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Moeller J, Bozhanova NG, Voehler M, Meiler J, Schoeder CT. Backbone chemical shift and secondary structure assignments for mouse siderocalin. BIOMOLECULAR NMR ASSIGNMENTS 2024; 18:79-84. [PMID: 38564159 PMCID: PMC11081974 DOI: 10.1007/s12104-024-10171-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/16/2024] [Indexed: 04/04/2024]
Abstract
The lipocalin protein family is a structurally conserved group of proteins with a variety of biological functions defined by their ability to bind small molecule ligands and interact with partner proteins. One member of this family is siderocalin, a protein found in mammals. Its role is discussed in inflammatory processes, iron trafficking, protection against bacterial infections and oxidative stress, cell migration, induction of apoptosis, and cancer. Though it seems to be involved in numerous essential pathways, the exact mechanisms are often not fully understood. The NMR backbone assignments for the human siderocalin and its rat ortholog have been published before. In this work we describe the backbone NMR assignments of siderocalin for another important model organism, the mouse - data that might become important for structure-based drug discovery. Secondary structure elements were predicted based on the assigned backbone chemical shifts using TALOS-N and CSI 3.0, revealing a high content of beta strands and one prominent alpha helical region. Our findings correlate well with the known crystal structure and the overall conserved fold of the lipocalin family.
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Affiliation(s)
- Johanna Moeller
- Institute for Drug Discovery, Leipzig University Medical School, 04103, Leipzig, Germany
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI) Dresden/Leipzig, Leipzig University, Leipzig, Germany
| | - Nina G Bozhanova
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37232, USA
| | - Markus Voehler
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37232, USA
| | - Jens Meiler
- Institute for Drug Discovery, Leipzig University Medical School, 04103, Leipzig, Germany
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37232, USA
| | - Clara T Schoeder
- Institute for Drug Discovery, Leipzig University Medical School, 04103, Leipzig, Germany.
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI) Dresden/Leipzig, Leipzig University, Leipzig, Germany.
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2
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Abdullah SJ, Mu Y, Bhattacharjya S. Structures, Interactions and Activity of the N-Terminal Truncated Variants of Antimicrobial Peptide Thanatin. Antibiotics (Basel) 2024; 13:74. [PMID: 38247633 PMCID: PMC10812785 DOI: 10.3390/antibiotics13010074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
Gram-negative bacteria are intrinsically more resistant to many frontline antibiotics, which is attributed to the permeability barrier of the outer membrane, drug efflux pumps and porins. Consequently, discovery of new small molecules antibiotics to kill drug-resistant Gram-negative bacteria presents a significant challenge. Thanatin, a 21-residue insect-derived antimicrobial peptide, is known for its potent activity against Enterobacter Gram-negative bacteria, including drug-resistant strains. Here, we investigated a 15-residue N-terminal truncated analog PM15 (P1IIYCNRRTGKCQRM15) of thanatin to determine modes of action and antibacterial activity. PM15 and the P1 to Y and A substituted variants PM15Y and PM15A delineated interactions and permeabilization of the LPS-outer membrane. In antibacterial assays, PM15 and the analogs showed growth inhibition of strains of Gram-negative bacteria that is largely dependent on the composition of the culture media. Atomic-resolution structures of PM15 and PM15Y in free solution and in complex with LPS micelle exhibited persistent β-hairpin structures similar to native thanatin. However, in complex with LPS, the structures of peptides are more compact, with extensive packing interactions among residues across the two anti-parallel strands of the β-hairpin. The docked complex of PM15/LPS revealed a parallel orientation of the peptide that may be sustained by potential ionic and van der Waals interactions with the lipid A moiety of LPS. Further, PM15 and PM15Y bind to LptAm, a monomeric functional variant of LptA, the periplasmic component of the seven-protein (A-G) complex involved in LPS transport. Taken together, the structures, target interactions and antibacterial effect of PM15 presented in the current study could be useful in designing thanatin-based peptide analogs.
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Affiliation(s)
| | | | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; (S.J.A.); (Y.M.)
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3
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Papageorgiou AC, Pospisilova M, Cibulka J, Ashraf R, Waudby CA, Kadeřávek P, Maroz V, Kubicek K, Prokop Z, Krejci L, Tripsianes K. Recognition and coacervation of G-quadruplexes by a multifunctional disordered region in RECQ4 helicase. Nat Commun 2023; 14:6751. [PMID: 37875529 PMCID: PMC10598209 DOI: 10.1038/s41467-023-42503-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 10/12/2023] [Indexed: 10/26/2023] Open
Abstract
Biomolecular polyelectrolyte complexes can be formed between oppositely charged intrinsically disordered regions (IDRs) of proteins or between IDRs and nucleic acids. Highly charged IDRs are abundant in the nucleus, yet few have been functionally characterized. Here, we show that a positively charged IDR within the human ATP-dependent DNA helicase Q4 (RECQ4) forms coacervates with G-quadruplexes (G4s). We describe a three-step model of charge-driven coacervation by integrating equilibrium and kinetic binding data in a global numerical model. The oppositely charged IDR and G4 molecules form a complex in the solution that follows a rapid nucleation-growth mechanism leading to a dynamic equilibrium between dilute and condensed phases. We also discover a physical interaction with Replication Protein A (RPA) and demonstrate that the IDR can switch between the two extremes of the structural continuum of complexes. The structural, kinetic, and thermodynamic profile of its interactions revealed a dynamic disordered complex with nucleic acids and a static ordered complex with RPA protein. The two mutually exclusive binding modes suggest a regulatory role for the IDR in RECQ4 function by enabling molecular handoffs. Our study extends the functional repertoire of IDRs and demonstrates a role of polyelectrolyte complexes involved in G4 binding.
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Affiliation(s)
- Anna C Papageorgiou
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Michaela Pospisilova
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jakub Cibulka
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Raghib Ashraf
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Pavel Kadeřávek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Volha Maroz
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Karel Kubicek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St Anne's University Hospital, Brno, Czech Republic
| | - Lumir Krejci
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.
- International Clinical Research Center, St Anne's University Hospital, Brno, Czech Republic.
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4
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Lee E, McLeod MJ, Redzic JS, Marcolin B, Thorne RE, Agarwal P, Eisenmesser EZ. Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle. Front Mol Biosci 2023; 10:1244587. [PMID: 37645217 PMCID: PMC10461185 DOI: 10.3389/fmolb.2023.1244587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/21/2023] [Indexed: 08/31/2023] Open
Abstract
Biliverdin Reductase B (BLVRB) is an NADPH-dependent reductase that catalyzes the reduction of multiple substrates and is therefore considered a critical cellular redox regulator. In this study, we sought to address whether both structural and dynamics changes occur between different intermediates of the catalytic cycle and whether these were relegated to just the active site or the entirety of the enzyme. Through X-ray crystallography, we determined the apo BLVRB structure for the first time, revealing subtle global changes compared to the holo structure and identifying the loss of a critical hydrogen bond that "clamps" the R78-loop over the coenzyme. Amide and Cα chemical shift perturbations were used to identify environmental and secondary structural changes between intermediates, with more distant global changes observed upon coenzyme binding compared to substrate interactions. NMR relaxation rate measurements provided insights into the dynamic behavior of BLVRB during the catalytic cycle. Specifically, the inherently dynamic R78-loop that becomes ordered upon coenzyme binding persists through the catalytic cycle while similar regions experience dynamic exchange. However, the dynamic exchange processes were found to differ through the catalytic cycle with several groups of residues exhibiting similar dynamic responses. Finally, both local and distal structural and dynamic changes occur within BLVRB that are dependent solely on the oxidative state of the coenzyme. Thus, through a comprehensive analysis here, this study revealed structural and dynamic alterations in BLVRB through its catalytic cycle that are not simply relegated to the active site, but instead, are allosterically coupled throughout the enzyme.
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Affiliation(s)
- Eunjeong Lee
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, CO, United States
| | - Matthew J. McLeod
- Laboratory of Atomic and Solid-State Physics, Cornell University, Ithaca, NY, United States
| | - Jasmina S. Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, CO, United States
| | - Barbara Marcolin
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, CO, United States
| | - Robert E. Thorne
- Laboratory of Atomic and Solid-State Physics, Cornell University, Ithaca, NY, United States
| | - Pratul Agarwal
- Department of Physiological Sciences and High Performance Computing Center, Oklahoma State University, Stillwater, OK, United States
| | - Elan Zohar Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, Aurora, CO, United States
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5
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Kovács D, Bodor A. The influence of random-coil chemical shifts on the assessment of structural propensities in folded proteins and IDPs. RSC Adv 2023; 13:10182-10203. [PMID: 37006359 PMCID: PMC10065145 DOI: 10.1039/d3ra00977g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/15/2023] [Indexed: 04/03/2023] Open
Abstract
In studying secondary structural propensities of proteins by nuclear magnetic resonance (NMR) spectroscopy, secondary chemical shifts (SCSs) serve as the primary atomic scale observables. For SCS calculation, the selection of an appropriate random coil chemical shift (RCCS) dataset is a crucial step, especially when investigating intrinsically disordered proteins (IDPs). The scientific literature is abundant in such datasets, however, the effect of choosing one over all the others in a concrete application has not yet been studied thoroughly and systematically. Hereby, we review the available RCCS prediction methods and to compare them, we conduct statistical inference by means of the nonparametric sum of ranking differences and comparison of ranks to random numbers (SRD-CRRN) method. We try to find the RCCS predictors best representing the general consensus regarding secondary structural propensities. The existence and the magnitude of resulting differences on secondary structure determination under varying sample conditions (temperature, pH) are demonstrated and discussed for globular proteins and especially IDPs.
