bank. Der p 5 is a three-helical bundle similar to Blo t 5, but the interactions of the helices are more similar to 2JMH than 2JRK. The crystallographic asymmetric unit contains three dimers of Der p 5 that are not exactly alike. Solution scattering techniques were used to assess the multimeric state of Der p 5 in vitro and showed that the predominant state was monomeric, similar to Blo t 5, but larger multimeric species are also present. In the crystal, the formation of the Der p 5 dimer creates a large hydrophobic cavity of approximately 3000 A(3) that could be a ligand-binding site. Many allergens are known to bind hydrophobic ligands, which are thought to stimulate the innate immune system and have adjuvant-like effects on IgE-mediated inflammatory responses.
Collapse
Affiliation(s)
- Geoffrey A Mueller
- Laboratory of Structural Biology, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Abstract
The dimerization of HIV reverse transcriptase (RT), required to obtain the active form of the enzyme, is influenced by mutations, non-nucleoside reverse transcriptase inhibitors (NNRTIs), nucleotide substrates, Mg ions, temperature, and specifically designed dimerization inhibitors. In this study, we have utilized nuclear magnetic resonance (NMR) spectroscopy of the [methyl-(13)C]methionine-labeled enzyme and small-angle X-ray scattering (SAXS) to investigate how several of these factors influence the dimerization behavior of the p51 subunit. The (1)H-(13)C HSQC spectrum of p51 obtained at micromolar concentrations indicates that a significant fraction of the p51 adopts a "p66-like" conformation. SAXS data obtained for p51 samples were used to determine the fractions of monomer and dimer in the sample and to evaluate the conformation of the fingers/thumb subdomain. All of the p51 monomer observed was found to adopt the compact, "p51C" conformation observed for the p51 subunit in the RT heterodimer. The NMR and SAXS data indicate that the p51 homodimer adopts a structure that is similar to the p66/p51 heterodimer, with one p51C subunit and a second p51 subunit in an extended, "p51E" conformation that resembles the p66 subunit of the heterodimer. The fractional dimer concentration and the fingers/thumb orientation are found to depend strongly on the experimental conditions and exhibit a qualitative dependence on nevirapine and ionic strength (KCl) that is similar to the behavior reported for the heterodimer and the p66 homodimer. The L289K mutation interferes with p51 homodimer formation as it does with formation of the heterodimer, despite its location far from the dimer interface. This effect is readily interpreted in terms of a conformational selection model, in which p51(L289K) has a much greater preference for the compact, p51C conformation. A reduced level of dimer formation then results from the reduced ratio of the p51E(L289K) to p51C(L289K) monomers.
Collapse
Affiliation(s)
- Xunhai Zheng
- Laboratory of Structural Biology, MR-01, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | | | | | | | | |
Collapse
|
44
|
McCormack T, Petrovich RM, Mercier KA, DeRose EF, Cuneo MJ, Williams J, Johnson KL, Lamb PW, London RE, Yakel JL. Identification and functional characterization of a novel acetylcholine-binding protein from the marine annelid Capitella teleta. Biochemistry 2010; 49:2279-87. [PMID: 20136097 DOI: 10.1021/bi902023y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [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
We identified a homologue of the molluscan acetylcholine-binding protein (AChBP) in the marine polychaete Capitella teleta, from the annelid phylum. The amino acid sequence of C. teleta AChBP (ct-AChBP) is 21-30% identical with those of known molluscan AChBPs. Sequence alignments indicate that ct-AChBP has a shortened Cys loop compared to other Cys loop receptors, and a variation on a conserved Cys loop triad, which is associated with ligand binding in other AChBPs and nicotinic ACh receptor (nAChR) alpha subunits. Within the D loop of ct-AChBP, a conserved aromatic residue (Tyr or Trp) in nAChRs and molluscan AChBPs, which has been implicated directly in ligand binding, is substituted with an isoleucine. Mass spectrometry results indicate that Asn122 and Asn216 of ct-AChBP are glycosylated when expressed using HEK293 cells. Small-angle X-ray scattering data suggest that the overall shape of ct-AChBP in the apo or unliganded state is similar to that of homologues with known pentameric crystal structures. NMR experiments show that acetylcholine, nicotine, and alpha-bungarotoxin bind to ct-AChBP with high affinity, with K(D) values of 28.7 microM, 209 nM, and 110 nM, respectively. Choline bound with a lower affinity (K(D) = 163 microM). Our finding of a functional AChBP in a marine annelid demonstrates that AChBPs may exhibit variations in hallmark motifs such as ligand-binding residues and Cys loop length and shows conclusively that this neurotransmitter binding protein is not limited to the phylum Mollusca.
