1
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Whitley MJ, Tran TH, Rigby M, Yi M, Dharmaiah S, Waybright TJ, Ramakrishnan N, Perkins S, Taylor T, Messing S, Esposito D, Nissley DV, McCormick F, Stephen AG, Turbyville T, Cornilescu G, Simanshu DK. Comparative analysis of KRAS4a and KRAS4b splice variants reveals distinctive structural and functional properties. Sci Adv 2024; 10:eadj4137. [PMID: 38354232 DOI: 10.1126/sciadv.adj4137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
KRAS, the most frequently mutated oncogene in human cancer, produces two isoforms, KRAS4a and KRAS4b, through alternative splicing. These isoforms differ in exon 4, which encodes the final 15 residues of the G-domain and hypervariable regions (HVRs), vital for trafficking and membrane localization. While KRAS4b has been extensively studied, KRAS4a has been largely overlooked. Our multidisciplinary study compared the structural and functional characteristics of KRAS4a and KRAS4b, revealing distinct structural properties and thermal stability. Position 151 influences KRAS4a's thermal stability, while position 153 affects binding to RAF1 CRD protein. Nuclear magnetic resonance analysis identified localized structural differences near sequence variations and provided a solution-state conformational ensemble. Notably, KRAS4a exhibits substantial transcript abundance in bile ducts, liver, and stomach, with transcript levels approaching KRAS4b in the colon and rectum. Functional disparities were observed in full-length KRAS variants, highlighting the impact of HVR variations on interaction with trafficking proteins and downstream effectors like RAF and PI3K within cells.
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Affiliation(s)
- Matthew J Whitley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Timothy H Tran
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Megan Rigby
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ming Yi
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Srisathiyanarayanan Dharmaiah
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Timothy J Waybright
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nitya Ramakrishnan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shelley Perkins
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Troy Taylor
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd Street, San Francisco, CA, USA
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Thomas Turbyville
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Gabriel Cornilescu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
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2
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Cornilescu G. 1D and 2D NMR for KRAS:Ligand Binding. Methods Mol Biol 2024; 2797:115-124. [PMID: 38570456 DOI: 10.1007/978-1-0716-3822-4_9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Fragment-based screening by ligand-observed 1D NMR and binding interface mapping by protein-observed 2D NMR are popular methods used in drug discovery. These methods allow researchers to detect compound binding over a wide range of affinities and offer a simultaneous assessment of solubility, purity, and chemical formula accuracy of the target compounds and the 15N-labeled protein when examined by 1D and 2D NMR, respectively. These methods can be applied for screening fragment binding to the active (GMPPNP-bound) and inactive (GDP-bound) states of oncogenic KRAS mutants.
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Affiliation(s)
- Gabriel Cornilescu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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3
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Chao FA, Chan AH, Dharmaiah S, Schwieters CD, Tran TH, Taylor T, Ramakrishnan N, Esposito D, Nissley DV, McCormick F, Simanshu DK, Cornilescu G. Reduced dynamic complexity allows structure elucidation of an excited state of KRAS G13D. Commun Biol 2023; 6:594. [PMID: 37268708 DOI: 10.1038/s42003-023-04960-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 05/19/2023] [Indexed: 06/04/2023] Open
Abstract
Localized dynamics of RAS, including regions distal to the nucleotide-binding site, is of high interest for elucidating the mechanisms by which RAS proteins interact with effectors and regulators and for designing inhibitors. Among several oncogenic mutants, methyl relaxation dispersion experiments reveal highly synchronized conformational dynamics in the active (GMPPNP-bound) KRASG13D, which suggests an exchange between two conformational states in solution. Methyl and 31P NMR spectra of active KRASG13D in solution confirm a two-state ensemble interconverting on the millisecond timescale, with a major Pγ atom peak corresponding to the dominant State 1 conformation and a secondary peak indicating an intermediate state different from the known State 2 conformation recognized by RAS effectors. High-resolution crystal structures of active KRASG13D and KRASG13D-RAF1 RBD complex provide snapshots of the State 1 and 2 conformations, respectively. We use residual dipolar couplings to solve and cross-validate the structure of the intermediate state of active KRASG13D, showing a conformation distinct from those of States 1 and 2 outside the known flexible switch regions. The dynamic coupling between the conformational exchange in the effector lobe and the breathing motion in the allosteric lobe is further validated by a secondary mutation in the allosteric lobe, which affects the conformational population equilibrium.
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Affiliation(s)
- Fa-An Chao
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA.
| | - Albert H Chan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
| | - Srisathiyanarayanan Dharmaiah
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
| | - Charles D Schwieters
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Building 12A, 20892-5624, Bethesda, MD, USA
| | - Timothy H Tran
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
| | - Troy Taylor
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
| | - Nitya Ramakrishnan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd Street, San Francisco, CA, 94158, USA
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA.
| | - Gabriel Cornilescu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD, 21701, USA.
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4
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Chao FA, Dharmaiah S, Taylor T, Messing S, Gillette W, Esposito D, Nissley DV, McCormick F, Byrd RA, Simanshu DK, Cornilescu G. Insights into the Cross Talk between Effector and Allosteric Lobes of KRAS from Methyl Conformational Dynamics. J Am Chem Soc 2022; 144:4196-4205. [PMID: 35213144 PMCID: PMC10430694 DOI: 10.1021/jacs.2c00007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 12/21/2022]
Abstract
KRAS is the most frequently mutated RAS protein in cancer patients, and it is estimated that about 20% of the cancer patients in the United States carried mutant RAS proteins. To accelerate therapeutic development, structures and dynamics of RAS proteins had been extensively studied by various biophysical techniques for decades. Although 31P NMR studies revealed population equilibrium of the two major states in the active GMPPNP-bound form, more complex conformational dynamics in RAS proteins and oncogenic mutants subtly modulate the interactions with their downstream effectors. We established a set of customized NMR relaxation dispersion techniques to efficiently and systematically examine the ms-μs conformational dynamics of RAS proteins. This method allowed us to observe varying synchronized motions that connect the effector and allosteric lobes in KRAS. We demonstrated the role of conformational dynamics of KRAS in controlling its interaction with the Ras-binding domain of the downstream effector RAF1, the first kinase in the MAPK pathway. This allows one to explain, as well as to predict, the altered binding affinities of various KRAS mutants, which was neither previously reported nor apparent from the structural perspective.
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Affiliation(s)
- Fa-An Chao
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland 21701, United States
| | - Srisathiyanarayanan Dharmaiah
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland 21701, United States
| | - Troy Taylor
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland 21701, United States
| | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland 21701, United States
| | - William Gillette
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland 21701, United States
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland 21701, United States
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland 21701, United States
| | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd Street, San Francisco, California 94158, United States
| | - R Andrew Byrd
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland 21701, United States
| | - Gabriel Cornilescu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland 21701, United States
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5
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Smith KP, Lee W, Tonelli M, Lee Y, Light SH, Cornilescu G, Chakravarthy S. Solution structure and dynamics of the mitochondrial-targeted GTPase-activating protein (GAP) VopE by an integrated NMR/SAXS approach. Protein Sci 2022; 31:e4282. [PMID: 35137487 PMCID: PMC9047041 DOI: 10.1002/pro.4282] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/17/2022] [Accepted: 01/27/2022] [Indexed: 11/11/2022]
Abstract
The bacterial pathogen Vibrio cholerae use a type III secretion system to inject effector proteins into a host cell. Recently, a putative Toxic GTPase Activating Protein (ToxGAP) called VopE was identified as a T3SS substrate and virulence factor that affected host mitochondrial dynamics and immune response. However, biophysical and structural characterization has been absent. Here, we describe solution NMR structure of the putative GAP domain (73-204) of VopE. Using SEC-SAXS and RDC data, we restrained the MD process to efficiently determine the overall fold and improve the quality of the output calculated structures. Comparing the structure of VopE with other ToxGAP's revealed a similar overall fold with several features unique to VopE. Specifically, the "Bulge 1", α1 helix, and noteworthy "backside linker" elements on the N-terminus are dissimilar to the other ToxGAP's. By using NMR relaxation dispersion experiments, we demonstrate that these regions undergo motions on a >6 s-1 timescale. Based on the disposition of these mobile regions relative to the putative catalytic arginine residue, we hypothesize the protein may undergo structural changes to bind cognate GTPases. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Kyle P Smith
- Current, Xilio Therapeutics, Waltham, MA, USA.,Former, Department of Cell & Developmental Biology, Northwestern University Chicago, IL, USA
| | - Woonghee Lee
- Department of Chemistry, University of Colorado-Denver, Denver, CO, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Yeongjoon Lee
- Department of Chemistry, University of Colorado-Denver, Denver, CO, USA
| | - Samuel H Light
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Gabriel Cornilescu
- Advanced Technology Research Facility, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., National Cancer Institute, National Institutes of Health, Frederick, MD, USA
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6
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Evans CM, Phillips M, Malone KL, Tonelli M, Cornilescu G, Cornilescu C, Holton SJ, Gorjánácz M, Wang L, Carlson S, Gay JC, Nix JC, Demeler B, Markley JL, Glass KC. Coordination of Di-Acetylated Histone Ligands by the ATAD2 Bromodomain. Int J Mol Sci 2021; 22:9128. [PMID: 34502039 PMCID: PMC8430952 DOI: 10.3390/ijms22179128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 07/26/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 12/15/2022] Open
Abstract
The ATPase Family, AAA domain-containing protein 2 (ATAD2) bromodomain (BRD) has a canonical bromodomain structure consisting of four α-helices. ATAD2 functions as a co-activator of the androgen and estrogen receptors as well as the MYC and E2F transcription factors. ATAD2 also functions during DNA replication, recognizing newly synthesized histones. In addition, ATAD2 is shown to be up-regulated in multiple forms of cancer including breast, lung, gastric, endometrial, renal, and prostate. Furthermore, up-regulation of ATAD2 is strongly correlated with poor prognosis in many types of cancer, making the ATAD2 bromodomain an innovative target for cancer therapeutics. In this study, we describe the recognition of histone acetyllysine modifications by the ATAD2 bromodomain. Residue-specific information on the complex formed between the histone tail and the ATAD2 bromodomain, obtained through nuclear magnetic resonance spectroscopy (NMR) and X-ray crystallography, illustrates key residues lining the binding pocket, which are involved in coordination of di-acetylated histone tails. Analytical ultracentrifugation, NMR relaxation data, and isothermal titration calorimetry further confirm the monomeric state of the functionally active ATAD2 bromodomain in complex with di-acetylated histone ligands. Overall, we describe histone tail recognition by ATAD2 BRD and illustrate that one acetyllysine group is primarily engaged by the conserved asparagine (N1064), the "RVF" shelf residues, and the flexible ZA loop. Coordination of a second acetyllysine group also occurs within the same binding pocket but is essentially governed by unique hydrophobic and electrostatic interactions making the di-acetyllysine histone coordination more specific than previously presumed.