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Affiliation(s)
- Dániel Kovács
- ELTE, Eötvös Loránd University, Institute of Chemistry, Analytical and BioNMR Laboratory Pázmány Péter sétány 1/A Budapest 1117 Hungary
- Eötvös Loránd University, Hevesy György PhD School of Chemistry Pázmány Péter sétány 1/A Budapest 1117 Hungary
| | - Andrea Bodor
- ELTE, Eötvös Loránd University, Institute of Chemistry, Analytical and BioNMR Laboratory Pázmány Péter sétány 1/A Budapest 1117 Hungary
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6
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Yu L, Hall DD, Zhao W, Song LS. NMR resonance assignments of the DNA binding domain of mouse Junctophilin-2. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:273-279. [PMID: 35665900 PMCID: PMC10394741 DOI: 10.1007/s12104-022-10091-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Junctophilin-2 (JP2) is a critical structural protein in the heart by stabilizing junctional membrane complexes between the plasma membrane and sarcoplasmic reticula responsible for precise Ca2+ regulation. Such complexes are essential for efficient cardiomyocyte contraction and adaptation to altered cardiac workload conditions. Mutations in the JPH2 gene that encodes JP2 are associated with inherited cardiomyopathies and arrhythmias, and disruption of JP2 function is lethal. Interestingly, cardiac stress promotes the proteolytic cleavage of JP2 that triggers the translocation of its N-terminal fragment into the nucleus to repress maladaptive gene transcription. We previously found that the central region of JP2 is responsible for mediating direct DNA binding interactions. Recent structural studies indicate that this region serves as a structural role in the cytosolic form of JP2 by folding into a single continuous α-helix. However, the structural basis of how this DNA-binding domain interacts with DNA is not known. Here, we report the backbone and sidechain assignments of the DNA-binding domain (residues 331-413) of mouse JP2. These assignments reveal that the JP2 DNA binding domain is an intrinsically disordered protein and contains two α-helices located in the C-terminal portion of the protein. Moreover, this protein binds to DNA in a similar manner to that shown previously by electrophoretic mobility shift assays. Therefore, these assignments provide a framework for further structural studies into the interaction of this JP2 domain with DNA for the elucidation of transcriptional regulation of stress-responsive genes as well as its role in the stabilization of junctional membrane complexes.
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Affiliation(s)
- Liping Yu
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, B291, CBRB, 285 Newton Road, Iowa City, IA, 52242, USA.
- CCOM NMR Core Facility, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA.
| | - Duane D Hall
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 285 Newton Road, Iowa City, IA, 52242, USA
| | - Weiyang Zhao
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 285 Newton Road, Iowa City, IA, 52242, USA
| | - Long-Sheng Song
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, B291, CBRB, 285 Newton Road, Iowa City, IA, 52242, USA.
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 285 Newton Road, Iowa City, IA, 52242, USA.
- Fraternal Order of Eagles Diabetes Research Center, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA.
- Iowa City Veterans Affairs Medical Center, Iowa City, IA, 52242, USA.
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7
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Lee E, Redzic JS, Nemkov T, Saviola AJ, Dzieciatkowska M, Hansen KC, D’Alessandro A, Dinarello C, Eisenmesser EZ. Human and Bacterial Toll-Interleukin Receptor Domains Exhibit Distinct Dynamic Features and Functions. Molecules 2022; 27:4494. [PMID: 35889366 PMCID: PMC9318647 DOI: 10.3390/molecules27144494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 02/04/2023] Open
Abstract
Toll-interleukin receptor (TIR) domains have emerged as critical players involved in innate immune signaling in humans but are also expressed as potential virulence factors within multiple pathogenic bacteria. However, there has been a shortage of structural studies aimed at elucidating atomic resolution details with respect to their interactions, potentially owing to their dynamic nature. Here, we used a combination of biophysical and biochemical studies to reveal the dynamic behavior and functional interactions of a panel of both bacterial TIR-containing proteins and mammalian receptor TIR domains. Regarding dynamics, all three bacterial TIR domains studied here exhibited an inherent exchange that led to severe resonance line-broadening, revealing their intrinsic dynamic nature on the intermediate NMR timescale. In contrast, the three mammalian TIR domains studied here exhibited a range in terms of their dynamic exchange that spans multiple timescales. Functionally, only the bacterial TIR domains were catalytic towards the cleavage of NAD+, despite the conservation of the catalytic nucleophile on human TIR domains. Our development of NMR-based catalytic assays allowed us to further identify differences in product formation for gram-positive versus gram-negative bacterial TIR domains. Differences in oligomeric interactions were also revealed, whereby bacterial TIR domains self-associated solely through their attached coil-coil domains, in contrast to the mammalian TIR domains that formed homodimers and heterodimers through reactive cysteines. Finally, we provide the first atomic-resolution studies of a bacterial coil-coil domain and provide the first atomic model of the TIR domain from a human anti-inflammatory IL-1R8 protein that undergoes a slow inherent exchange.
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Affiliation(s)
- Eunjeong Lee
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| | - Jasmina S. Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| | - Anthony J. Saviola
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| | - Angelo D’Alessandro
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
| | - Charles Dinarello
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA;
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Elan Z. Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, Aurora, CO 80045, USA; (E.L.); (J.S.R.); (T.N.); (A.J.S.); (M.D.); (K.C.H.); (A.D.)
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8
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Ahlawat S, Mote KR, Lakomek NA, Agarwal V. Solid-State NMR: Methods for Biological Solids. Chem Rev 2022; 122:9643-9737. [PMID: 35238547 DOI: 10.1021/acs.chemrev.1c00852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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Baskaran K, Craft DL, Eghbalnia HR, Gryk MR, Hoch JC, Maciejewski MW, Schuyler AD, Wedell JR, Wilburn CW. Merging NMR Data and Computation Facilitates Data-Centered Research. Front Mol Biosci 2022; 8:817175. [PMID: 35111815 PMCID: PMC8802229 DOI: 10.3389/fmolb.2021.817175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/23/2021] [Indexed: 12/01/2022] Open
Abstract
The Biological Magnetic Resonance Data Bank (BMRB) has served the NMR structural biology community for 40 years, and has been instrumental in the development of many widely-used tools. It fosters the reuse of data resources in structural biology by embodying the FAIR data principles (Findable, Accessible, Inter-operable, and Re-usable). NMRbox is less than a decade old, but complements BMRB by providing NMR software and high-performance computing resources, facilitating the reuse of software resources. BMRB and NMRbox both facilitate reproducible research. NMRbox also fosters the development and deployment of complex meta-software. Combining BMRB and NMRbox helps speed and simplify workflows that utilize BMRB, and enables facile federation of BMRB with other data repositories. Utilization of BMRB and NMRbox in tandem will enable additional advances, such as machine learning, that are poised to become increasingly powerful.
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Affiliation(s)
| | | | - Hamid R. Eghbalnia
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | | | - Jeffrey C. Hoch
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
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10
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Miao Z, Wang Q, Xiao X, Kamal GM, Song L, Zhang X, Li C, Zhou X, Jiang B, Liu M. CSI-LSTM: a web server to predict protein secondary structure using bidirectional long short term memory and NMR chemical shifts. JOURNAL OF BIOMOLECULAR NMR 2021; 75:393-400. [PMID: 34510297 DOI: 10.1007/s10858-021-00383-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
Protein secondary structure provides rich structural information, hence the description and understanding of protein structure relies heavily on it. Identification or prediction of secondary structures therefore plays an important role in protein research. In protein NMR studies, it is more convenient to predict secondary structures from chemical shifts as compared to the traditional determination methods based on inter-nuclear distances provided by NOESY experiment. In recent years, there was a significant improvement observed in deep neural networks, which had been applied in many research fields. Here we proposed a deep neural network based on bidirectional long short term memory (biLSTM) to predict protein 3-state secondary structure using NMR chemical shifts of backbone nuclei. While comparing with the existing methods the proposed method showed better prediction accuracy. Based on the proposed method, a web server has been built to provide protein secondary structure prediction service.
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Affiliation(s)
- Zhiwei Miao
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, 430071, Wuhan, China
| | - Qianqian Wang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, 430071, Wuhan, China
| | - Xiongjie Xiao
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, 430071, Wuhan, China
| | - Ghulam Mustafa Kamal
- Department of Chemistry, Khwaja Fareed University of Engineering & Information Technology, Rahim Yar Khan, Punjab, 64200, Pakistan
| | - Linhong Song
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, 430071, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Xu Zhang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, 430071, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Conggang Li
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, 430071, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Xin Zhou
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, 430071, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Bin Jiang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, 430071, Wuhan, China.
- University of Chinese Academy of Sciences, Beijing, 10049, China.
| | - Maili Liu
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, 430071, Wuhan, China.
- University of Chinese Academy of Sciences, Beijing, 10049, China.