Collapse
Affiliation(s)
- Thomas McCormack
- Laboratory of Neurobiology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, P.O. Box 12233, Research Triangle Park, North Carolina 27709, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Cuneo MJ, Beese LS, Hellinga HW. Structural analysis of semi-specific oligosaccharide recognition by a cellulose-binding protein of thermotoga maritima reveals adaptations for functional diversification of the oligopeptide periplasmic binding protein fold. J Biol Chem 2009; 284:33217-23. [PMID: 19801540 PMCID: PMC2785164 DOI: 10.1074/jbc.m109.041624] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [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: 07/06/2009] [Revised: 09/10/2009] [Indexed: 11/06/2022] Open
Abstract
Periplasmic binding proteins (PBPs) constitute a protein superfamily that binds a wide variety of ligands. In prokaryotes, PBPs function as receptors for ATP-binding cassette or tripartite ATP-independent transporters and chemotaxis systems. In many instances, PBPs bind their cognate ligands with exquisite specificity, distinguishing, for example, between sugar epimers or structurally similar anions. By contrast, oligopeptide-binding proteins bind their ligands through interactions with the peptide backbone but do not distinguish between different side chains. The extremophile Thermotoga maritima possesses a remarkable array of carbohydrate-processing metabolic systems, including the hydrolysis of cellulosic polymers. Here, we present the crystal structure of a T. maritima cellobiose-binding protein (tm0031) that is homologous to oligopeptide-binding proteins. T. maritima cellobiose-binding protein binds a variety of lengths of beta(1-->4)-linked glucose oligomers, ranging from two rings (cellobiose) to five (cellopentaose). The structure reveals that binding is semi-specific. The disaccharide at the nonreducing end binds specifically; the other rings are located in a large solvent-filled groove, where the reducing end makes several contacts with the protein, thereby imposing an upper limit of the oligosaccharides that are recognized. Semi-specific recognition, in which a molecular class rather than individual species is selected, provides an efficient solution for the uptake of complex mixtures.
Collapse
Affiliation(s)
- Matthew J. Cuneo
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
| | - Lorena S. Beese
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
| | - Homme W. Hellinga
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
| |
Collapse
|
46
|
Cuneo MJ, Changela A, Beese LS, Hellinga HW. Structural Adaptations that Modulate Monosaccharide, Disaccharide, and Trisaccharide Specificities in Periplasmic Maltose-Binding Proteins. J Mol Biol 2009; 389:157-66. [DOI: 10.1016/j.jmb.2009.04.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 04/02/2009] [Accepted: 04/03/2009] [Indexed: 11/25/2022]
|
47
|
Cuneo MJ, Beese LS, Hellinga HW. Ligand-induced conformational changes in a thermophilic ribose-binding protein. BMC Struct Biol 2008; 8:50. [PMID: 19019243 PMCID: PMC2630998 DOI: 10.1186/1472-6807-8-50] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Accepted: 11/19/2008] [Indexed: 01/07/2023]
Abstract
BACKGROUND Members of the periplasmic binding protein (PBP) superfamily are involved in transport and signaling processes in both prokaryotes and eukaryotes. Biological responses are typically mediated by ligand-induced conformational changes in which the binding event is coupled to a hinge-bending motion that brings together two domains in a closed form. In all PBP-mediated biological processes, downstream partners recognize the closed form of the protein. This motion has also been exploited in protein engineering experiments to construct biosensors that transduce ligand binding to a variety of physical signals. Understanding the mechanistic details of PBP conformational changes, both global (hinge bending, twisting, shear movements) and local (rotamer changes, backbone motion), therefore is not only important for understanding their biological function but also for protein engineering experiments. RESULTS Here we present biochemical characterization and crystal structure determination of the periplasmic ribose-binding protein (RBP) from the hyperthermophile Thermotoga maritima in its ribose-bound and unliganded state. The T. maritima RBP (tmRBP) has 39% sequence identity and is considerably more resistant to thermal denaturation (app Tm value is 108 degrees C) than the mesophilic Escherichia coli homolog (ecRBP) (app Tm value is 56 degrees C). Polar ligand interactions and ligand-induced global conformational changes are conserved among ecRBP and tmRBP; however local structural rearrangements involving side-chain motions in the ligand-binding site are not conserved. CONCLUSION Although the large-scale ligand-induced changes are mediated through similar regions, and are produced by similar backbone movements in tmRBP and ecRBP, the small-scale ligand-induced structural rearrangements differentiate the mesophile and thermophile. This suggests there are mechanistic differences in the manner by which these two proteins bind their ligands and are an example of how two structurally similar proteins utilize different mechanisms to form a ligand-bound state.