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Affiliation(s)
- Chiara M. Evans
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
| | - Margaret Phillips
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Kiera L. Malone
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.T.); (G.C.); (C.C.); (J.L.M.)
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.T.); (G.C.); (C.C.); (J.L.M.)
| | - Claudia Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.T.); (G.C.); (C.C.); (J.L.M.)
| | - Simon J. Holton
- Bayer AG, Pharmaceuticals, Research & Early Development Oncology, 13353 Berlin, Germany; (S.J.H.); (M.G.)
| | - Mátyás Gorjánácz
- Bayer AG, Pharmaceuticals, Research & Early Development Oncology, 13353 Berlin, Germany; (S.J.H.); (M.G.)
| | - Liping Wang
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (L.W.); (B.D.)
| | - Samuel Carlson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
| | - Jamie C. Gay
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
| | - Jay C. Nix
- Molecular Biology Consortium, Advanced Light Source, Berkeley, CA 94720, USA;
| | - Borries Demeler
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (L.W.); (B.D.)
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - John L. Markley
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.T.); (G.C.); (C.C.); (J.L.M.)
| | - Karen C. Glass
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
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7
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Lloyd JT, McLaughlin K, Lubula MY, Gay JC, Dest A, Gao C, Phillips M, Tonelli M, Cornilescu G, Marunde MR, Evans CM, Boyson SP, Carlson S, Keogh MC, Markley JL, Frietze S, Glass KC. Structural Insights into the Recognition of Mono- and Diacetylated Histones by the ATAD2B Bromodomain. J Med Chem 2020; 63:12799-12813. [PMID: 33084328 DOI: 10.1021/acs.jmedchem.0c01178] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Bromodomains exhibit preferences for specific patterns of post-translational modifications on core and variant histone proteins. We examined the ligand specificity of the ATAD2B bromodomain and compared it to its closely related paralogue in ATAD2. We show that the ATAD2B bromodomain recognizes mono- and diacetyllysine modifications on histones H4 and H2A. A structure-function approach was used to identify key residues in the acetyllysine-binding pocket that dictate the molecular recognition process, and we examined the binding of an ATAD2 bromodomain inhibitor by ATAD2B. Our analysis demonstrated that critical contacts required for bromodomain inhibitor coordination are conserved between the ATAD2/B bromodomains, with many residues playing a dual role in acetyllysine recognition. We further characterized an alternative splice variant of ATAD2B that results in a loss of function. Our results outline the structural and functional features of the ATAD2B bromodomain and identify a novel mechanism regulating the interaction of the ATAD2B protein with chromatin.
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Affiliation(s)
- Jonathan T Lloyd
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, United States
| | - Kyle McLaughlin
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont 05405, United States
| | - Mulu Y Lubula
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, United States
| | - Jamie C Gay
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, United States
| | - Andrea Dest
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont 05405, United States
| | - Cong Gao
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont 05405, United States
| | - Margaret Phillips
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, United States
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison and Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison and Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | | | - Chiara M Evans
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, United States
| | - Samuel P Boyson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, United States
| | - Samuel Carlson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, United States
| | | | - John L Markley
- National Magnetic Resonance Facility at Madison and Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont 05405, United States
| | - Karen C Glass
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 261 Mountain View Drive, Colchester, Vermont 05446, United States
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8
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Lee W, Tonelli M, Frederick RO, Haruta M, Cornilescu G, Cornilescu CC, Sussman MR, Markley JL. Solution Structure Determination of Arabidopsis Thaliana RALF8 Illustrates the use of Cutting-Edge Software Developed at the National Magnetic Resonance Facility at Madison. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.514] [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: 10/25/2022] Open
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9
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Yang Y, Lin J, Harrington A, Cornilescu G, Lau GW, Tal-Gan Y. Designing cyclic competence-stimulating peptide (CSP) analogs with pan-group quorum-sensing inhibition activity in Streptococcus pneumoniae. Proc Natl Acad Sci U S A 2020; 117:1689-1699. [PMID: 31915298 PMCID: PMC6983377 DOI: 10.1073/pnas.1915812117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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] [Indexed: 12/15/2022] Open
Abstract
Streptococcus pneumoniae is an opportunistic human pathogen that utilizes the competence regulon, a quorum-sensing circuitry, to acquire antibiotic resistance genes and initiate its attack on the human host. Interception of the competence regulon can therefore be utilized to study S. pneumoniae cell-cell communication and behavioral changes, as well as attenuate S. pneumoniae infectivity. Herein we report the design and synthesis of cyclic dominant negative competence-stimulating peptide (dnCSP) analogs capable of intercepting the competence regulon in both S. pneumoniae specificity groups with activities at the low nanomolar range. Structural analysis of lead analogs provided important insights as to the molecular mechanism that drives CSP receptor binding and revealed that the pan-group cyclic CSPs exhibit a chimeric hydrophobic patch conformation that resembles the hydrophobic patches required for both ComD1 and ComD2 binding. Moreover, the lead cyclic dnCSP, CSP1-E1A-cyc(Dap6E10), was found to possess superior pharmacological properties, including improved resistance to enzymatic degradation, while remaining nontoxic. Lastly, CSP1-E1A-cyc(Dap6E10) was capable of attenuating mouse mortality during acute pneumonia caused by both group 1 and group 2 S. pneumoniae strains. This cyclic pan-group dnCSP is therefore a promising drug lead scaffold against S. pneumoniae infections that could be administered individually or utilized in combination therapy to augment the effects of current antimicrobial agents.
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Affiliation(s)
- Yifang Yang
- Department of Chemistry, University of Nevada, Reno, Reno, NV 89557
| | - Jingjun Lin
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL 61802
| | | | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706
| | - Gee W Lau
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL 61802;
| | - Yftah Tal-Gan
- Department of Chemistry, University of Nevada, Reno, Reno, NV 89557;
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10
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Vasquez JK, West KHJ, Yang T, Polaske TJ, Cornilescu G, Tonelli M, Blackwell HE. Conformational Switch to a β-Turn in a Staphylococcal Quorum Sensing Signal Peptide Causes a Dramatic Increase in Potency. J Am Chem Soc 2020; 142:750-761. [PMID: 31859506 DOI: 10.1021/jacs.9b05513] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We report the solution-phase structures of native signal peptides and related analogs capable of either strongly agonizing or antagonizing the AgrC quorum sensing (QS) receptor in the emerging pathogen Staphylococcus epidermidis. Chronic S. epidermidis infections are often recalcitrant to traditional therapies due to antibiotic resistance and formation of robust biofilms. The accessory gene regulator (agr) QS system plays an important role in biofilm formation in this opportunistic pathogen, and the binding of an autoinducing peptide (AIP) signal to its cognate transmembrane receptor (AgrC) is responsible for controlling agr. Small molecules or peptides capable of modulating this binding event are of significant interest as probes to investigate both the agr system and QS as a potential antivirulence target. We used NMR spectroscopy to characterize the structures of the three native S. epidermidis AIP signals and five non-native analogs with distinct activity profiles in the AgrC-I receptor from S. epidermidis. These studies revealed a suite of structural motifs critical for ligand activity. Interestingly, a unique β-turn was present in the macrocycles of the two most potent AgrC-I modulators, in both an agonist and an antagonist, which was distinct from the macrocycle conformation in the less-potent AgrC-I modulators and in the native AIP-I itself. This previously unknown β-turn provides a structural rationale for these ligands' respective biological activity profiles. Development of analogs to reinforce the β-turn resulted in our first antagonist with subnanomolar potency in AgrC-I, while analogs designed to contain a disrupted β-turn were dramatically less potent relative to their parent compounds. Collectively, these studies provide new insights into the AIP:AgrC interactions crucial for QS activation in S. epidermidis and advance the understanding of QS at the molecular level.
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Affiliation(s)
- Joseph K Vasquez
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Korbin H J West
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Tian Yang
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Thomas J Polaske
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Helen E Blackwell
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
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11
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Frederick RO, Haruta M, Tonelli M, Lee W, Cornilescu G, Cornilescu CC, Sussman MR, Markley JL. Function and solution structure of the Arabidopsis thaliana RALF8 peptide. Protein Sci 2019; 28:1115-1126. [PMID: 31004454 PMCID: PMC6511734 DOI: 10.1002/pro.3628] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 02/08/2019] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 12/31/2022]
Abstract
We report the recombinant preparation from Escherichia coli cells of samples of two closely related, small, secreted cysteine-rich plant peptides: rapid alkalinization factor 1 (RALF1) and rapid alkalinization factor 8 (RALF8). Purified samples of the native sequence of RALF8 exhibited well-resolved nuclear magnetic resonance (NMR) spectra and also biological activity through interaction with a plant receptor kinase, cytoplasmic calcium mobilization, and in vivo root growth suppression. By contrast, RALF1 could only be isolated from inclusion bodies as a construct containing an N-terminal His-tag; its poorly resolved NMR spectrum was indicative of aggregation. We prepared samples of the RALF8 peptide labeled with 15 N and 13 C for NMR analysis and obtained near complete 1 H, 13 C, and 15 N NMR assignments; determined the disulfide pairing of its four cysteine residues; and examined its solution structure. RALF8 is mostly disordered except for the two loops spanned by each of its two disulfide bridges.
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Affiliation(s)
- Ronnie O. Frederick
- National Magnetic Resonance Facility at MadisonUniversity of Wisconsin‐MadisonMadisonWisconsin53706
| | - Miyoshi Haruta
- Biotechnology CenterUniversity of Wisconsin‐MadisonMadisonWisconsin53706
| | - Marco Tonelli
- National Magnetic Resonance Facility at MadisonUniversity of Wisconsin‐MadisonMadisonWisconsin53706
| | - Woonghee Lee
- National Magnetic Resonance Facility at MadisonUniversity of Wisconsin‐MadisonMadisonWisconsin53706
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at MadisonUniversity of Wisconsin‐MadisonMadisonWisconsin53706
| | - Claudia C. Cornilescu
- National Magnetic Resonance Facility at MadisonUniversity of Wisconsin‐MadisonMadisonWisconsin53706
| | - Michael R. Sussman
- Biotechnology CenterUniversity of Wisconsin‐MadisonMadisonWisconsin53706
- Department of BiochemistryUniversity of Wisconsin‐MadisonMadisonWisconsin53706
| | - John L. Markley
- National Magnetic Resonance Facility at MadisonUniversity of Wisconsin‐MadisonMadisonWisconsin53706
- Department of BiochemistryUniversity of Wisconsin‐MadisonMadisonWisconsin53706
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12
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Warden MS, Cai K, Cornilescu G, Burke JE, Ponniah K, Butcher SE, Pascal SM. Conformational flexibility in the enterovirus RNA replication platform. RNA 2019; 25:376-387. [PMID: 30578285 PMCID: PMC6380274 DOI: 10.1261/rna.069476.118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/19/2018] [Indexed: 05/06/2023]
Abstract
A presumed RNA cloverleaf (5'CL), located at the 5'-most end of the noncoding region of the enterovirus genome, is the primary established site for initiation of genomic replication. Stem-loop B (SLB) and stem-loop D (SLD), the two largest stem-loops within the 5'CL, serve as recognition sites for protein interactions that are essential for replication. Here we present the solution structure of rhinovirus serotype 14 5'CL using a combination of nuclear magnetic resonance spectroscopy and small-angle X-ray scattering. In the absence of magnesium, the structure adopts an open, somewhat extended conformation. In the presence of magnesium, the structure compacts, bringing SLB and SLD into close contact, a geometry that creates an extensive accessible major groove surface, and permits interaction between the proteins that target each stem-loop.