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11
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Redzic JS, Lee E, Born A, Issaian A, Henen MA, Nichols PJ, Blue A, Hansen KC, D'Alessandro A, Vögeli B, Eisenmesser EZ. The Inherent Dynamics and Interaction Sites of the SARS-CoV-2 Nucleocapsid N-Terminal Region. J Mol Biol 2021; 433:167108. [PMID: 34161778 PMCID: PMC8214912 DOI: 10.1016/j.jmb.2021.167108] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/16/2022]
Abstract
The nucleocapsid protein is one of four structural proteins encoded by SARS-CoV-2 and plays a central role in packaging viral RNA and manipulating the host cell machinery, yet its dynamic behavior and promiscuity in nucleotide binding has made standard structural methods to address its atomic-resolution details difficult. To begin addressing the SARS-CoV-2 nucleocapsid protein interactions with both RNA and the host cell along with its dynamic behavior, we have specifically focused on the folded N-terminal domain (NTD) and its flanking regions using nuclear magnetic resonance solution studies. Studies performed here reveal a large repertoire of interactions, which includes a temperature-dependent self-association mediated by the disordered flanking regions that also serve as binding sites for host cell cyclophilin-A while nucleotide binding is largely mediated by the central NTD core. NMR studies that include relaxation experiments have revealed the complicated dynamic nature of this viral protein. Specifically, while much of the N-terminal core domain exhibits micro-millisecond motions, a central β-hairpin shows elevated inherent flexibility on the pico-nanosecond timescale and the serine/arginine-rich region of residues 176-209 undergoes multiple exchange phenomena. Collectively, these studies have begun to reveal the complexities of the nucleocapsid protein dynamics and its preferred interaction sites with its biological targets.
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Affiliation(s)
- Jasmina S Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States
| | - Eunjeong Lee
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States
| | - Alexandra Born
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States
| | - Aaron Issaian
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States; Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Parker J Nichols
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States
| | - Ashley Blue
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, United States
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States.
| | - Elan Zohar Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States.
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12
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Vincenzi M, Mercurio FA, Leone M. NMR Spectroscopy in the Conformational Analysis of Peptides: An Overview. Curr Med Chem 2021; 28:2729-2782. [PMID: 32614739 DOI: 10.2174/0929867327666200702131032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/21/2020] [Accepted: 05/28/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND NMR spectroscopy is one of the most powerful tools to study the structure and interaction properties of peptides and proteins from a dynamic perspective. Knowing the bioactive conformations of peptides is crucial in the drug discovery field to design more efficient analogue ligands and inhibitors of protein-protein interactions targeting therapeutically relevant systems. OBJECTIVE This review provides a toolkit to investigate peptide conformational properties by NMR. METHODS Articles cited herein, related to NMR studies of peptides and proteins were mainly searched through PubMed and the web. More recent and old books on NMR spectroscopy written by eminent scientists in the field were consulted as well. RESULTS The review is mainly focused on NMR tools to gain the 3D structure of small unlabeled peptides. It is more application-oriented as it is beyond its goal to deliver a profound theoretical background. However, the basic principles of 2D homonuclear and heteronuclear experiments are briefly described. Protocols to obtain isotopically labeled peptides and principal triple resonance experiments needed to study them, are discussed as well. CONCLUSION NMR is a leading technique in the study of conformational preferences of small flexible peptides whose structure can be often only described by an ensemble of conformations. Although NMR studies of peptides can be easily and fast performed by canonical protocols established a few decades ago, more recently we have assisted to tremendous improvements of NMR spectroscopy to investigate instead large systems and overcome its molecular weight limit.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
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13
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Sanz-Hernández M, De Simone A. Backbone NMR assignments of the C-terminal domain of the human prion protein and its disease-associated T183A variant. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:193-196. [PMID: 33590433 PMCID: PMC7974147 DOI: 10.1007/s12104-021-10005-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
Transmissible spongiform encephalopathies (TSEs) are fatal neurodegenerative disorders associated with the misfolding and aggregation of the human prion protein (huPrP). Despite efforts into investigating the process of huPrP aggregation, the mechanisms triggering its misfolding remain elusive. A number of TSE-associated mutations of huPrP have been identified, but their role at the onset and progression of prion diseases is unclear. Here we report the NMR assignments of the C-terminal globular domain of the wild type huPrP and the pathological mutant T183A. The differences in chemical shifts between the two variants reveal conformational alterations in some structural elements of the mutant, whereas the analyses of secondary shifts and random coil index provide indications on the putative mechanisms of misfolding of T183A huPrP.
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Affiliation(s)
- Máximo Sanz-Hernández
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, UK.
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy.
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14
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Okuda M, Ekimoto T, Kurita JI, Ikeguchi M, Nishimura Y. Structural and dynamical insights into the PH domain of p62 in human TFIIH. Nucleic Acids Res 2021; 49:2916-2930. [PMID: 33211877 PMCID: PMC7969019 DOI: 10.1093/nar/gkaa1045] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 09/30/2020] [Accepted: 10/22/2020] [Indexed: 11/15/2022] Open
Abstract
TFIIH is a crucial transcription and DNA repair factor consisting of the seven-subunit core. The core subunit p62 contains a pleckstrin homology domain (PH-D), which is essential for locating TFIIH at transcription initiation and DNA damage sites, and two BSD (BTF2-like transcription factors, synapse-associated proteins and DOS2-like proteins) domains. A recent cryo-electron microscopy (cryo-EM) structure of human TFIIH visualized most parts of core, except for the PH-D. Here, by nuclear magnetic resonance spectroscopy we have established the solution structure of human p62 PH-D connected to the BSD1 domain by a highly flexible linker, suggesting the flexibility of PH-D in TFIIH. Based on this dynamic character, the PH-D was modeled in the cryo-EM structure to obtain the whole human TFIIH core structure, which indicates that the PH-D moves around the surface of core with a specific but limited spatial distribution; these dynamic structures were refined by molecular dynamics (MD) simulations. Furthermore, we built models, also refined by MD simulations, of TFIIH in complex with five p62-binding partners, including transcription factors TFIIEα, p53 and DP1, and nucleotide excision repair factors XPC and UVSSA. The models explain why the PH-D is crucially targeted by these factors, which use their intrinsically disordered acidic regions for TFIIH recruitment.
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Affiliation(s)
- Masahiko Okuda
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Toru Ekimoto
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Jun-Ichi Kurita
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,RIKEN Medical Sciences Innovation Hub Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima 739-8258, Japan
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15
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Liu S, Refaei M, Liu S, Decker A, Hinerman JM, Herr AB, Howell M, Musier-Forsyth K, Tsang P. Hairpin RNA-induced conformational change of a eukaryotic-specific lysyl-tRNA synthetase extension and role of adjacent anticodon-binding domain. J Biol Chem 2020; 295:12071-12085. [PMID: 32611767 PMCID: PMC7443506 DOI: 10.1074/jbc.ra120.013852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 06/26/2020] [Indexed: 11/06/2022] Open
Abstract
Human lysyl-tRNA synthetase (hLysRS) is essential for aminoacylation of tRNALys Higher eukaryotic LysRSs possess an N-terminal extension (Nterm) previously shown to facilitate high-affinity tRNA binding and aminoacylation. This eukaryote-specific appended domain also plays a critical role in hLysRS nuclear localization, thus facilitating noncanonical functions of hLysRS. The structure is intrinsically disordered and therefore remains poorly characterized. Findings of previous studies are consistent with the Nterm domain undergoing a conformational transition to an ordered structure upon nucleic acid binding. In this study, we used NMR to investigate how the type of RNA, as well as the presence of the adjacent anticodon-binding domain (ACB), influences the Nterm conformation. To explore the latter, we used sortase A ligation to produce a segmentally labeled tandem-domain protein, Nterm-ACB. In the absence of RNA, Nterm remained disordered regardless of ACB attachment. Both alone and when attached to ACB, Nterm structure remained unaffected by titration with single-stranded RNAs. The central region of the Nterm domain adopted α-helical structure upon titration of Nterm and Nterm-ACB with RNA hairpins containing double-stranded regions. Nterm binding to the RNA hairpins resulted in CD spectral shifts consistent with an induced helical structure. NMR and fluorescence anisotropy revealed that Nterm binding to hairpin RNAs is weak but that the binding affinity increases significantly upon covalent attachment to ACB. We conclude that the ACB domain facilitates induced-fit conformational changes and confers high-affinity RNA hairpin binding, which may be advantageous for functional interactions of LysRS with a variety of different binding partners.
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Affiliation(s)
- Sheng Liu
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA
| | - Maryanne Refaei
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA
| | - Shuohui Liu
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, Ohio, USA
| | - Aaron Decker
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA
| | - Jennifer M. Hinerman
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Andrew B. Herr
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Mike Howell
- Protein Express, Inc., Cincinnati, Ohio, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, Ohio, USA
| | - Pearl Tsang
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA
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16
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Goldbourt A. Structural characterization of bacteriophage viruses by NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 114-115:192-210. [PMID: 31779880 DOI: 10.1016/j.pnmrs.2019.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/03/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
Magic-angle spinning (MAS) solid-state NMR has provided structural insights into various bacteriophage systems including filamentous, spherical, and tailed bacteriophage viruses. A variety of methodologies have been utilized including elementary two and three-dimensional assignment experiments, proton-detection techniques at fast spinning speeds, non-uniform sampling, structure determination protocols, conformational dynamics revealed by recoupling of anisotropic interactions, and enhancement by dynamic nuclear polarization. This review summarizes most of the studies performed during the last decade by MAS techniques and makes comparisons with prior knowledge obtained from static and solution NMR techniques. Chemical shifts for the capsids of the various systems are reported and analyzed, and DNA shifts are reported and discussed in the context of general high molecular-weight DNA molecules. Chemical shift and torsion angle prediction techniques are compared and applied to the various phage systems. The structures of the intact M13 filamentous bacteriophage and that of the Acinetobacter phage AP205 capsid, determined using MAS-based experimental data, are presented. Finally, filamentous phages, which are highly rigid systems, show interesting dynamics at the interface of the capsid and DNA, and their mutual electrostatic interactions are shown to be mediated by highly mobile positively charged residues. Novel results obtained from recoupling the chemical shift anisotropy of a single arginine in IKe phage, which is in contact with its DNA, further demonstrate this point. MAS NMR thus provides many new insights into phage structure, and on the other hand the richness, complexity and variety of bacteriophage systems provide opportunities for new NMR methodologies and technique developments.