Collapse
Affiliation(s)
- Matthew J Cuneo
- The Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710, USA
| | - Lorena S Beese
- The Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710, USA
| | - Homme W Hellinga
- The Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710, USA
| |
Collapse
|
48
|
Cuneo MJ, Changela A, Miklos AE, Beese LS, Krueger JK, Hellinga HW. Structural analysis of a periplasmic binding protein in the tripartite ATP-independent transporter family reveals a tetrameric assembly that may have a role in ligand transport. J Biol Chem 2008; 283:32812-20. [PMID: 18723845 DOI: 10.1074/jbc.m803595200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Several bacterial solute transport mechanisms involve members of the periplasmic binding protein (PBP) superfamily that bind and deliver ligand to integral membrane transport proteins in the ATP-binding cassette, tripartite tricarboxylate transporter, or tripartite ATP-independent (TRAP) families. PBPs involved in ATP-binding cassette transport systems have been well characterized, but only a few PBPs involved in TRAP transport have been studied. We have measured the thermal stability, determined the oligomerization state by small angle x-ray scattering, and solved the x-ray crystal structure to 1.9 A resolution of a TRAP-PBP (open reading frame tm0322) from the hyperthermophilic bacterium Thermotoga maritima (TM0322). The overall fold of TM0322 is similar to other TRAP transport related PBPs, although the structural similarity of backbone atoms (2.5-3.1 A root mean square deviation) is unusually low for PBPs within the same group. Individual monomers within the tetrameric asymmetric unit of TM0322 exhibit high root mean square deviation (0.9 A) to each other as a consequence of conformational heterogeneity in their binding pockets. The gel filtration elution profile and the small angle x-ray scattering analysis indicate that TM0322 assembles as dimers in solution that in turn assemble into a dimer of dimers in the crystallographic asymmetric unit. Tetramerization has been previously observed in another TRAP-PBP (the Rhodobacter sphaeroides alpha-keto acid-binding protein) where quaternary structure formation is postulated to be an important requisite for the transmembrane transport process.
Collapse
Affiliation(s)
- Matthew J Cuneo
- Department of Biochemistry, Duke University, Medical Center, Durham, North Carolina 27710, USA
| | | | | | | | | | | |
Collapse
|
49
|
Cuneo MJ, Tian Y, Allert M, Hellinga HW. The backbone structure of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein is essentially identical to its mesophilic E. coli homolog. BMC Struct Biol 2008; 8:20. [PMID: 18373848 PMCID: PMC2315655 DOI: 10.1186/1472-6807-8-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Accepted: 03/28/2008] [Indexed: 11/16/2022]
Abstract
Background Comparison of experimentally determined mesophilic and thermophilic homologous protein structures is an important tool for understanding the mechanisms that contribute to thermal stability. Of particular interest are pairs of homologous structures that are structurally very similar, but differ significantly in thermal stability. Results We report the X-ray crystal structure of a Thermoanaerobacter tengcongensis ribose binding protein (tteRBP) determined to 1.9 Å resolution. We find that tteRBP is significantly more stable (appTm value ~102°C) than the mesophilic Escherichia coli ribose binding protein (ecRBP) (appTm value ~56°C). The tteRBP has essentially the identical backbone conformation (0.41 Å RMSD of 235/271 Cα positions and 0.65 Å RMSD of 270/271 Cα positions) as ecRBP. Classification of the amino acid substitutions as a function of structure therefore allows the identification of amino acids which potentially contribute to the observed thermal stability of tteRBP in the absence of large structural heterogeneities. Conclusion The near identity of backbone structures of this pair of proteins entails that the significant differences in their thermal stabilities are encoded exclusively by the identity of the amino acid side-chains. Furthermore, the degree of sequence divergence is strongly correlated with structure; with a high degree of conservation in the core progressing to increased diversity in the boundary and surface regions. Different factors that may possibly contribute to thermal stability appear to be differentially encoded in each of these regions of the protein. The tteRBP/ecRBP pair therefore offers an opportunity to dissect contributions to thermal stability by side-chains alone in the absence of large structural differences.
Collapse
Affiliation(s)
- Matthew J Cuneo
- The Institute for Biological Structure and Design and the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, 27710, USA.
| | | | | | | |
Collapse
|
50
|
Tian Y, Cuneo MJ, Changela A, Höcker B, Beese LS, Hellinga HW. Structure-based design of robust glucose biosensors using a Thermotoga maritima periplasmic glucose-binding protein. Protein Sci 2007; 16:2240-50. [PMID: 17766373 PMCID: PMC2204141 DOI: 10.1110/ps.072969407] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [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: 12/22/2022]
Abstract
We report the design and engineering of a robust, reagentless fluorescent glucose biosensor based on the periplasmic glucose-binding protein obtained from Thermotoga maritima (tmGBP). The gene for this protein was cloned from genomic DNA and overexpressed in Escherichia coli, the identity of its cognate sugar was confirmed, ligand binding was studied, and the structure of its glucose complex was solved to 1.7 Angstrom resolution by X-ray crystallography. TmGBP is specific for glucose and exhibits high thermostability (midpoint of thermal denaturation is 119 +/- 1 degrees C and 144 +/- 2 degrees C in the absence and presence of 1 mM glucose, respectively). A series of fluorescent conjugates was constructed by coupling single, environmentally sensitive fluorophores to unique cysteines introduced by site-specific mutagenesis at positions predicted to be responsive to ligand-induced conformational changes based on the structure. These conjugates were screened to identify engineered tmGBPs that function as reagentless fluorescent glucose biosensors. The Y13C*Cy5 conjugate is bright, gives a large response to glucose over concentration ranges appropriate for in vivo monitoring of blood glucose levels (1-30 mM), and can be immobilized in an orientation-specific manner in microtiter plates to give a reversible response to glucose. The immobilized protein retains its response after long-term storage at room temperature.
Collapse
Affiliation(s)
- Yaji Tian
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
| | | | | | | | | | | |
Collapse
|