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Affiliation(s)
- Meghan S Warden
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529, USA
| | - Kai Cai
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Jordan E Burke
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Komala Ponniah
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Steven M Pascal
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529, USA
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13
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Yang Y, Cornilescu G, Tal-Gan Y. Structural Characterization of Competence-Stimulating Peptide Analogues Reveals Key Features for ComD1 and ComD2 Receptor Binding in Streptococcus pneumoniae. Biochemistry 2018; 57:5359-5369. [PMID: 30125091 DOI: 10.1021/acs.biochem.8b00653] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Streptococcus pneumoniae is an important pathogen that utilizes quorum sensing (QS) to regulate genetic transformation, virulence, and biofilm formation. The competence-stimulating peptide (CSP) is a 17-amino acid signal peptide that is used by S. pneumoniae to trigger QS. S. pneumoniae strains can be divided into two main specificity groups based on the CSP signal they produce (CSP1 or CSP2) and their compatible receptors (ComD1 or ComD2, respectively). Modulation of QS in S. pneumoniae can be achieved by targeting the CSP:ComD interaction using synthetic CSP analogues. However, to rationally design CSP-based QS modulators with enhanced activities, an in-depth understanding of the structural features that are required for receptor binding is needed. Herein, we report a comprehensive in-solution three-dimensional structural characterization of eight CSP1 and CSP2 analogues with varied biological activities using nuclear magnetic resonance spectroscopy. Analysis of these structures revealed two distinct hydrophobic patches required for effective ComD1 and ComD2 binding.
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Affiliation(s)
- Yifang Yang
- Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison , University of Wisconsin-Madison , 433 Babcock Drive , Madison , Wisconsin 53706 , United States
| | - Yftah Tal-Gan
- Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States
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14
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Wyche TP, Alvarenga RFR, Piotrowski JS, Duster MN, Warrack SR, Cornilescu G, De Wolfe TJ, Hou Y, Braun DR, Ellis GA, Simpkins SW, Nelson J, Myers CL, Steele J, Mori H, Safdar N, Markley JL, Rajski SR, Bugni TS. Chemical Genomics, Structure Elucidation, and in Vivo Studies of the Marine-Derived Anticlostridial Ecteinamycin. ACS Chem Biol 2017; 12:2287-2295. [PMID: 28708379 DOI: 10.1021/acschembio.7b00388] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A polyether antibiotic, ecteinamycin (1), was isolated from a marine Actinomadura sp., cultivated from the ascidian Ecteinascidia turbinata. 13C enrichment, high resolution NMR spectroscopy, and molecular modeling enabled elucidation of the structure of 1, which was validated on the basis of comparisons with its recently reported crystal structure. Importantly, ecteinamycin demonstrated potent activity against the toxigenic strain of Clostridium difficile NAP1/B1/027 (MIC = 59 ng/μL), as well as other toxigenic and nontoxigenic C. difficile isolates both in vitro and in vivo. Additionally, chemical genomics studies using Escherichia coli barcoded deletion mutants led to the identification of sensitive mutants such as trkA and kdpD involved in potassium cation transport and homeostasis supporting a mechanistic proposal that ecteinamycin acts as an ionophore antibiotic. This is the first antibacterial agent whose mechanism of action has been studied using E. coli chemical genomics. On the basis of these data, we propose ecteinamycin as an ionophore antibiotic that causes C. difficile detoxification and cell death via potassium transport dysregulation.
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Affiliation(s)
- Thomas P. Wyche
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - René F. Ramos Alvarenga
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | | | - Megan N. Duster
- Department
of Medicine, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Simone R. Warrack
- Department
of Medicine, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Gabriel Cornilescu
- National
Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Travis J. De Wolfe
- Department
of Food Science, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Yanpeng Hou
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Doug R. Braun
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Gregory A. Ellis
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Scott W. Simpkins
- Department
of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Justin Nelson
- Department
of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Chad L. Myers
- Department
of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, Minnesota 55455, United States
| | - James Steele
- Department
of Food Science, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Hirotada Mori
- Graduate
School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
| | - Nasia Safdar
- Department
of Medicine, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - John L. Markley
- National
Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Scott R. Rajski
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Tim S. Bugni
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
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15
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Cornilescu G, Ramos Alvarenga RF, Wyche TP, Bugni TS, Gil RR, Cornilescu CC, Westler WM, Markley JL, Schwieters CD. Progressive Stereo Locking (PSL): A Residual Dipolar Coupling Based Force Field Method for Determining the Relative Configuration of Natural Products and Other Small Molecules. ACS Chem Biol 2017; 12:2157-2163. [PMID: 28617580 DOI: 10.1021/acschembio.7b00281] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Establishing the relative configuration of a bioactive natural product represents the most challenging part in determining its structure. Residual dipolar couplings (RDCs) are sensitive probes of the relative spatial orientation of internuclear vectors. We adapted a force field structure calculation methodology to allow free sampling of both R and S configurations of the stereocenters of interest. The algorithm uses a floating alignment tensor in a simulated annealing protocol to identify the conformations and configurations that best fit experimental RDC and distance restraints (from NOE and J-coupling data). A unique configuration (for rigid molecules) or a very small number of configurations (for less rigid molecules) of the structural models having the lowest chiral angle energies and reasonable magnitudes of the alignment tensor are provided as the best predictions of the unknown configuration. For highly flexible molecules, the progressive locking of their stereocenters into their statistically dominant R or S state dramatically reduces the number of possible relative configurations. The result is verified by checking that the same configuration is obtained by initiating the locking from different regions of the molecule. For all molecules tested having known configurations (with conformations ranging from mostly rigid to highly flexible), the method accurately determined the correct configuration.
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Affiliation(s)
| | - René F. Ramos Alvarenga
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Thomas P. Wyche
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Biological
Chemistry and Molecular Pharmacology Department, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Tim S. Bugni
- Pharmaceutical
Sciences Division, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Roberto R. Gil
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | | | | | | | - Charles D. Schwieters
- Center for
Information Technology, National Institutes of Health, Bethesda, Maryland 20892-5624, United States
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16
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Warden MS, Tonelli M, Cornilescu G, Liu D, Hopersberger LJ, Ponniah K, Pascal SM. Structure of RNA Stem Loop B from the Picornavirus Replication Platform. Biochemistry 2017; 56:2549-2557. [PMID: 28459542 DOI: 10.1021/acs.biochem.7b00141] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The presumptive RNA cloverleaf at the start of the 5'-untranslated region of the picornavirus genome is an essential element in replication. Stem loop B (SLB) of the cloverleaf is a recognition site for the host polyC-binding protein, which initiates a switch from translation to replication. Here we present the solution structure of human rhinovirus isotype 14 SLB using nuclear magnetic resonance spectroscopy. SLB adopts a predominantly A-form helical structure. The stem contains five Watson-Crick base pairs and one wobble base pair and is capped by an eight-nucleotide loop. The wobble base pair introduces perturbations into the helical parameters but does not appear to introduce flexibility. However, the helix major groove appears to be accessible. Flexibility is seen throughout the loop and in the terminal nucleotides. The pyrimidine-rich region of the loop, the apparent recognition site for the polyC-binding protein, is the most disordered region of the structure.
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Affiliation(s)
- Meghan S Warden
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Dong Liu
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
| | - Lorelei J Hopersberger
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
| | - Komala Ponniah
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
| | - Steven M Pascal
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
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17
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Vasquez JK, Tal-Gan Y, Cornilescu G, Tyler KA, Blackwell HE. Simplified AIP-II Peptidomimetics Are Potent Inhibitors of Staphylococcus aureus AgrC Quorum Sensing Receptors. Chembiochem 2017; 18:413-423. [PMID: 28006082 DOI: 10.1002/cbic.201600516] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [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: 09/20/2016] [Indexed: 01/13/2023]
Abstract
The bacterial pathogen Staphylococcus aureus controls many aspects of virulence by using the accessory gene regulator (agr) quorum sensing (QS) system. The agr system is activated by a macrocyclic peptide signal known as an autoinducing peptide (AIP). We sought to develop structurally simplified mimetics of AIPs for use as chemical tools to study QS in S. aureus. Herein, we report new peptidomimetic AgrC receptor inhibitors based on a tail-truncated AIP-II peptide that have almost analogous inhibitory activities to the parent peptide. Structural comparison of one of these peptidomimetics to the parent peptide and a highly potent, all-peptide-derived, S. aureus agr inhibitor (AIP-III D4A) revealed a conserved hydrophobic motif and overall amphipathic nature. Our results suggest that the AIP scaffold is amenable to structural mimicry and minimization for the development of synthetic agr inhibitors.
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Affiliation(s)
- Joseph K Vasquez
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA
| | - Yftah Tal-Gan
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA.,Present address: Department of Chemistry, University of Nevada, 1664 N. Virginia Street, Reno, NV, 89557, USA
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Kimberly A Tyler
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI, 53706, USA
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18
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Abstract
Metal ions are critical for RNA structure and enzymatic activity. We present the structure of an asymmetric RNA loop that binds metal ions and has an essential function in a bacteriophage packaging motor. Prohead RNA is a noncoding RNA that is required for genome packaging activity in phi29-like bacteriophage. The loops in GA1 and phi29 bacteriophage share a conserved adenine that forms a base triple, although the structural context for the base triple differs. NMR relaxation studies and femtosecond time-resolved fluorescence spectroscopy reveal the dynamic behavior of the loop in the metal ion bound and unbound forms. The mechanism of metal ion binding appears to be an induced conformational change between two dynamic ensembles rather than a conformational capture mechanism. These results provide experimental benchmarks for computational models of RNA-metal ion interactions.