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Affiliation(s)
- Amir Goldbourt
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.
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17
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Nie Y, Li S, Zhu J, Hu R, Liu M, He T, Yang Y. Chemical shift assignments of a camelid nanobody against aflatoxin B 1. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:75-78. [PMID: 30328057 DOI: 10.1007/s12104-018-9855-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 10/11/2018] [Indexed: 06/08/2023]
Abstract
Nanobodies (Nbs) are the variable domain of the heavy-chain antibodies produced from Camelidae, which possess comparable binding affinities and specificity to conventional antibodies. Nbs have become valuable and versatile tools for numerous biotechnology applications due to their small size (12-15 kDa), high solubility, exceptional stability, and facile genetic manipulation. The interactions between Nbs and protein antigens have been well-studied, but less work has been done to characterize their ability to bind small molecule haptens. Here we present the backbone and side-chain assignments of the 1H, 13C and 15N resonances of Nb26 (123 amino acids), a nanobody that recognizes the hapten aflatoxin B1 (AFB1). These assignments are preliminary work towards the determination of the structure of free Nb26 using NMR spectroscopy, which will provide useful information about the complex structure of "Nb26-AFB1" and the recognition mechanism about how Nb26 binds to AFB1.
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Affiliation(s)
- Yao Nie
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuangli Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Ting He
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China.
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18
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Local unfolding of the HSP27 monomer regulates chaperone activity. Nat Commun 2019; 10:1068. [PMID: 30842409 PMCID: PMC6403371 DOI: 10.1038/s41467-019-08557-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 12/20/2018] [Indexed: 12/21/2022] Open
Abstract
The small heat-shock protein HSP27 is a redox-sensitive molecular chaperone that is expressed throughout the human body. Here, we describe redox-induced changes to the structure, dynamics, and function of HSP27 and its conserved α-crystallin domain (ACD). While HSP27 assembles into oligomers, we show that the monomers formed upon reduction are highly active chaperones in vitro, but are susceptible to self-aggregation. By using relaxation dispersion and high-pressure nuclear magnetic resonance (NMR) spectroscopy, we observe that the pair of β-strands that mediate dimerisation partially unfold in the monomer. We note that numerous HSP27 mutations associated with inherited neuropathies cluster to this dynamic region. High levels of sequence conservation in ACDs from mammalian sHSPs suggest that the exposed, disordered interface present in free monomers or oligomeric subunits may be a general, functional feature of sHSPs. The small heat-shock protein HSP27 occurs predominantly in oligomeric forms, which makes its structural characterisation challenging. Here the authors employ CPMG and high-pressure NMR with native mass spectrometry and biophysical assays to show that the active monomeric form of HSP27 is substantially disordered and highly chaperone-active.
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19
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MacCarthy E, Perry D, Kc DB. Advances in Protein Super-Secondary Structure Prediction and Application to Protein Structure Prediction. Methods Mol Biol 2019; 1958:15-45. [PMID: 30945212 DOI: 10.1007/978-1-4939-9161-7_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Due to the advancement in various sequencing technologies, the gap between the number of protein sequences and the number of experimental protein structures is ever increasing. Community-wide initiatives like CASP have resulted in considerable efforts in the development of computational methods to accurately model protein structures from sequences. Sequence-based prediction of super-secondary structure has direct application in protein structure prediction, and there have been significant efforts in the prediction of super-secondary structure in the last decade. In this chapter, we first introduce the protein structure prediction problem and highlight some of the important progress in the field of protein structure prediction. Next, we discuss recent methods for the prediction of super-secondary structures. Finally, we discuss applications of super-secondary structure prediction in structure prediction/analysis of proteins. We also discuss prediction of protein structures that are composed of simple super-secondary structure repeats and protein structures that are composed of complex super-secondary structure repeats. Finally, we also discuss the recent trends in the field.
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Affiliation(s)
- Elijah MacCarthy
- Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC, USA
| | - Derrick Perry
- Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC, USA
| | - Dukka B Kc
- Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC, USA.
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20
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Sticht J, Bertazzon M, Henning LM, Licha JR, Abualrous ET, Freund C. FBP21's C-Terminal Domain Remains Dynamic When Wrapped around the c-Sec63 Unit of Brr2 Helicase. Biophys J 2018; 116:406-418. [PMID: 30558886 DOI: 10.1016/j.bpj.2018.11.3123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 10/12/2018] [Accepted: 11/19/2018] [Indexed: 01/20/2023] Open
Abstract
Based on our recent finding that FBP21 regulates human Brr2 helicase activity involved in the activation of the spliceosomal B-complex, we investigated the structural and dynamic contribution of FBP21 to the interaction. By using NMR spectroscopy, we could show that the 50 C-terminal residues of FBP21 (FBP21326-376), which are sufficient to fully form the interaction with the C-terminal Sec63 unit of Brr2 (Brr2C-Sec63), adopt a random-coil conformation in their unbound state. Upon interaction with Brr2C-Sec63, 42 residues of FBP21326-376 cover the large binding site on Brr2C-Sec63 in an extended conformation. Short charged motifs are steering complex formation, still allowing the bound state to retain dynamics. Based on fragment docking in combination with experimental restraints, we present models of the complex structure. The FBP21326-376/Brr2C-Sec63 interaction thus presents an example of an intrinsically disordered protein/ordered-protein interaction in which a large binding site provides high specificity and, in combination with conformational disorder, displays a relatively high affinity.
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Affiliation(s)
- Jana Sticht
- Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany; Core Facility BioSupraMol, Freie Universität Berlin, Berlin, Germany.
| | - Miriam Bertazzon
- Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Lisa M Henning
- Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Jan R Licha
- Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Esam T Abualrous
- Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany; Computational Molecular Biology Group, Freie Universität Berlin, Berlin, Germany
| | - Christian Freund
- Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany.
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21
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Sturlese M, Manta B, Bertarello A, Bonilla M, Lelli M, Zambelli B, Grunberg K, Mammi S, Comini MA, Bellanda M. The lineage-specific, intrinsically disordered N-terminal extension of monothiol glutaredoxin 1 from trypanosomes contains a regulatory region. Sci Rep 2018; 8:13716. [PMID: 30209332 PMCID: PMC6135854 DOI: 10.1038/s41598-018-31817-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 08/23/2018] [Indexed: 12/31/2022] Open
Abstract
Glutaredoxins (Grx) are small proteins conserved throughout all the kingdoms of life that are engaged in a wide variety of biological processes and share a common thioredoxin-fold. Among them, class II Grx are redox-inactive proteins involved in iron-sulfur (FeS) metabolism. They contain a single thiol group in their active site and use low molecular mass thiols such as glutathione as ligand for binding FeS-clusters. In this study, we investigated molecular aspects of 1CGrx1 from the pathogenic parasite Trypanosoma brucei brucei, a mitochondrial class II Grx that fulfills an indispensable role in vivo. Mitochondrial 1CGrx1 from trypanosomes differs from orthologues in several features including the presence of a parasite-specific N-terminal extension (NTE) whose role has yet to be elucidated. Previously we have solved the structure of a truncated form of 1CGrx1 containing only the conserved glutaredoxin domain but lacking the NTE. Our aim here is to investigate the effect of the NTE on the conformation of the protein. We therefore solved the NMR structure of the full-length protein, which reveals subtle but significant differences with the structure of the NTE-less form. By means of different experimental approaches, the NTE proved to be intrinsically disordered and not involved in the non-redox dependent protein dimerization, as previously suggested. Interestingly, the portion comprising residues 65–76 of the NTE modulates the conformational dynamics of the glutathione-binding pocket, which may play a role in iron-sulfur cluster assembly and delivery. Furthermore, we disclosed that the class II-strictly conserved loop that precedes the active site is critical for stabilizing the protein structure. So far, this represents the first communication of a Grx containing an intrinsically disordered region that defines a new protein subgroup within class II Grx.
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Affiliation(s)
- Mattia Sturlese
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy.,Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy
| | - Bruno Manta
- Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay.,Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Igua 4425, 11400, Montevideo, Uruguay.,New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA
| | - Andrea Bertarello
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Mariana Bonilla
- Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Moreno Lelli
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino (FI), Italy.,Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino (FI), Italy.,Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Barbara Zambelli
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin 40, 40127, Bologna, Italy
| | - Karin Grunberg
- Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Stefano Mammi
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Marcelo A Comini
- Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Massimo Bellanda
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy.
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22
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Paukovich N, Xue M, Elder JR, Redzic JS, Blue A, Pike H, Miller BG, Pitts TM, Pollock DD, Hansen K, D'Alessandro A, Eisenmesser EZ. Biliverdin Reductase B Dynamics Are Coupled to Coenzyme Binding. J Mol Biol 2018; 430:3234-3250. [PMID: 29932944 DOI: 10.1016/j.jmb.2018.06.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/05/2018] [Accepted: 06/06/2018] [Indexed: 12/28/2022]
Abstract
Biliverdin reductase B (BLVRB) is a newly identified cellular redox regulator that catalyzes the NADPH-dependent reduction of multiple substrates. Through mass spectrometry analysis, we identified high levels of BLVRB in mature red blood cells, highlighting the importance of BLVRB in redox regulation. The BLVRB conformational changes that occur during conezyme/substrate binding and the role of dynamics in BLVRB function, however, remain unknown. Through a combination of NMR, kinetics, and isothermal titration calorimetry studies, we determined that BLVRB binds its coenzyme 500-fold more tightly than its substrate. While the active site of apo BLVRB is highly dynamic on multiple timescales, active site dynamics are largely quenched within holo BLVRB, in which dynamics are redistributed to other regions of the enzyme. We show that a single point mutation of Arg78➔Ala leads to both an increase in active site micro-millisecond motions and an increase in the microscopic rate constants of coenzyme binding. This demonstrates that altering BLVRB active site dynamics can directly cause a change in functional characteristics. Our studies thus address the solution behavior of apo and holo BLVRB and identify a role of enzyme dynamics in coenzyme binding.