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Affiliation(s)
- Xiaobo Gu
- Department of Chemistry & Biochemistry and Department of Microbiology & Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Sun-Young Park
- Department of Physics, Ohio State University, Columbus, Ohio 43210, United States
| | - Marco Tonelli
- NMRFAM, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Gabriel Cornilescu
- NMRFAM, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Tianbing Xia
- Department of Molecular and Cell Biology, University of Texas, Dallas, Texas 75080, United States
| | - Dongping Zhong
- Department of Physics, Ohio State University, Columbus, Ohio 43210, United States
| | - Susan J. Schroeder
- Department of Chemistry & Biochemistry and Department of Microbiology & Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
- Corresponding Author.
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19
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Wessel SR, Cornilescu CC, Cornilescu G, Metz A, Leroux M, Hu K, Sandler SJ, Markley JL, Keck JL. Structure and Function of the PriC DNA Replication Restart Protein. J Biol Chem 2016; 291:18384-96. [PMID: 27382050 DOI: 10.1074/jbc.m116.738781] [Citation(s) in RCA: 11] [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] [Received: 05/17/2016] [Indexed: 11/06/2022] Open
Abstract
Collisions between DNA replication complexes (replisomes) and barriers such as damaged DNA or tightly bound protein complexes can dissociate replisomes from chromosomes prematurely. Replisomes must be reloaded under these circumstances to avoid incomplete replication and cell death. Bacteria have evolved multiple pathways that initiate DNA replication restart by recognizing and remodeling abandoned replication forks and reloading the replicative helicase. In vitro, the simplest of these pathways is mediated by the single-domain PriC protein, which, along with the DnaC helicase loader, can load the DnaB replicative helicase onto DNA bound by the single-stranded DNA (ssDNA)-binding protein (SSB). Previous biochemical studies have identified PriC residues that mediate interactions with ssDNA and SSB. However, the mechanisms by which PriC drives DNA replication restart have remained poorly defined due to the limited structural information available for PriC. Here, we report the NMR structure of full-length PriC from Cronobacter sakazakii PriC forms a compact bundle of α-helices that brings together residues involved in ssDNA and SSB binding at adjacent sites on the protein surface. Disruption of these interaction sites and of other conserved residues leads to decreased DnaB helicase loading onto SSB-bound DNA. We also demonstrate that PriC can directly interact with DnaB and the DnaB·DnaC complex. These data lead to a model in which PriC acts as a scaffold for recruiting DnaB·DnaC to SSB/ssDNA sites present at stalled replication forks.
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Affiliation(s)
- Sarah R Wessel
- From the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Claudia C Cornilescu
- the National Magnetic Resonance Facility at Madison and the Biochemistry Department, University of Wisconsin, Madison, Wisconsin 53706, and
| | - Gabriel Cornilescu
- the National Magnetic Resonance Facility at Madison and the Biochemistry Department, University of Wisconsin, Madison, Wisconsin 53706, and
| | - Alice Metz
- the Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003
| | - Maxime Leroux
- the Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003
| | - Kaifeng Hu
- the National Magnetic Resonance Facility at Madison and the Biochemistry Department, University of Wisconsin, Madison, Wisconsin 53706, and
| | - Steven J Sandler
- the Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003
| | - John L Markley
- the National Magnetic Resonance Facility at Madison and the Biochemistry Department, University of Wisconsin, Madison, Wisconsin 53706, and
| | - James L Keck
- From the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706,
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20
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Tal-Gan Y, Ivancic M, Cornilescu G, Yang T, Blackwell HE. Highly Stable, Amide-Bridged Autoinducing Peptide Analogues that Strongly Inhibit the AgrC Quorum Sensing Receptor in Staphylococcus aureus. Angew Chem Int Ed Engl 2016; 55:8913-7. [PMID: 27276693 DOI: 10.1002/anie.201602974] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [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: 03/25/2016] [Revised: 05/19/2016] [Indexed: 12/20/2022]
Abstract
Blocking quorum sensing (QS) pathways has attracted considerable interest as an approach to suppress virulence in bacterial pathogens. Toward this goal, we recently developed analogues of a native autoinducing peptide (AIP-III) signal that can inhibit AgrC-type QS receptors and attenuate virulence phenotypes in Staphylococcus aureus. Application of these compounds is limited, however, as they contain hydrolytically unstable thioester linkages and have only low aqueous solubilities. Herein, we report amide-linked AIP analogues with greatly enhanced hydrolytic stabilities and solubilities relative to our prior analogues, whilst maintaining strong potencies as AgrC receptor inhibitors in S. aureus. These compounds represent powerful tools for the study of QS.
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Affiliation(s)
- Yftah Tal-Gan
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
- Current address: Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia St., Reno, NV, 89557, USA
| | - Monika Ivancic
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
- Current address: Department of Chemistry, University of Vermont, 82 University Pl., Burlington, VT, 05405, USA
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility, University of Wisconsin-Madison, 433 Babcock Dr., Madison, WI, 53706, USA
| | - Tian Yang
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA.
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21
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Tal-Gan Y, Ivancic M, Cornilescu G, Yang T, Blackwell HE. Highly Stable, Amide-Bridged Autoinducing Peptide Analogues that Strongly Inhibit the AgrC Quorum Sensing Receptor inStaphylococcus aureus. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602974] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yftah Tal-Gan
- Department of Chemistry; University of Wisconsin-Madison; 1101 University Ave. Madison WI 53706 USA
- Current address: Department of Chemistry; University of Nevada, Reno; 1664 N. Virginia St. Reno NV 89557 USA
| | - Monika Ivancic
- Department of Chemistry; University of Wisconsin-Madison; 1101 University Ave. Madison WI 53706 USA
- Current address: Department of Chemistry; University of Vermont; 82 University Pl. Burlington VT 05405 USA
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility; University of Wisconsin-Madison; 433 Babcock Dr. Madison WI 53706 USA
| | - Tian Yang
- Department of Chemistry; University of Wisconsin-Madison; 1101 University Ave. Madison WI 53706 USA
| | - Helen E. Blackwell
- Department of Chemistry; University of Wisconsin-Madison; 1101 University Ave. Madison WI 53706 USA
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Kim S, Natesan S, Cornilescu G, Carlson S, Tonelli M, McClurg UL, Binda O, Robson CN, Markley JL, Balaz S, Glass KC. Mechanism of Histone H3K4me3 Recognition by the Plant Homeodomain of Inhibitor of Growth 3. J Biol Chem 2016; 291:18326-41. [PMID: 27281824 PMCID: PMC5000080 DOI: 10.1074/jbc.m115.690651] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Indexed: 12/23/2022] Open
Abstract
Aberrant access to genetic information disrupts cellular homeostasis and can lead to cancer development. One molecular mechanism that regulates access to genetic information includes recognition of histone modifications, which is carried out by protein modules that interact with chromatin and serve as landing pads for enzymatic activities that regulate gene expression. The ING3 tumor suppressor protein contains a plant homeodomain (PHD) that reads the epigenetic code via recognition of histone H3 tri-methylated at lysine 4 (H3K4me3), and this domain is lost or mutated in various human cancers. However, the molecular mechanisms targeting ING3 to histones and the role of this interaction in the cell remain elusive. Thus, we employed biochemical and structural biology approaches to investigate the interaction of the ING3 PHD finger (ING3PHD) with the active transcription mark H3K4me3. Our results demonstrate that association of the ING3PHD with H3K4me3 is in the sub-micromolar range (KD ranging between 0.63 and 0.93 μm) and is about 200-fold stronger than with the unmodified histone H3. NMR and computational studies revealed an aromatic cage composed of Tyr-362, Ser-369, and Trp-385 that accommodate the tri-methylated side chain of H3K4. Mutational analysis confirmed the critical importance of Tyr-362 and Trp-385 in mediating the ING3PHD-H3K4me3 interaction. Finally, the biological relevance of ING3PHD-H3K4me3 binding was demonstrated by the failure of ING3PHD mutant proteins to enhance ING3-mediated DNA damage-dependent cell death. Together, our results reveal the molecular mechanism of H3K4me3 selection by the ING3PHD and suggest that this interaction is important for mediating ING3 tumor suppressive activities.
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Affiliation(s)
- Sophia Kim
- From the Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, Vermont 05446
| | - Senthil Natesan
- From the Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, Vermont 05446
| | - Gabriel Cornilescu
- the National Magnetic Resonance Facility at Madison and Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, and
| | - Samuel Carlson
- From the Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, Vermont 05446
| | - Marco Tonelli
- the National Magnetic Resonance Facility at Madison and Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, and
| | - Urszula L McClurg
- the Newcastle Cancer Centre at the Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne NE2 4HH, United Kingdom
| | - Olivier Binda
- the Newcastle Cancer Centre at the Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne NE2 4HH, United Kingdom
| | - Craig N Robson
- the Newcastle Cancer Centre at the Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne NE2 4HH, United Kingdom
| | - John L Markley
- the National Magnetic Resonance Facility at Madison and Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, and
| | - Stefan Balaz
- From the Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, Vermont 05446
| | - Karen C Glass
- From the Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, Vermont 05446,
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Lee W, Petit CM, Cornilescu G, Stark JL, Markley JL. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data. J Biomol NMR 2016; 65:51-7. [PMID: 27169728 PMCID: PMC4921114 DOI: 10.1007/s10858-016-0036-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 05/06/2016] [Indexed: 05/21/2023]
Abstract
We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25 kDa that had 27-98 % sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models.
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Affiliation(s)
- Woonghee Lee
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Chad M Petit
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jaime L Stark
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - John L Markley
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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Lee W, Cornilescu G, Dashti H, Eghbalnia HR, Tonelli M, Westler WM, Butcher SE, Henzler-Wildman KA, Markley JL. Integrative NMR for biomolecular research. J Biomol NMR 2016; 64:307-32. [PMID: 27023095 PMCID: PMC4861749 DOI: 10.1007/s10858-016-0029-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 03/21/2016] [Indexed: 05/05/2023]
Abstract
NMR spectroscopy is a powerful technique for determining structural and functional features of biomolecules in physiological solution as well as for observing their intermolecular interactions in real-time. However, complex steps associated with its practice have made the approach daunting for non-specialists. We introduce an NMR platform that makes biomolecular NMR spectroscopy much more accessible by integrating tools, databases, web services, and video tutorials that can be launched by simple installation of NMRFAM software packages or using a cross-platform virtual machine that can be run on any standard laptop or desktop computer. The software package can be downloaded freely from the NMRFAM software download page ( http://pine.nmrfam.wisc.edu/download_packages.html ), and detailed instructions are available from the Integrative NMR Video Tutorial page ( http://pine.nmrfam.wisc.edu/integrative.html ).
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Affiliation(s)
- Woonghee Lee
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Hesam Dashti
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Hamid R Eghbalnia
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - William M Westler
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Samuel E Butcher
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Katherine A Henzler-Wildman
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - John L Markley
- National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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Dashti H, Tonelli M, Lee W, Westler WM, Cornilescu G, Ulrich EL, Markley JL. Probabilistic validation of protein NMR chemical shift assignments. J Biomol NMR 2016; 64:17-25. [PMID: 26724815 PMCID: PMC4744101 DOI: 10.1007/s10858-015-0007-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 12/20/2015] [Indexed: 05/05/2023]
Abstract
Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data . ARECA has been evaluated through its application to 26 case studies and has been shown to be complementary to, and usually more reliable than, approaches based on chemical shift databases. ARECA is available online at http://areca.nmrfam.wisc.edu/.
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Affiliation(s)
- Hesam Dashti
- Graduate Program in Biophysics, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Marco Tonelli
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Woonghee Lee
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - William M Westler
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Gabriel Cornilescu
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Eldon L Ulrich
- BioMagResBank, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA
| | - John L Markley
- Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA.
- BioMagResBank, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA.
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26
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27
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Jureka AS, Kleinpeter AB, Cornilescu G, Cornilescu CC, Petit CM. Structural Basis for a Novel Interaction between the NS1 Protein Derived from the 1918 Influenza Virus and RIG-I. Structure 2015; 23:2001-10. [PMID: 26365801 PMCID: PMC4635043 DOI: 10.1016/j.str.2015.08.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 08/12/2015] [Accepted: 08/14/2015] [Indexed: 10/23/2022]
Abstract
The influenza non-structural protein 1 (NS1) plays a critical role in antagonizing the innate immune response to infection. One interaction that facilitates this function is between NS1 and RIG-I, one of the main sensors of influenza virus infection. While NS1 and RIG-I are known to interact, it is currently unclear whether this interaction is direct or if it is mediated by other biomolecules. Here we demonstrate a direct, strain-dependent interaction between the NS1 RNA binding domain (NS1(RBD)) of the influenza A/Brevig Mission/1918 H1N1 (1918(H1N1)) virus and the second caspase activation and recruitment domain of RIG-I. Solving the solution structure of the 1918(H1N1) NS1(RBD) revealed features in a functionally novel region that may facilitate the observed interaction. The biophysical and structural data herein suggest a possible mechanism by which strain-specific differences in NS1 modulate influenza virulence.
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Affiliation(s)
- Alexander S Jureka
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Alex B Kleinpeter
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Claudia C Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Chad M Petit
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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28
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Kung VM, Cornilescu G, Gellman SH. Impact of Strand Number on Parallel β-Sheet Stability. Angew Chem Int Ed Engl 2015; 54:14336-9. [PMID: 26457984 DOI: 10.1002/anie.201506448] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 08/27/2015] [Indexed: 11/10/2022]
Abstract
We have examined whether parallel β-sheet secondary structure becomes more stable as the number of β-strands increases, via comparisons among peptides designed to adopt two- or three-stranded parallel β-sheet conformations in aqueous solution. Our three-strand design is the first experimental model of a triple-stranded parallel β-sheet. Analysis of the designed peptides by nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy supports the hypothesis that increasing the number of β-strands, from two to three, increases the stability of the parallel β-sheet. We present the first experimental evidence for cooperativity in the folding of a triple-stranded parallel β-sheet, and we show how minimal model systems may enable experimental documentation of characteristic properties, such as CD spectra, of parallel β-sheets.
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Affiliation(s)
- Vanessa M Kung
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI 53706 (USA)
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, 433 Babcock Dr., Madison, WI 53706 (USA)
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI 53706 (USA).
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29
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Tal-Gan Y, Ivancic M, Cornilescu G, Blackwell HE. Characterization of structural elements in native autoinducing peptides and non-native analogues that permit the differential modulation of AgrC-type quorum sensing receptors in Staphylococcus aureus. Org Biomol Chem 2015; 14:113-21. [PMID: 26416476 DOI: 10.1039/c5ob01735a] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Staphylococcus aureus uses short macrocyclic peptides (i.e., autoinducing peptides, or AIPs) to assess its local population density in a cell-cell signaling mechanism called quorum sensing (QS). At high cell numbers, this pathogen can initiate many virulent behaviors that allow for the establishment of infection. Binding of the AIP signal to its cognate transmembrane AgrC-type receptor is a critical event in the QS signaling cascade; consequently, interference of AIP:receptor interactions may have the potential to prevent and eradicate certain S. aureus infections. To date, four pairs of AIP:AgrC receptors have been identified in S. aureus, each pair being utilized by a specific S. aureus group (I-IV). Other staphylococcal species also use closely related, but distinct, AIP:AgrC pairs to control QS. We seek to develop non-native ligands capable of intercepting AIP:AgrC binding in each S. aureus group and in related species. As these bacteria may use their respective AIP signal to attenuate the QS systems of other groups/species, such ligands would provide valuable chemical tools to probe possible interference mechanisms in a range of contexts. In the current study, we used solution-phase NMR techniques to characterize the 3-D structures of a set of known native and non-native peptides that have differential modulatory activity in certain AgrC receptors. Analysis of these structures revealed several distinct structural motifs that belay differential activity in selected S. aureus AgrC receptors (i.e., AgrC-I, AgrC-II, and AgrC-III). The results of this study can be leveraged for the design of new synthetic ligands with enhanced selectivities and potencies for these AgrC receptors.
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Affiliation(s)
- Yftah Tal-Gan
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
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Dashti H, Lee W, Tonelli M, Cornilescu CC, Cornilescu G, Assadi-Porter FM, Westler WM, Eghbalnia HR, Markley JL. NMRFAM-SDF: a protein structure determination framework. J Biomol NMR 2015; 62:481-95. [PMID: 25900069 PMCID: PMC4569665 DOI: 10.1007/s10858-015-9933-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/15/2015] [Indexed: 05/21/2023]
Abstract
The computationally demanding nature of automated NMR structure determination necessitates a delicate balancing of factors that include the time complexity of data collection, the computational complexity of chemical shift assignments, and selection of proper optimization steps. During the past two decades the computational and algorithmic aspects of several discrete steps of the process have been addressed. Although no single comprehensive solution has emerged, the incorporation of a validation protocol has gained recognition as a necessary step for a robust automated approach. The need for validation becomes even more pronounced in cases of proteins with higher structural complexity, where potentially larger errors generated at each step can propagate and accumulate in the process of structure calculation, thereby significantly degrading the efficacy of any software framework. This paper introduces a complete framework for protein structure determination with NMR--from data acquisition to the structure determination. The aim is twofold: to simplify the structure determination process for non-NMR experts whenever feasible, while maintaining flexibility by providing a set of modules that validate each step, and to enable the assessment of error propagations. This framework, called NMRFAM-SDF (NMRFAM-Structure Determination Framework), and its various components are available for download from the NMRFAM website (http://nmrfam.wisc.edu/software.htm).
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Affiliation(s)
- Hesam Dashti
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - Woonghee Lee
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - Claudia C Cornilescu
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - Fariba M Assadi-Porter
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - William M Westler
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - Hamid R Eghbalnia
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA
| | - John L Markley
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA.
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Cornilescu CC, Cornilescu G, Burgie ES, Markley JL, Ulijasz AT, Vierstra RD. Dynamic structural changes underpin photoconversion of a blue/green cyanobacteriochrome between its dark and photoactivated states. J Biol Chem 2013; 289:3055-65. [PMID: 24337572 DOI: 10.1074/jbc.m113.531053] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The phytochrome superfamily of photoreceptors exploits reversible light-driven changes in the bilin chromophore to initiate a variety of signaling cascades. The nature of these alterations and how they impact the protein moiety remain poorly resolved and might include several species-specific routes. Here, we provide a detailed picture of photoconversion for the photosensing cGMP phosphodiesterase/adenylyl cyclase/FhlA (GAF) domain from Thermosynechococcus elongatus (Te) PixJ, a member of the cyanobacteriochrome clade. Solution NMR structures of the blue light-absorbing dark state Pb and green light-absorbing photoactivated state Pg, combined with paired crystallographic models, revealed that the bilin and GAF domain dynamically transition via breakage of the C10/Cys-494 thioether bond, opposite rotations of the A and D pyrrole rings, sliding of the bilin in the GAF pocket, and the appearance of an extended region of disorder that includes Cys-494. Changes in GAF domain backbone dynamics were also observed that are likely important for inter-domain signal propagation. Taken together, photoconversion of T. elongatus PixJ from Pb to Pg involves complex structural changes within the GAF domain pocket that transduce light into a mechanical signal, many aspects of which should be relevant to others within the extended phytochrome superfamily.
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Affiliation(s)
- Claudia C Cornilescu
- From the National Magnetic Resonance Facility at Madison, Department of Biochemistry and
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32
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Tal-Gan Y, Ivancic M, Cornilescu G, Cornilescu CC, Blackwell HE. Structural characterization of native autoinducing peptides and abiotic analogues reveals key features essential for activation and inhibition of an AgrC quorum sensing receptor in Staphylococcus aureus. J Am Chem Soc 2013; 135:18436-44. [PMID: 24219181 DOI: 10.1021/ja407533e] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Staphylococcus aureus is a major human pathogen that uses quorum sensing (QS) to control virulence. Its QS system is regulated by macrocyclic peptide signals (or autoinducing peptides (AIPs)) and their cognate transmembrane receptors (AgrCs). Four different specificity groups of S. aureus have been identified to date (groups I-IV), each of which uses a different AIP:AgrC pair. Non-native ligands capable of intercepting AIP:AgrC binding, and thereby QS, in S. aureus have attracted considerable interest as chemical tools to study QS pathways and as possible antivirulence strategies for the treatment of infection. We recently reported a set of analogues of the group-III AIP that are capable of strongly modulating the activity of all four AgrC receptors. Critical to the further development of such ligands is a detailed understanding of the structural features of both native AIPs and non-native analogues that are essential for activity. Herein, we report the first three-dimensional structural analysis of the known native AIP signals (AIPs-I-IV) and several AIP-III analogues with varied biological activities using NMR spectroscopy. Integration of these NMR studies with the known agonism and antagonism profiles of these peptides in AgrC-III revealed two key structural elements that control AIP-III (and non-native peptide) activity: (1) a tri-residue hydrophobic "knob" essential for both activation and inhibition and (2) a fourth anchor point on the exocyclic tail needed for receptor activation. These results provide strong structural support for a mechanism of AIP-mediated AgrC activation and inhibition in S. aureus , and should facilitate the design of new AgrC ligands with enhanced activities (as agonists or antagonists) and simplified chemical structures.