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Affiliation(s)
- Natasia Paukovich
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
| | - Mengjun Xue
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
| | - James R Elder
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
| | - Jasmina S Redzic
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
| | - Ashley Blue
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Hamish Pike
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
| | - Brian G Miller
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32310, USA
| | - Todd M Pitts
- Division of Medical Oncology, School of Medicine, Aurora, CO 80045, USA
| | - David D Pollock
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
| | - Kirk Hansen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
| | - Elan Zohar Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA.
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23
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Abayev M, Rodrigues JPGLM, Srivastava G, Arshava B, Jaremko Ł, Jaremko M, Naider F, Levitt M, Anglister J. The solution structure of monomeric CCL5 in complex with a doubly sulfated N-terminal segment of CCR5. FEBS J 2018; 285:1988-2003. [PMID: 29619777 PMCID: PMC6433596 DOI: 10.1111/febs.14460] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/12/2018] [Accepted: 03/31/2018] [Indexed: 12/30/2022]
Abstract
The inflammatory chemokine CCL5, which binds the chemokine receptor CCR5 in a two-step mechanism so as to activate signaling pathways in hematopoetic cells, plays an important role in immune surveillance, inflammation, and development as well as in several immune system pathologies. The recently published crystal structure of CCR5 bound to a high-affinity variant of CCL5 lacks the N-terminal segment of the receptor that is post-translationally sulfated and is known to be important for high-affinity binding. Here, we report the NMR solution structure of monomeric CCL5 bound to a synthetic doubly sulfated peptide corresponding to the missing first 27 residues of CCR5. Our structures show that two sulfated tyrosine residues, sY10 and sY14, as well as the unsulfated Y15 form a network of strong interactions with a groove on a surface of CCL5 that is formed from evolutionarily conserved basic and hydrophobic amino acids. We then use our NMR structures, in combination with available crystal data, to create an atomic model of full-length wild-type CCR5:CCL5. Our findings reveal the structural determinants involved in the recognition of CCL5 by the CCR5 N terminus. These findings, together with existing structural data, provide a complete structural framework with which to understand the specificity of receptor:chemokine interactions. DATABASE Structural data are available in the PDB under the accession number 6FGP.
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Affiliation(s)
- Meital Abayev
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Gautam Srivastava
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Boris Arshava
- Department of Chemistry and Macromolecular Assembly Institute, College of Staten Island of the City University of New York, Staten Island, NY, USA
- The Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, NY, USA
| | - Łukasz Jaremko
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Gottingen, Germany
| | - Mariusz Jaremko
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Gottingen, Germany
| | - Fred Naider
- Department of Chemistry and Macromolecular Assembly Institute, College of Staten Island of the City University of New York, Staten Island, NY, USA
- The Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, NY, USA
| | - Michael Levitt
- Department of Structural Biology, Stanford University School of Medicine, CA, USA
| | - Jacob Anglister
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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24
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Johnson BA. From Raw Data to Protein Backbone Chemical Shifts Using NMRFx Processing and NMRViewJ Analysis. Methods Mol Biol 2018; 1688:257-310. [PMID: 29151214 DOI: 10.1007/978-1-4939-7386-6_13] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Assignment of the chemical shifts of the backbone atoms (HN, N, CA, CB, and C) of proteins is often a prerequisite to using NMR information in the study of proteins. These chemical shifts and their perturbations are the basis for the analysis of protein dynamics, ligand binding, and backbone conformation. They are generally assigned prior to full side-chain assignments and the determination of the complete three-dimensional molecular structure. This chapter describes the use of two software packages, NMRFx Processor and NMRViewJ, in going from raw NMR data to backbone assignments. The step-by-step procedure describes processing of the data and the use of manual and automated features of the RunAbout tool in NMRViewJ to perform the assignments.
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Affiliation(s)
- Bruce A Johnson
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA.
- One Moon Scientific, Inc., Westfield, NJ, 07090, USA.
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25
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Hafsa NE, Berjanskii MV, Arndt D, Wishart DS. Rapid and reliable protein structure determination via chemical shift threading. JOURNAL OF BIOMOLECULAR NMR 2018; 70:33-51. [PMID: 29196969 DOI: 10.1007/s10858-017-0154-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/14/2017] [Indexed: 06/07/2023]
Abstract
Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often < 10 min/structure) and to significantly outperform other shift-based or threading-based structure determination methods (in terms of top template model accuracy)-with an average TM-score performance of 0.68 (vs. 0.50-0.62 for other methods). Coupled with recent developments in chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca .
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Affiliation(s)
- Noor E Hafsa
- Department of Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada
| | - Mark V Berjanskii
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - David Arndt
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - David S Wishart
- Department of Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada.
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
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26
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Wang M, Quinn CM, Perilla JR, Zhang H, Shirra R, Hou G, Byeon IJ, Suiter CL, Ablan S, Urano E, Nitz TJ, Aiken C, Freed EO, Zhang P, Schulten K, Gronenborn AM, Polenova T. Quenching protein dynamics interferes with HIV capsid maturation. Nat Commun 2017; 8:1779. [PMID: 29176596 PMCID: PMC5701193 DOI: 10.1038/s41467-017-01856-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 10/19/2017] [Indexed: 11/14/2022] Open
Abstract
Maturation of HIV-1 particles encompasses a complex morphological transformation of Gag via an orchestrated series of proteolytic cleavage events. A longstanding question concerns the structure of the C-terminal region of CA and the peptide SP1 (CA–SP1), which represents an intermediate during maturation of the HIV-1 virus. By integrating NMR, cryo-EM, and molecular dynamics simulations, we show that in CA–SP1 tubes assembled in vitro, which represent the features of an intermediate assembly state during maturation, the SP1 peptide exists in a dynamic helix–coil equilibrium, and that the addition of the maturation inhibitors Bevirimat and DFH-055 causes stabilization of a helical form of SP1. Moreover, the maturation-arresting SP1 mutation T8I also induces helical structure in SP1 and further global dynamical and conformational changes in CA. Overall, our results show that dynamics of CA and SP1 are critical for orderly HIV-1 maturation and that small molecules can inhibit maturation by perturbing molecular motions. The process of HIV particle maturation involves complex molecular transitions. Here the authors combine NMR spectroscopy, cryo-EM, and molecular dynamics simulations to provide insight into the conformational equilibria in CA-SP1 assemblies relevant to HIV-1 maturation intermediates formation.
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Affiliation(s)
- Mingzhang Wang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA
| | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA. .,University of Illinois, Theoretical and Computational Biophysics Group, Urbana, IL, 61801, USA.
| | - Huilan Zhang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA
| | - Randall Shirra
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA.,Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA
| | - Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA
| | - In-Ja Byeon
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA.,Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA
| | - Christopher L Suiter
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA
| | - Sherimay Ablan
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Emiko Urano
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | | | - Christopher Aiken
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Eric O Freed
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Peijun Zhang
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA.,Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA.,Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK
| | - Klaus Schulten
- University of Illinois, Theoretical and Computational Biophysics Group, Urbana, IL, 61801, USA
| | - Angela M Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA. .,Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA.
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA. .,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA.
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27
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Hibino E, Inoue R, Sugiyama M, Kuwahara J, Matsuzaki K, Hoshino M. Identification of heteromolecular binding sites in transcription factors Sp1 and TAF4 using high-resolution nuclear magnetic resonance spectroscopy. Protein Sci 2017; 26:2280-2290. [PMID: 28857320 PMCID: PMC5654864 DOI: 10.1002/pro.3287] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/26/2017] [Accepted: 08/28/2017] [Indexed: 01/17/2023]
Abstract
The expression of eukaryotic genes is precisely controlled by interactions between general transcriptional factors and promoter-specific transcriptional activators. The fourth element of TATA-box binding protein-associated factor (TAF4), an essential subunit of the general transcription factor TFIID, serves as a coactivator for various promoter-specific transcriptional regulators. Interactions between TAF4 and site-specific transcriptional activators, such as Sp1, are important for regulating the expression levels of genes of interest. However, only limited information is available on the molecular mechanisms underlying the interactions between these transcriptional regulatory proteins. We herein analyzed the interaction between the transcriptional factors Sp1 and TAF4 using high-resolution solution nuclear magnetic resonance spectroscopy. We found that four glutamine-rich (Q-rich) regions in TAF4 were largely disordered under nearly physiological conditions. Among them, the first Q-rich region in TAF4 was essential for the interaction with another Q-rich region in the Sp1 molecule, most of which was largely disordered. The residues responsible for this interaction were specific and highly localized in a defined region within a range of 20-30 residues. Nevertheless, a detailed analysis of 13 C-chemical shift values suggested that no significant conformational change occurred upon binding. These results indicate a prominent and exceptional binding mode for intrinsically disordered proteins other than the well-accepted concept of "coupled folding and binding."