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Affiliation(s)
- Yftah Tal-Gan
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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Cornilescu CC, Cornilescu G, Rao H, Porter SF, Tonelli M, DeRider ML, Markley JL, Assadi-Porter FM. Temperature-dependent conformational change affecting Tyr11 and sweetness loops of brazzein. Proteins 2013; 81:919-25. [PMID: 23349025 PMCID: PMC3982881 DOI: 10.1002/prot.24259] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [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: 11/01/2012] [Accepted: 01/11/2013] [Indexed: 10/27/2022]
Abstract
The sweet protein brazzein, a member of the Csβα fold family, contains four disulfide bonds that lend a high degree of thermal and pH stability to its structure. Nevertheless, a variable temperature study has revealed that the protein undergoes a local, reversible conformational change between 37 and 3°C with a midpoint about 27°C that changes the orientations and side-chain hydrogen bond partners of Tyr8 and Tyr11. To test the functional significance of this effect, we used NMR saturation transfer to investigate the interaction between brazzein and the amino terminal domain of the sweet receptor subunit T1R2; the results showed a stronger interaction at 7°C than at 37°C. Thus the low temperature conformation, which alters the orientations of two loops known to be critical for the sweetness of brazzein, may represent the bound state of brazzein in the complex with the human sweet receptor.
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Affiliation(s)
- Claudia C. Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Wisconsin 53706
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Wisconsin 53706
| | - Hongyu Rao
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Sarah F. Porter
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Wisconsin 53706
| | - Michele L. DeRider
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - John L. Markley
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Wisconsin 53706
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Fariba M. Assadi-Porter
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Wisconsin 53706
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
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Farago B, Li J, Cornilescu G, Callaway DJE, Bu Z. Activation of nanoscale allosteric protein domain motion revealed by neutron spin echo spectroscopy. Biophys J 2011; 99:3473-82. [PMID: 21081097 DOI: 10.1016/j.bpj.2010.09.058] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 09/09/2010] [Accepted: 09/30/2010] [Indexed: 11/15/2022] Open
Abstract
NHERF1 is a multidomain scaffolding protein that assembles signaling complexes, and regulates the cell surface expression and endocytic recycling of a variety of membrane proteins. The ability of the two PDZ domains in NHERF1 to assemble protein complexes is allosterically modulated by the membrane-cytoskeleton linker protein ezrin, whose binding site is located as far as 110 Ångstroms away from the PDZ domains. Here, using neutron spin echo (NSE) spectroscopy, selective deuterium labeling, and theoretical analyses, we reveal the activation of interdomain motion in NHERF1 on nanometer length-scales and on submicrosecond timescales upon forming a complex with ezrin. We show that a much-simplified coarse-grained model suffices to describe interdomain motion of a multidomain protein or protein complex. We expect that future NSE experiments will benefit by exploiting our approach of selective deuteration to resolve the specific domain motions of interest from a plethora of global translational and rotational motions. Our results demonstrate that the dynamic propagation of allosteric signals to distal sites involves changes in long-range coupled domain motions on submicrosecond timescales, and that these coupled motions can be distinguished and characterized by NSE.
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Yao L, Grishaev A, Cornilescu G, Bax A. The impact of hydrogen bonding on amide 1H chemical shift anisotropy studied by cross-correlated relaxation and liquid crystal NMR spectroscopy. J Am Chem Soc 2010; 132:10866-75. [PMID: 20681720 PMCID: PMC2915638 DOI: 10.1021/ja103629e] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [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] [Indexed: 11/29/2022]
Abstract
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Site-specific 1H chemical shift anisotropy (CSA) tensors have been derived for the well-ordered backbone amide moieties in the B3 domain of protein G (GB3). Experimental input data include residual chemical shift anisotropy (RCSA), measured in six mutants that align differently relative to the static magnetic field when dissolved in a liquid crystalline Pf1 suspension, and cross-correlated relaxation rates between the 1HN CSA tensor and either the 1H−15N, the 1H−13C′, or the 1H−13Cα dipolar interactions. Analyses with the assumption that the 1HN CSA tensor is symmetric with respect to the peptide plane (three-parameter fit) or without this premise (five-parameter fit) yield very similar results, confirming the robustness of the experimental input data, and that, to a good approximation, one of the principal components orients orthogonal to the peptide plane. 1HN CSA tensors are found to deviate strongly from axial symmetry, with the most shielded tensor component roughly parallel to the N−H vector, and the least shielded component orthogonal to the peptide plane. DFT calculations on pairs of N-methyl acetamide and acetamide in H-bonded geometries taken from the GB3 X-ray structure correlate with experimental data and indicate that H-bonding effects dominate variations in the 1HN CSA. Using experimentally derived 1HN CSA tensors, the optimal relaxation interference effect needed for narrowest 1HN TROSY line widths is found at ∼1200 MHz.
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Affiliation(s)
- Lishan Yao
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266061, China
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36
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Yao L, Grishaev A, Cornilescu G, Bax A. Site-specific backbone amide (15)N chemical shift anisotropy tensors in a small protein from liquid crystal and cross-correlated relaxation measurements. J Am Chem Soc 2010; 132:4295-309. [PMID: 20199098 PMCID: PMC2847892 DOI: 10.1021/ja910186u] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Site-specific (15)N chemical shift anisotropy (CSA) tensors have been derived for the well-ordered backbone amide (15)N nuclei in the B3 domain of protein G (GB3) from residual chemical shift anisotropy (RCSA) measured in six different mutants that retain the native structure but align differently relative to the static magnetic field when dissolved in a liquid crystalline Pf1 suspension. This information is complemented by measurement of cross-correlated relaxation rates between the (15)N CSA tensor and either the (15)N-(1)H or (15)N-(13)C' dipolar interaction. In agreement with recent solid state NMR measurements, the (15)N CSA tensors exhibit only a moderate degree of variation from averaged values, but have larger magnitudes in alpha-helical (-173 +/- 7 ppm) than in beta-sheet (-162 +/- 6 ppm) residues, a finding also confirmed by quantum computations. The orientations of the least shielded tensor component cluster tightly around an in-peptide-plane vector that makes an angle of 19.6 +/- 2.5 degrees with the N-H bond, with the asymmetry of the (15)N CSA tensor being slightly smaller in alpha-helix (eta = 0.23 +/- 0.17) than in beta-sheet (eta = 0.31 +/- 0.11). The residue-specific (15)N CSA values are validated by improved agreement between computed and experimental (15)N R(1rho) relaxation rates measured for (15)N-{(2)H} sites in GB3, which are dominated by the CSA mechanism. Use of residue-specific (15)N CSA values also results in more uniform generalized order parameters, S(2), and predicts considerable residue-by-residue variations in the magnetic field strengths where TROSY line narrowing is most effective.
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Affiliation(s)
- Lishan Yao
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD 20892-0520
| | - Alexander Grishaev
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD 20892-0520
| | | | - Ad Bax
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD 20892-0520
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Tonelli M, Masterson LR, Cornilescu G, Markley JL, Veglia G. One-sample approach to determine the relative orientations of proteins in ternary and binary complexes from residual dipolar coupling measurements. J Am Chem Soc 2009; 131:14138-9. [PMID: 19764746 DOI: 10.1021/ja904766g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [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 present a procedure that supports the acquisition of (1)H-(15)N residual dipolar coupling (RDC) values for individual subunits in binary or ternary protein assemblies from a single experimental sample. Our method relies on asymmetric labeling of each subunit with the following scheme: species A uniformly with (15)N, species B uniformly with (15)N and (13)C, and species C uniformly with (15)N but selectively with (13)C' or (13)C(alpha). Because only a single sample is required, the approach obviates the need for preparing multiple samples and eliminates potential errors introduced from differences in sample conditions. Because numerous biological processes rely on protein assemblies or transient interactions, this method should be well suited for a wide range of future applications.
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Affiliation(s)
- Marco Tonelli
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1544, USA
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38
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Ulijasz AT, Cornilescu G, von Stetten D, Cornilescu C, Velazquez Escobar F, Zhang J, Stankey RJ, Rivera M, Hildebrandt P, Vierstra RD. Cyanochromes are blue/green light photoreversible photoreceptors defined by a stable double cysteine linkage to a phycoviolobilin-type chromophore. J Biol Chem 2009; 284:29757-72. [PMID: 19671704 DOI: 10.1074/jbc.m109.038513] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Phytochromes are a collection of bilin-containing photoreceptors that regulate a diverse array of processes in microorganisms and plants through photoconversion between two stable states, a red light-absorbing Pr form, and a far red light-absorbing Pfr form. Recently, a novel set of phytochrome-like chromoproteins was discovered in cyanobacteria, designated here as cyanochromes, that instead photoconvert between stable blue and green light-absorbing forms Pb and Pg, respectively. Here, we show that the distinctive absorption properties of cyanochromes are facilitated through the binding of phycocyanobilin via two stable cysteine-based thioether linkages within the cGMP phosphodiesterase/adenyl cyclase/FhlA domain. Absorption, resonance Raman and infrared spectroscopy, and molecular modeling of the Te-PixJ GAF (cGMP phosphodiesterase/adenyl cyclase/FhlA) domain assembled with phycocyanobilin are consistent with attachments to the C3(1) carbon of the ethylidene side chain and the C4 or C5 carbons in the A-B methine bridge to generate a double thioether-linked phycoviolobilin-type chromophore. These spectroscopic methods combined with NMR data show that the bilin is fully protonated in the Pb and Pg states and that numerous conformation changes occur during Pb --> Pg photoconversion. Also identified were a number of photochromically inactive mutants with strong yellow or red fluorescence that may be useful for fluorescence-based cell biological assays. Phylogenetic analyses detected cyanochromes capable of different signaling outputs in a wide range of cyanobacterial species. One unusual case is the Synechocystis cyanochrome Etr1 that also binds ethylene, suggesting that it works as a hybrid receptor to simultaneously integrate light and hormone signals.
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Affiliation(s)
- Andrew T Ulijasz
- Department of Genetics, University of Wisconsin, Madison, WI 53706, USA
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39
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Shen Y, Delaglio F, Cornilescu G, Bax A. TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 2009; 44:213-23. [PMID: 19548092 PMCID: PMC2726990 DOI: 10.1007/s10858-009-9333-z] [Citation(s) in RCA: 2085] [Impact Index Per Article: 139.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Accepted: 05/28/2009] [Indexed: 05/03/2023]
Abstract
NMR chemical shifts in proteins depend strongly on local structure. The program TALOS establishes an empirical relation between 13C, 15N and 1H chemical shifts and backbone torsion angles phi and psi (Cornilescu et al. J Biomol NMR 13 289-302, 1999). Extension of the original 20-protein database to 200 proteins increased the fraction of residues for which backbone angles could be predicted from 65 to 74%, while reducing the error rate from 3 to 2.5%. Addition of a two-layer neural network filter to the database fragment selection process forms the basis for a new program, TALOS+, which further enhances the prediction rate to 88.5%, without increasing the error rate. Excluding the 2.5% of residues for which TALOS+ makes predictions that strongly differ from those observed in the crystalline state, the accuracy of predicted phi and psi angles, equals +/-13 degrees . Large discrepancies between predictions and crystal structures are primarily limited to loop regions, and for the few cases where multiple X-ray structures are available such residues are often found in different states in the different structures. The TALOS+ output includes predictions for individual residues with missing chemical shifts, and the neural network component of the program also predicts secondary structure with good accuracy.
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Affiliation(s)
- Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, U.S.A
| | - Frank Delaglio
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, U.S.A
| | | | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, U.S.A
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Cornilescu G, Ulijasz AT, Cornilescu CC, Markley JL, Vierstra RD. Solution structure of a cyanobacterial phytochrome GAF domain in the red-light-absorbing ground state. J Mol Biol 2008; 383:403-13. [PMID: 18762196 DOI: 10.1016/j.jmb.2008.08.034] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Revised: 08/11/2008] [Accepted: 08/14/2008] [Indexed: 01/31/2023]
Abstract
The unique photochromic absorption behavior of phytochromes (Phys) depends on numerous reversible interactions between the bilin chromophore and the associated polypeptide. To help define these dynamic interactions, we determined by NMR spectroscopy the first solution structure of the chromophore-binding cGMP phosphodiesterase/adenylcyclase/FhlA (GAF) domain from a cyanobacterial Phy assembled with phycocyanobilin (PCB). The three-dimensional NMR structure of Synechococcus OS-B' cyanobacterial Phy 1 in the red-light-absorbing state of Phy (Pr) revealed that PCB is bound to Cys138 of the GAF domain via the A-ring ethylidene side chain and is buried within the GAF domain in a ZZZsyn,syn,anti configuration. The D ring of the chromophore sits within a hydrophobic pocket and is tilted by approximately 80 degrees relative to the B/C rings by contacts with Lys52 and His169. The solution structure revealed remarkable flexibility for PCB and several adjacent amino acids, indicating that the Pr chromophore has more freedom in the binding pocket than anticipated. The propionic acid side chains of rings B and C and Arg101 and Arg133 nearby are especially mobile and can assume several distinct and energetically favorable conformations. Mutagenic studies on these arginines, which are conserved within the Phy superfamily, revealed that they have opposing roles, with Arg101 and Arg133 helping stabilize and destabilize the far-red-light-absorbing state of Phy (Pfr), respectively. Given the fact that the Synechococcus OS-B' GAF domain can, by itself, complete the Pr --> Pfr photocycle, it should now be possible to determine the solution structure of the Pfr chromophore and surrounding pocket using this Pr structure as a framework.
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Affiliation(s)
- Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin, Madison, WI 53706, USA
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41
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Füzéry AK, Tonelli M, Ta DT, Cornilescu G, Vickery LE, Markley JL. Solution structure of the iron-sulfur cluster cochaperone HscB and its binding surface for the iron-sulfur assembly scaffold protein IscU. Biochemistry 2008; 47:9394-404. [PMID: 18702525 PMCID: PMC2627783 DOI: 10.1021/bi800502r] [Citation(s) in RCA: 36] [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: 12/01/2022]
Abstract
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The interaction between IscU and HscB is critical for successful assembly of iron−sulfur clusters. NMR experiments were performed on HscB to investigate which of its residues might be part of the IscU binding surface. Residual dipolar couplings (1DHN and 1DCαHα) indicated that the crystal structure of HscB [Cupp-Vickery, J. R., and Vickery, L. E. (2000) Crystal structure of Hsc20, a J-type cochaperone from Escherichia coli, J. Mol. Biol. 304, 835−845] faithfully represents its solution state. NMR relaxation rates (15N R1, R2) and 1H−15N heteronuclear NOE values indicated that HscB is rigid along its entire backbone except for three short regions which exhibit flexibility on a fast time scale. Changes in the NMR spectrum of HscB upon addition of IscU mapped to the J-domain/C-domain interface, the interdomain linker, and the C-domain. Sequence conservation is low in the interface and in the linker, and NMR changes observed for these residues likely result from indirect effects of IscU binding. NMR changes observed in the conserved patch of residues in the C-domain (L92, M93, L96, E97, E100, E104, and F153) were suggestive of a direct interaction with IscU. To test this, we replaced several of these residues with alanine and assayed for the ability of HscB to interact with IscU and to stimulate HscA ATPase activity. HscB(L92A,M93A,F153A) and HscB(E97A,E100A,E104A) both showed decreased binding affinity for IscU; the (L92A,M93A,F153A) substitution also strongly perturbed the allosteric interaction within the HscA·IscU·HscB ternary complex. We propose that the conserved patch in the C-domain of HscB is the principal binding site for IscU.
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Affiliation(s)
- Anna K Füzéry
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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42
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Ulijasz AT, Cornilescu G, von Stetten D, Kaminski S, Mroginski MA, Zhang J, Bhaya D, Hildebrandt P, Vierstra RD. Characterization of two thermostable cyanobacterial phytochromes reveals global movements in the chromophore-binding domain during photoconversion. J Biol Chem 2008; 283:21251-66. [PMID: 18480055 PMCID: PMC3258942 DOI: 10.1074/jbc.m801592200] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [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: 02/27/2008] [Revised: 04/30/2008] [Indexed: 11/06/2022] Open
Abstract
Photointerconversion between the red light-absorbing (Pr) form and the far-red light-absorbing (Pfr) form is the central feature that allows members of the phytochrome (Phy) superfamily to act as reversible switches in light perception. Whereas the chromophore structure and surrounding binding pocket of Pr have been described, those for Pfr have remained enigmatic for various technical reasons. Here we describe a novel pair of Phys from two thermophilic cyanobacteria, Synechococcus sp. OS-A and OS-B', that overcome several of these limitations. Like other cyanobacterial Phys, SyA-Cph1 and SyB-Cph1 covalently bind the bilin phycocyanobilin via their cGMP phosphodiesterase/adenyl cyclase/FhlA (GAF) domains and then assume the photointerconvertible Pr and Pfr states with absorption maxima at 630 and 704 nm, respectively. However, they are naturally missing the N-terminal Per/Arndt/Sim domain common to others in the Phy superfamily. Importantly, truncations containing only the GAF domain are monomeric, photochromic, and remarkably thermostable. Resonance Raman and NMR spectroscopy show that all four pyrrole ring nitrogens of phycocyanobilin are protonated both as Pr and following red light irradiation, indicating that the GAF domain by itself can complete the Pr to Pfr photocycle. (1)H-(15)N two-dimensional NMR spectra of isotopically labeled preparations of the SyB-Cph1 GAF domain revealed that a number of amino acids change their environment during photoconversion of Pr to Pfr, which can be reversed by subsequent photoconversion back to Pr. Through three-dimensional NMR spectroscopy before and after light photoexcitation, it should now be possible to define the movements of the chromophore and binding pocket during photoconversion. We also generated a series of strongly red fluorescent derivatives of SyB-Cph1, which based on their small size and thermostability may be useful as cell biological reporters.
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Affiliation(s)
- Andrew T. Ulijasz
- Department of Genetics and
National Magnetic Resonance Facility,
University of Wisconsin, Madison, Wisconsin 53706, the
Technische Universität, D-10623
Berlin, Germany, and the Department of
Plant Biology, Carnegie Institution of Washington, Stanford, California
94305
| | - Gabriel Cornilescu
- Department of Genetics and
National Magnetic Resonance Facility,
University of Wisconsin, Madison, Wisconsin 53706, the
Technische Universität, D-10623
Berlin, Germany, and the Department of
Plant Biology, Carnegie Institution of Washington, Stanford, California
94305
| | - David von Stetten
- Department of Genetics and
National Magnetic Resonance Facility,
University of Wisconsin, Madison, Wisconsin 53706, the
Technische Universität, D-10623
Berlin, Germany, and the Department of
Plant Biology, Carnegie Institution of Washington, Stanford, California
94305
| | - Steve Kaminski
- Department of Genetics and
National Magnetic Resonance Facility,
University of Wisconsin, Madison, Wisconsin 53706, the
Technische Universität, D-10623
Berlin, Germany, and the Department of
Plant Biology, Carnegie Institution of Washington, Stanford, California
94305
| | - Maria Andrea Mroginski
- Department of Genetics and
National Magnetic Resonance Facility,
University of Wisconsin, Madison, Wisconsin 53706, the
Technische Universität, D-10623
Berlin, Germany, and the Department of
Plant Biology, Carnegie Institution of Washington, Stanford, California
94305
| | - Junrui Zhang
- Department of Genetics and
National Magnetic Resonance Facility,
University of Wisconsin, Madison, Wisconsin 53706, the
Technische Universität, D-10623
Berlin, Germany, and the Department of
Plant Biology, Carnegie Institution of Washington, Stanford, California
94305
| | - Devaki Bhaya
- Department of Genetics and
National Magnetic Resonance Facility,
University of Wisconsin, Madison, Wisconsin 53706, the
Technische Universität, D-10623
Berlin, Germany, and the Department of
Plant Biology, Carnegie Institution of Washington, Stanford, California
94305
| | - Peter Hildebrandt
- Department of Genetics and
National Magnetic Resonance Facility,
University of Wisconsin, Madison, Wisconsin 53706, the
Technische Universität, D-10623
Berlin, Germany, and the Department of
Plant Biology, Carnegie Institution of Washington, Stanford, California
94305
| | - Richard D. Vierstra
- Department of Genetics and
National Magnetic Resonance Facility,
University of Wisconsin, Madison, Wisconsin 53706, the
Technische Universität, D-10623
Berlin, Germany, and the Department of
Plant Biology, Carnegie Institution of Washington, Stanford, California
94305
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43
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Juranić N, Dannenberg JJ, Cornilescu G, Salvador P, Atanasova E, Ahn HC, Macura S, Markley JL, Prendergast FG. Structural dependencies of protein backbone 2JNC' couplings. Protein Sci 2008; 17:768-76. [PMID: 18305196 DOI: 10.1110/ps.073331608] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Protein folding can introduce strain in peptide covalent geometry, including deviations from planarity that are difficult to detect, especially for a protein in solution. We have found dependencies in protein backbone (2)J(NC') couplings on the planarity and the relative orientation of the sequential peptide planes. These dependences were observed in experimental (2)J(NC') couplings from seven proteins, and also were supported by DFT calculations for a model tripeptide. Findings indicate that elevated (2)J(NC') couplings may serve as reporters of structural strain in the protein backbone imposed by protein folds. Such information, supplemented with the H-bond strengths derived from (h3)J(NC') couplings, provides useful insight into the overall energy profile of the protein backbone in solution.