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Affiliation(s)
- Emi Hibino
- Graduate School of Pharmaceutical SciencesKyoto UniversityKyotoSakyo‐ku606‐8501Japan
| | - Rintaro Inoue
- Research Reactor Institute, Kyoto UniversitySennan‐gunOsaka590‐0494Japan
| | - Masaaki Sugiyama
- Research Reactor Institute, Kyoto UniversitySennan‐gunOsaka590‐0494Japan
| | - Jun Kuwahara
- Faculty of Pharmaceutical SciencesDoshisha Women's UniversityKyotanabe cityKyoto610‐0395Japan
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical SciencesKyoto UniversityKyotoSakyo‐ku606‐8501Japan
| | - Masaru Hoshino
- Graduate School of Pharmaceutical SciencesKyoto UniversityKyotoSakyo‐ku606‐8501Japan
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28
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Kobayashi A, Kanaba T, Satoh R, Ito Y, Sugiura R, Mishima M. Chemical shift assignments of the first and second RRMs of Nrd1, a fission yeast MAPK-target RNA binding protein. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:123-126. [PMID: 28284018 DOI: 10.1007/s12104-017-9731-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/17/2017] [Indexed: 06/06/2023]
Abstract
Negative regulator differentiation 1 (Nrd1), a fission yeast RNA binding protein, modulates cytokinesis and sexual development and contributes to stress granule formation in response to environmental stresses. Nrd1 comprises four RRM domains and binds and stabilizes Cdc4 mRNA that encodes the myosin II light chain. Nrd1 binds the Cpc2 fission-yeast RACK1 homolog, and the interaction promotes Nrd1 localization to stress granules. Interestingly, Pmk1 mitogen-activated protein kinase phosphorylates Thr40 in the unstructured N-terminal region and Thr126 in the first RRM domain of Nrd1. Phosphorylation significantly reduces RNA-binding activity and likely modulates Nrd1 function. To reveal the relationship between the structure and function of Nrd1 and how phosphorylation affects structure, we used heteronuclear NMR techniques to investigate the three-dimensional structure of Nrd1. Here we report the 1H, 13C, and 15N resonance assignments of RRM1-RRM2 (residues 108-284) comprising the first and second RRMs obtained using heteronuclear NMR techniques. Secondary structures derived from the chemical shifts are reported. These data should contribute to the understanding of the three-dimensional structure of the RRM1-RRM2 region of Nrd1 and the perturbation caused by phosphorylation.
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Affiliation(s)
- Ayaho Kobayashi
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, 192-0397, Japan
| | - Teppei Kanaba
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, 192-0397, Japan
- Bruker BioSpin K. K., 3-9, Moriya-cho, Kanagawa, Yokohama, 221-0022, Japan
| | - Ryosuke Satoh
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University, 3-4-1 Kowake, Higashi-Osaka, 577-8502, Japan
| | - Yutaka Ito
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, 192-0397, Japan
| | - Reiko Sugiura
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University, 3-4-1 Kowake, Higashi-Osaka, 577-8502, Japan
| | - Masaki Mishima
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, 192-0397, Japan.
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29
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Currie SL, Lau DKW, Doane JJ, Whitby FG, Okon M, McIntosh LP, Graves BJ. Structured and disordered regions cooperatively mediate DNA-binding autoinhibition of ETS factors ETV1, ETV4 and ETV5. Nucleic Acids Res 2017; 45:2223-2241. [PMID: 28161714 PMCID: PMC5389675 DOI: 10.1093/nar/gkx068] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/29/2017] [Indexed: 12/21/2022] Open
Abstract
Autoinhibition enables spatial and temporal regulation of cellular processes by coupling protein activity to surrounding conditions, often via protein partnerships or signaling pathways. We report the molecular basis of DNA-binding autoinhibition of ETS transcription factors ETV1, ETV4 and ETV5, which are often overexpressed in prostate cancer. Inhibitory elements that cooperate to repress DNA binding were identified in regions N- and C-terminal of the ETS domain. Crystal structures of these three factors revealed an α-helix in the C-terminal inhibitory domain that packs against the ETS domain and perturbs the conformation of its DNA-recognition helix. Nuclear magnetic resonance spectroscopy demonstrated that the N-terminal inhibitory domain (NID) is intrinsically disordered, yet utilizes transient intramolecular interactions with the DNA-recognition helix of the ETS domain to mediate autoinhibition. Acetylation of selected lysines within the NID activates DNA binding. This investigation revealed a distinctive mechanism for DNA-binding autoinhibition in the ETV1/4/5 subfamily involving a network of intramolecular interactions not present in other ETS factors. These distinguishing inhibitory elements provide a platform through which cellular triggers, such as protein–protein interactions or post-translational modifications, may specifically regulate the function of these oncogenic proteins.
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Affiliation(s)
- Simon L Currie
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112-5550, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112-5550, USA
| | - Desmond K W Lau
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver BC, V6T 1Z3, Canada
| | - Jedediah J Doane
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112-5550, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112-5550, USA
| | - Frank G Whitby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112-5650, USA
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver BC, V6T 1Z3, Canada
| | - Lawrence P McIntosh
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver BC, V6T 1Z3, Canada
| | - Barbara J Graves
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112-5550, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112-5550, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
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30
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Unraveling the meaning of chemical shifts in protein NMR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1564-1576. [PMID: 28716441 DOI: 10.1016/j.bbapap.2017.07.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/29/2017] [Accepted: 07/07/2017] [Indexed: 12/14/2022]
Abstract
Chemical shifts are among the most informative parameters in protein NMR. They provide wealth of information about protein secondary and tertiary structure, protein flexibility, and protein-ligand binding. In this report, we review the progress in interpreting and utilizing protein chemical shifts that has occurred over the past 25years, with a particular focus on the large body of work arising from our group and other Canadian NMR laboratories. More specifically, this review focuses on describing, assessing, and providing some historical context for various chemical shift-based methods to: (1) determine protein secondary and super-secondary structure; (2) derive protein torsion angles; (3) assess protein flexibility; (4) predict residue accessible surface area; (5) refine 3D protein structures; (6) determine 3D protein structures and (7) characterize intrinsically disordered proteins. This review also briefly covers some of the methods that we previously developed to predict chemical shifts from 3D protein structures and/or protein sequence data. It is hoped that this review will help to increase awareness of the considerable utility of NMR chemical shifts in structural biology and facilitate more widespread adoption of chemical-shift based methods by the NMR spectroscopists, structural biologists, protein biophysicists, and biochemists worldwide. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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31
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Davies HA, Rigden DJ, Phelan MM, Madine J. Probing Medin Monomer Structure and its Amyloid Nucleation Using 13C-Direct Detection NMR in Combination with Structural Bioinformatics. Sci Rep 2017; 7:45224. [PMID: 28327552 PMCID: PMC5361114 DOI: 10.1038/srep45224] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 02/20/2017] [Indexed: 12/21/2022] Open
Abstract
Aortic medial amyloid is the most prevalent amyloid found to date, but remarkably little is known about it. It is characterised by aberrant deposition of a 5.4 kDa protein called medin within the medial layer of large arteries. Here we employ a combined approach of ab initio protein modelling and 13C-direct detection NMR to generate a model for soluble monomeric medin comprising a stable core of three β-strands and shorter more labile strands at the termini. Molecular dynamics simulations suggested that detachment of the short, C-terminal β-strand from the soluble fold exposes key amyloidogenic regions as a potential site of nucleation enabling dimerisation and subsequent fibril formation. This mechanism resembles models proposed for several other amyloidogenic proteins suggesting that despite variations in sequence and protomer structure these proteins may share a common pathway for amyloid nucleation and subsequent protofibril and fibril formation.
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Affiliation(s)
- Hannah A. Davies
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, L69 7ZB, UK
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, L69 7ZB, UK
| | - Marie M. Phelan
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, L69 7ZB, UK
| | - Jillian Madine
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, L69 7ZB, UK
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32
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Lehnert E, Mao J, Mehdipour AR, Hummer G, Abele R, Glaubitz C, Tampé R. Antigenic Peptide Recognition on the Human ABC Transporter TAP Resolved by DNP-Enhanced Solid-State NMR Spectroscopy. J Am Chem Soc 2016; 138:13967-13974. [DOI: 10.1021/jacs.6b07426] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | | | - Ahmad Reza Mehdipour
- Department
of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str.
3, 60438 Frankfurt
am Main, Germany
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str.
3, 60438 Frankfurt
am Main, Germany
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33
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Amin N, Nietlispach D, Qamar S, Coyle J, Chiarparin E, Williams G. NMR backbone resonance assignment and solution secondary structure determination of human NSD1 and NSD2. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:315-320. [PMID: 27356987 DOI: 10.1007/s12104-016-9691-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 06/22/2016] [Indexed: 06/06/2023]
Abstract
Proteins of the NSD family are histone-methyl transferases with critical functions in the regulation of chromatin structure and function. NSD1 and NSD2 are homologous proteins that function as epigenetic regulators of transcription through their abilities to catalyse histone methylation. Misregulation of NSD1 and NSD2 expression or mutations in their genes are linked to a number of human diseases such as Sotos syndrome, and cancers including acute myeloid leukemia, multiple myeloma, and lung cancer. The catalytic domain of both proteins contains a conserved SET domain which is involved in histone methylation. Here we report the backbone resonance assignments and secondary structure information of the catalytic domains of human NSD1 and NSD2.
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Affiliation(s)
- Nader Amin
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK
- Nuffield Department of Population Health, University of Oxford, Richard Doll Building, Oxford, OX3 7LF, UK
| | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge, CB2 1GA, UK
| | - Seema Qamar
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK
| | - Joe Coyle
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK
| | - Elisabetta Chiarparin
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK
- AstraZeneca, 310 Cambridge Science Park, Cambridge, CB4 0WG, UK
| | - Glyn Williams
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK.
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34
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Wang CC, Lai WC, Chuang WJ. Predicting the redox state and secondary structure of cysteine residues using multi-dimensional classification analysis of NMR chemical shifts. JOURNAL OF BIOMOLECULAR NMR 2016; 66:55-68. [PMID: 27613298 DOI: 10.1007/s10858-016-0057-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/02/2016] [Indexed: 06/06/2023]
Abstract
A tool for predicting the redox state and secondary structure of cysteine residues using multi-dimensional analyses of different combinations of nuclear magnetic resonance (NMR) chemical shifts has been developed. A data set of cysteine [Formula: see text], (13)C(α), (13)C(β), (1)H(α), (1)H(N), and (15)N(H) chemical shifts was created, classified according to redox state and secondary structure, using a library of 540 re-referenced BioMagResBank (BMRB) entries. Multi-dimensional analyses of three, four, five, and six chemical shifts were used to derive rules for predicting the structural states of cysteine residues. The results from 60 BMRB entries containing 122 cysteines showed that four-dimensional analysis of the C(α), C(β), H(α), and N(H) chemical shifts had the highest prediction accuracy of 100 and 95.9 % for the redox state and secondary structure, respectively. The prediction of secondary structure using 3D, 5D, and 6D analyses had the accuracy of ~90 %, suggesting that H(N) and [Formula: see text] chemical shifts may be noisy and made the discrimination worse. A web server (6DCSi) was established to enable users to submit NMR chemical shifts, either in BMRB or key-in formats, for prediction. 6DCSi displays predictions using sets of 3, 4, 5, and 6 chemical shifts, which shows their consistency and allows users to draw their own conclusions. This web-based tool can be used to rapidly obtain structural information regarding cysteine residues directly from experimental NMR data.
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Affiliation(s)
- Ching-Cheng Wang
- Institute of Manufacturing Information and Systems, National Cheng Kung University College of Electrical Engineering and Computer Science, Tainan, 701, Taiwan
| | - Wen-Chung Lai
- Institute of Manufacturing Information and Systems, National Cheng Kung University College of Electrical Engineering and Computer Science, Tainan, 701, Taiwan
| | - Woei-Jer Chuang
- Department of Biochemistry and Molecular Biology, National Cheng Kung University College of Medicine, Tainan, 701, Taiwan.
- Department of Biochemistry, National Cheng Kung University College of Medicine, Tainan, 701, Taiwan.
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35
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Pucheta-Martinez E, D’Amelio N, Lelli M, Martinez-Torrecuadrada JL, Sudol M, Saladino G, Gervasio FL. Changes in the folding landscape of the WW domain provide a molecular mechanism for an inherited genetic syndrome. Sci Rep 2016; 6:30293. [PMID: 27456546 PMCID: PMC4960638 DOI: 10.1038/srep30293] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/01/2016] [Indexed: 10/25/2022] Open
Abstract
WW domains are small domains present in many human proteins with a wide array of functions and acting through the recognition of proline-rich sequences. The WW domain belonging to polyglutamine tract-binding protein 1 (PQBP1) is of particular interest due to its direct involvement in several X chromosome-linked intellectual disabilities, including Golabi-Ito-Hall (GIH) syndrome, where a single point mutation (Y65C) correlates with the development of the disease. The mutant cannot bind to its natural ligand WBP11, which regulates mRNA processing. In this work we use high-field high-resolution NMR and enhanced sampling molecular dynamics simulations to gain insight into the molecular causes the disease. We find that the wild type protein is partially unfolded exchanging among multiple beta-strand-like conformations in solution. The Y65C mutation further destabilizes the residual fold and primes the protein for the formation of a disulphide bridge, which could be at the origin of the loss of function.
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Affiliation(s)
| | - Nicola D’Amelio
- Research Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom
| | - Moreno Lelli
- University of Florence, Department of Chemistry, Magnetic Resonance Center (CERM), 50019 Sesto Fiorentino (FI), Italy
| | - Jorge L. Martinez-Torrecuadrada
- Crystallography and Protein Engineering Unit, Spanish National Cancer Research Centre (CNIO), C/Melchor Fernandez Almagro 3, 28029, Madrid, Spain
| | - Marius Sudol
- Institute of Molecular and Cell Biology A*STAR, 61 Biopolis, Singapore 138673, Republic of Singapore
- Mechanobiology Institute, 5A Engineering Drive 1, Singapore 117411, Republic of Singapore
- National University of Singapore, Department of Physiology, The Yong Loo Li School of Medicine, 2 Medical Drive, Singapore 117597, Republic of Singapore
| | - Giorgio Saladino
- Department of Chemistry, University College London, London WC1E 6BT, United Kingdom
- Research Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom
| | - Francesco Luigi Gervasio
- Department of Chemistry, University College London, London WC1E 6BT, United Kingdom
- Research Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom
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36
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Dick M, Hartmann R, Weiergräber OH, Bisterfeld C, Classen T, Schwarten M, Neudecker P, Willbold D, Pietruszka J. Mechanism-based inhibition of an aldolase at high concentrations of its natural substrate acetaldehyde: structural insights and protective strategies. Chem Sci 2016; 7:4492-4502. [PMID: 30155096 PMCID: PMC6016325 DOI: 10.1039/c5sc04574f] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 03/29/2016] [Indexed: 11/21/2022] Open
Abstract
2-Deoxy-d-ribose-5-phosphate aldolase (DERA) is used in organic synthesis for the enantioselective reaction between acetaldehyde and a broad range of other aldehydes as acceptor molecules. Nevertheless, its application is hampered by a poor tolerance towards high concentrations of acetaldehyde, its natural substrate. While numerous studies have been performed searching for new, more acetaldehyde-resistant DERAs, the mechanism underlying this deactivation process has remained elusive. By using NMR spectroscopy on both the protein and the small-molecule scale, we could show that a reaction product binds to the inner part of the enzyme, and that this effect can be partly reversed via heating. The crystal structure of DERA before and after acetaldehyde incubation was determined at high resolution, revealing a covalently bound reaction product bridging the catalytically active lysine (K167) to a nearby cysteine (C47) in the deactivated enzyme. A reaction mechanism is proposed where crotonaldehyde as the aldol product of two acetaldehyde molecules after water elimination forms a Schiff base with the lysine side chain, followed by Michael addition of the cysteine thiol group to the Cβ atom of the inhibitor. In support of this mechanism, direct incubation of DERA with crotonaldehyde results in a more than 100-fold stronger inhibition, compared to acetaldehyde, whereas mutation of C47 gives rise to a fully acetaldehyde-resistant DERA. Thus this variant appears perfectly suited for synthetic applications. A similar diagnostic and preventive strategy should be applicable to other biocatalysts suffering from mechanism-based inhibition by a reactive substrate, a condition that may be more common than currently appreciated in biotechnology.
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Affiliation(s)
- Markus Dick
- Institute of Bioorganic Chemistry , Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich , 52426 Jülich , Germany .
| | - Rudolf Hartmann
- Institute of Complex Systems , ICS-6: Structural Biochemistry , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
| | - Oliver H Weiergräber
- Institute of Complex Systems , ICS-6: Structural Biochemistry , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
| | - Carolin Bisterfeld
- Institute of Bioorganic Chemistry , Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich , 52426 Jülich , Germany .
| | - Thomas Classen
- Institute of Bio- and Geosciences , IBG-1: Biotechnology , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
| | - Melanie Schwarten
- Institute of Complex Systems , ICS-6: Structural Biochemistry , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
| | - Philipp Neudecker
- Institute of Complex Systems , ICS-6: Structural Biochemistry , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
- Institut für Physikalische Biologie , Heinrich-Heine-Universität Düsseldorf , 40225 Düsseldorf , Germany
| | - Dieter Willbold
- Institute of Complex Systems , ICS-6: Structural Biochemistry , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
- Institut für Physikalische Biologie , Heinrich-Heine-Universität Düsseldorf , 40225 Düsseldorf , Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry , Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich , 52426 Jülich , Germany .
- Institute of Bio- and Geosciences , IBG-1: Biotechnology , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
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37
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Characterisation of the conformational preference and dynamics of the intrinsically disordered N-terminal region of Beclin 1 by NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1128-1137. [PMID: 27288992 DOI: 10.1016/j.bbapap.2016.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/23/2016] [Accepted: 06/07/2016] [Indexed: 11/21/2022]
Abstract
Beclin 1 is a 450 amino acid protein that plays critical roles in the early stages of autophagosome formation. We recently reported the successful expression, purification and structural characterisation of the entire N-terminal region of Beclin 1 (residues 1-150), including its backbone NMR chemical shift assignments. Based on assigned backbone NMR chemical shifts, it has been established that the N-terminal region of Beclin 1 (1-150), including the BH3 domain (112-123), is intrinsically disordered in the absence of its interaction partners. Here, a detailed study of its conformational preference and backbone dynamics obtained from an analysis of its secondary structure populations using the δ2D method, and the measurements of effective hydrodynamic radius as well as (1)H temperature coefficients, (1)H solvent exchange rates, and (15)N relaxation parameters of backbone amides using NMR spectroscopy is reported. These data provide further evidence for the intrinsically disordered nature of the N-terminal region of Beclin 1 and support the view that the helical conformation adopted by the Beclin 1 BH3 domain upon interaction with binding partners such as BCL-2 pro-survival proteins is likely induced rather than pre-existing.