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Affiliation(s)
- Nenad Juranić
- Department of Biochemistry and Molecular Biology, Mayo Clinic and Foundation, Rochester, Minnesota 55905, USA
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44
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Cornilescu G, Bahrami A, Tonelli M, Markley JL, Eghbalnia HR. HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections. J Biomol NMR 2007; 38:341-51. [PMID: 17610130 DOI: 10.1007/s10858-007-9173-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Revised: 06/11/2007] [Accepted: 06/13/2007] [Indexed: 05/16/2023]
Abstract
We describe a novel method for the robust, rapid, and reliable determination of J couplings in multi-dimensional NMR coupling data, including small couplings from larger proteins. The method, "High-resolution Iterative Frequency Identification of Couplings" (HIFI-C) is an extension of the adaptive and intelligent data collection approach introduced earlier in HIFI-NMR. HIFI-C collects one or more optimally tilted two-dimensional (2D) planes of a 3D experiment, identifies peaks, and determines couplings with high resolution and precision. The HIFI-C approach, demonstrated here for the 3D quantitative J method, offers vital features that advance the goal of rapid and robust collection of NMR coupling data. (1) Tilted plane residual dipolar couplings (RDC) data are collected adaptively in order to offer an intelligent trade off between data collection time and accuracy. (2) Data from independent planes can provide a statistical measure of reliability for each measured coupling. (3) Fast data collection enables measurements in cases where sample stability is a limiting factor (for example in the presence of an orienting medium required for residual dipolar coupling measurements). (4) For samples that are stable, or in experiments involving relatively stronger couplings, robust data collection enables more reliable determinations of couplings in shorter time, particularly for larger biomolecules. As a proof of principle, we have applied the HIFI-C approach to the 3D quantitative J experiment to determine N-C' RDC values for three proteins ranging from 56 to 159 residues (including a homodimer with 111 residues in each subunit). A number of factors influence the robustness and speed of data collection. These factors include the size of the protein, the experimental set up, and the coupling being measured, among others. To exhibit a lower bound on robustness and the potential for time saving, the measurement of dipolar couplings for the N-C' vector represents a realistic "worst case analysis". These couplings are among the smallest currently measured, and their determination in both isotropic and anisotropic media demands the highest measurement precision. The new approach yielded excellent quantitative agreement with values determined independently by the conventional 3D quantitative J NMR method (in cases where sample stability in oriented media permitted these measurements) but with a factor of 2-5 in time savings. The statistical measure of reliability, measuring the quality of each RDC value, offers valuable adjunct information even in cases where modest time savings may be realized.
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Affiliation(s)
- Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Abstract
The spliceosome is a dynamic ribonucleoprotein complex responsible for the removal of intron sequences from pre-messenger RNA. The highly conserved 5' end of the U2 small nuclear RNA (snRNA) makes key base-pairing interactions with the intron branch point sequence and U6 snRNA. U2 stem I, a stem-loop located in the 5' region of U2, has been implicated in spliceosome assembly and may modulate the folding of the U2 and U6 snRNAs in the spliceosome active site. Here we present the NMR structures of U2 stem I from human and Saccharomyces cerevisiae. These sequences represent the two major classes of U2 stem I, distinguished by the identity of tandem wobble pairs (UU/UU in yeast and CA/GU in human) and the presence of post-transcriptional modifications (four 2'-O-methyl groups and two pseudouracils in human). The structures reveal that the UU/UU and CA/GU tandem wobble pairs are nearly isosteric. The tandem wobble pairs separate two thermodynamically distinct regions of Watson-Crick base pairs, with the modified nucleotides in human stem I conferring a significant increase in stability. We hypothesize that the separate thermodynamic stabilities of U2 stem I exist to allow the structure to transition through different folded conformations during spliceosome assembly and catalysis.
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Affiliation(s)
- Dipali G Sashital
- Department of Biochemistry, University of Wisconsin-Madison 53706, USA
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46
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Cornilescu G, Hadley EB, Woll MG, Markley JL, Gellman SH, Cornilescu CC. Solution structure of a small protein containing a fluorinated side chain in the core. Protein Sci 2007; 16:14-9. [PMID: 17123960 PMCID: PMC2222841 DOI: 10.1110/ps.062557707] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [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: 09/13/2006] [Revised: 10/06/2006] [Accepted: 10/10/2006] [Indexed: 10/23/2022]
Abstract
We report the first high-resolution structure for a protein containing a fluorinated side chain. Recently we carried out a systematic evaluation of phenylalanine to pentafluorophenylalanine (Phe --> F(5)-Phe) mutants for the 35-residue chicken villin headpiece subdomain (c-VHP), the hydrophobic core of which features a cluster of three Phe side chains (residues 6, 10, and 17). Phe --> F(5)-Phe mutations are interesting because aryl-perfluoroaryl interactions of optimal geometry are intrinsically more favorable than either aryl-aryl or perfluoroaryl-perfluoroaryl interactions, and because perfluoroaryl units are more hydrophobic than are analogous aryl units. Only one mutation, Phe10 --> F(5)-Phe, was found to provide enhanced tertiary structural stability relative to the native core (by approximately 1 kcal/mol, according to guanidinium chloride denaturation studies). The NMR structure of this mutant, described here, reveals very little variation in backbone conformation or side chain packing relative to the wild type. Thus, although Phe --> F(5)-Phe mutations offer the possibility of greater tertiary structural stability from side chain-side chain attraction and/or side chain desolvation, the constraints associated with the native c-VHP fold apparently prevent the modified polypeptide from taking advantage of this possibility. Our findings are important because they complement several studies that have shown that fluorination of saturated side chain carbon atoms can provide enhanced conformational stability.
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Affiliation(s)
- Gabriel Cornilescu
- NMRFAM, Department of biochemistry, University of Wisconsin, Madison, WI 53706, USA
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47
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Cornilescu G, Vinarov DA, Tyler EM, Markley JL, Cornilescu CC. Solution structure of a single-domain thiosulfate sulfurtransferase from Arabidopsis thaliana. Protein Sci 2006; 15:2836-41. [PMID: 17088324 PMCID: PMC2242445 DOI: 10.1110/ps.062395206] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [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: 10/23/2022]
Abstract
We describe the three-dimensional structure of the product of Arabidopsis thaliana gene At5g66040.1 as determined by NMR spectroscopy. This protein is categorized as single-domain sulfurtransferase and is annotated as a senescence-associated protein (sen1-like protein) and ketoconazole resistance protein (http://arabidopsis.org/info/genefamily/STR_genefamily.html). The sequence of At5g66040.1 is virtually identical to that of a protein from Arabidopsis found by others to confer ketoconazole resistance in yeast. Comparison of the three-dimensional structure with those in the Protein Data Bank revealed that At5g66040.1 contains an additional mobile beta-hairpin not found in other rhodaneses that may function in binding specific substrates. This represents the first structure of a single-domain plant sulfurtransferase. The enzymatically active cysteine-containing domain belongs to the CDC25 class of phosphatases, sulfide dehydrogenases, and stress proteins such as senescence specific protein 1 in plants, PspE and GlpE in bacteria, and cyanide and arsenate resistance proteins. Versions of this domain that lack the active site cysteine are found in other proteins, such as phosphatases, ubiquitin hydrolases, and sulfuryltransferases.
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Affiliation(s)
- Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin 53706-1544, USA.
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Singh S, Cornilescu CC, Tyler RC, Cornilescu G, Tonelli M, Lee MS, Markley JL. Solution structure of a late embryogenesis abundant protein (LEA14) from Arabidopsis thaliana, a cellular stress-related protein. Protein Sci 2005; 14:2601-9. [PMID: 16155204 PMCID: PMC2253292 DOI: 10.1110/ps.051579205] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [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: 10/25/2022]
Abstract
We report the three-dimensional structure of a late embryogenesis abundant (LEA) protein from Arabidopsis thaliana gene At1g01470.1. This protein is a member of Pfam cluster PF03168, and has been classified as a LEA14 protein. LEA proteins are expressed under conditions of cellular stress, such as desiccation, cold, osmotic stress, and heat. The structure, which was determined by NMR spectroscopy, revealed that the At1g01470.1 protein has an alphabeta-fold consisting of one alpha-helix and seven beta-strands that form two antiparallel beta-sheets. The closest structural homologs were discovered to be fibronectin Type III domains, which have <7% sequence identity. Because fibronectins from animal cells have been shown to be involved in cell adhesion, cell motility, wound healing, and maintenance of cell shape, it is interesting to note that in plants wounding or stress results in the overexpression of a protein with fibronectin Type III structural features.
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Affiliation(s)
- Shanteri Singh
- Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
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Sashital DG, Cornilescu G, McManus CJ, Brow DA, Butcher SE. U2-U6 RNA folding reveals a group II intron-like domain and a four-helix junction. Nat Struct Mol Biol 2004; 11:1237-42. [PMID: 15543154 DOI: 10.1038/nsmb863] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.7] [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: 08/12/2004] [Accepted: 09/30/2004] [Indexed: 11/10/2022]
Abstract
Intron removal in nuclear precursor mRNA is catalyzed through two transesterification reactions by a multi-megaDalton ribonucleoprotein machine called the spliceosome. A complex between U2 and U6 small nuclear RNAs is a core component of the spliceosome. Here we present an NMR structural analysis of a protein-free U2-U6 complex from Saccharomyces cerevisiae. The observed folding of the U2-U6 complex is a four-helix junction, in which the catalytically important AGC triad base-pairs only within U6 and not with U2. The base-pairing of the AGC triad extends the U6 intramolecular stem-loop (U6 ISL), and the NMR structure of this extended U6 ISL reveals structural similarities with domain 5 of group II self-splicing introns. The observed conformation of the four-helix junction could be relevant to the first, but not the second, step of splicing and may help to position the U6 ISL adjacent to the 5' splice site.
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Affiliation(s)
- Dipali G Sashital
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
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Cornilescu G, Cornilescu CC, Zhao Q, Frederick RO, Peterson FC, Thao S, Markley JL. Solution structure of a homodimeric hypothetical protein, At5g22580, a structural genomics target from Arabidopsis thaliana. J Biomol NMR 2004; 29:387-390. [PMID: 15213437 DOI: 10.1023/b:jnmr.0000032525.70677.16] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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