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38
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To V, Dzananovic E, McKenna SA, O’Neil J. The Dynamic Landscape of the Full-Length HIV-1 Transactivator of Transcription. Biochemistry 2016; 55:1314-25. [DOI: 10.1021/acs.biochem.5b01178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vu To
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Edis Dzananovic
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Sean A. McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Joe O’Neil
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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39
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Lee EF, Perugini MA, Pettikiriarachchi A, Evangelista M, Keizer DW, Yao S, Fairlie WD. The BECN1 N-terminal domain is intrinsically disordered. Autophagy 2016; 12:460-71. [PMID: 27046249 PMCID: PMC4836020 DOI: 10.1080/15548627.2016.1140292] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 12/16/2015] [Accepted: 01/04/2016] [Indexed: 10/22/2022] Open
Abstract
BECN1/Beclin 1 has a critical role in the early stages of autophagosome formation. Recently, structures of its central and C-terminal domains were reported, however, little structural information is available on the N-terminal domain, comprising a third of the protein. This lack of structural information largely stems from the inability to produce this region in a purified form. Here, we describe the expression and purification of the N-terminal domain of BECN1 (residues 1 to 150) and detailed biophysical characterization, including NMR spectroscopy. Combined, our studies demonstrated at the atomic level that the BECN1 N-terminal domain is intrinsically disordered, and apart from the BH3 subdomain, remains disordered following interaction with a binding partner, BCL2L1/BCL-XL. In addition, the BH3 domain α-helix induced upon interaction with BCL2L1 reverts to a disordered state when the complex is dissociated by exposure to a competitive inhibitor. No significant interactions between N- and C-terminal domains were detected.
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Affiliation(s)
- Erinna F. Lee
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, Melbourne, Victoria, Australia
| | - Matthew A. Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | | | - Marco Evangelista
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
| | - David W. Keizer
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Shenggen Yao
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - W. Douglas Fairlie
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, Melbourne, Victoria, Australia
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40
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Aumayr M, Fedosyuk S, Ruzicska K, Sousa-Blin C, Kontaxis G, Skern T. NMR analysis of the interaction of picornaviral proteinases Lb and 2A with their substrate eukaryotic initiation factor 4GII. Protein Sci 2015; 24:1979-96. [PMID: 26384734 PMCID: PMC4815241 DOI: 10.1002/pro.2807] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/14/2015] [Accepted: 09/17/2015] [Indexed: 11/09/2022]
Abstract
Messenger RNA is recruited to the eukaryotic ribosome by a complex including the eukaryotic initiation factor (eIF) 4E (the cap-binding protein), the scaffold protein eIF4G and the RNA helicase eIF4A. To shut-off host-cell protein synthesis, eIF4G is cleaved during picornaviral infection by a virally encoded proteinase; the structural basis of this reaction and its stimulation by eIF4E is unclear. We have structurally and biochemically investigated the interaction of purified foot-and-mouth disease virus (FMDV) leader proteinase (Lb(pro)), human rhinovirus 2 (HRV2) 2A proteinase (2A(pro)) and coxsackievirus B4 (CVB4) 2A(pro) with purified eIF4GII, eIF4E and the eIF4GII/eIF4E complex. Using nuclear magnetic resonance (NMR), we completed (13)C/(15) N sequential backbone assignment of human eIF4GII residues 551-745 and examined their binding to murine eIF4E. eIF4GII551-745 is intrinsically unstructured and remains so when bound to eIF4E. NMR and biophysical techniques for determining stoichiometry and binding constants revealed that the papain-like Lb(pro) only forms a stable complex with eIF4GII(551-745) in the presence of eIF4E, with KD values in the low nanomolar range; Lb(pro) contacts both eIF4GII and eIF4E. Furthermore, the unrelated chymotrypsin-like 2A(pro) from HRV2 and CVB4 also build a stable complex with eIF4GII/eIF4E, but with K(D) values in the low micromolar range. The HRV2 enzyme also forms a stable complex with eIF4E; however, none of the proteinases tested complex stably with eIF4GII alone. Thus, these three picornaviral proteinases have independently evolved to establish distinct triangular heterotrimeric protein complexes that may actively target ribosomes involved in mRNA recruitment to ensure efficient host cell shut-off.
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Affiliation(s)
- Martina Aumayr
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9/3, Vienna, A-1030, Austria
| | - Sofiya Fedosyuk
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9/3, Vienna, A-1030, Austria
| | - Katharina Ruzicska
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9/3, Vienna, A-1030, Austria
| | - Carla Sousa-Blin
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9/3, Vienna, A-1030, Austria
| | - Georg Kontaxis
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna, A-1030, Austria
| | - Tim Skern
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9/3, Vienna, A-1030, Austria
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41
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Quilici G, Berardi A, Gaudesi D, Gourlay LJ, Bolognesi M, Musco G. Backbone and side-chain (1)H, (15)N, (13)C assignment and secondary structure of BPSL1445 from Burkholderia pseudomallei. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:347-350. [PMID: 25893672 DOI: 10.1007/s12104-015-9607-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 04/11/2015] [Indexed: 06/04/2023]
Abstract
BPSL1445 is a lipoprotein produced by the Gram-negative bacterium Burkholderia pseudomallei (B. pseudomallei), the etiological agent of melioidosis. Immunodetection assays against sera patients using protein microarray suggest BPSL1445 involvement in melioidosis. Herein we report backbone, side chain NMR assignment and secondary structure for the recombinant protein.
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Affiliation(s)
- Giacomo Quilici
- Biomolecular NMR Unit, c/o S. Raffaele Scientific Institute, Via Olgettina, 58, Milan, Italy
| | - Andrea Berardi
- Biomolecular NMR Unit, c/o S. Raffaele Scientific Institute, Via Olgettina, 58, Milan, Italy
| | - Davide Gaudesi
- Biomolecular NMR Unit, c/o S. Raffaele Scientific Institute, Via Olgettina, 58, Milan, Italy
| | - Louise J Gourlay
- Department of Biosciences, University of Milan, Via Celoria, 26, 20133, Milan, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milan, Via Celoria, 26, 20133, Milan, Italy
| | - Giovanna Musco
- Biomolecular NMR Unit, c/o S. Raffaele Scientific Institute, Via Olgettina, 58, Milan, Italy.
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42
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Macdonald R, Sarkar D, Amer BR, Clubb RT. Solution structure of the PhoP DNA-binding domain from Mycobacterium tuberculosis. JOURNAL OF BIOMOLECULAR NMR 2015; 63:111-117. [PMID: 26209027 PMCID: PMC4714862 DOI: 10.1007/s10858-015-9965-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 07/10/2015] [Indexed: 06/05/2023]
Abstract
Tuberculosis caused by Mycobacterium tuberculosis is a leading cause of death world-wide. The PhoP protein is required for virulence and is part of the PhoPR two-component system that regulates gene expression. The NMR-derived solution structure of the PhoP C-terminal DNA-binding domain is reported. Residues 150 to 246 form a structured domain that contains a winged helix-turn-helix motif. We provide evidence that the transactivation loop postulated to contact RNA polymerase is partially disordered in solution, and that the polypeptide that connects the DNA-binding domain to the regulatory domain is unstructured.
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Affiliation(s)
- Ramsay Macdonald
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 602 Boyer Hall, Los Angeles, CA, 90095, USA
- UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA, 90095, USA
| | - Dibyendu Sarkar
- CSIR-Institute of Microbial Technology, Sector-39A, Chandigarh, 160036, India
| | - Brendan R Amer
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 602 Boyer Hall, Los Angeles, CA, 90095, USA
- UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA, 90095, USA
| | - Robert T Clubb
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 602 Boyer Hall, Los Angeles, CA, 90095, USA.
- Molecular Biology Institute, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA, 90095, USA.
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43
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Rad-Malekshahi M, Visscher KM, Rodrigues JPGLM, de Vries R, Hennink WE, Baldus M, Bonvin AMJJ, Mastrobattista E, Weingarth M. The Supramolecular Organization of a Peptide-Based Nanocarrier at High Molecular Detail. J Am Chem Soc 2015; 137:7775-84. [DOI: 10.1021/jacs.5b02919] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mazda Rad-Malekshahi
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Koen M. Visscher
- NMR
Spectroscopy, Bijvoet Center for Biomolecular Research, Department
of Chemistry, Faculty of Science, Utrecht University, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - João P. G. L. M. Rodrigues
- NMR
Spectroscopy, Bijvoet Center for Biomolecular Research, Department
of Chemistry, Faculty of Science, Utrecht University, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Renko de Vries
- Laboratory
of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands
| | - Wim E. Hennink
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Marc Baldus
- NMR
Spectroscopy, Bijvoet Center for Biomolecular Research, Department
of Chemistry, Faculty of Science, Utrecht University, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Alexandre M. J. J. Bonvin
- NMR
Spectroscopy, Bijvoet Center for Biomolecular Research, Department
of Chemistry, Faculty of Science, Utrecht University, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Enrico Mastrobattista
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Markus Weingarth
- NMR
Spectroscopy, Bijvoet Center for Biomolecular Research, Department
of Chemistry, Faculty of Science, Utrecht University, Padualaan
8, 3584 CH Utrecht, The Netherlands
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44
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Hafsa NE, Arndt D, Wishart DS. CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts. Nucleic Acids Res 2015; 43:W370-7. [PMID: 25979265 PMCID: PMC4489240 DOI: 10.1093/nar/gkv494] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/02/2015] [Indexed: 11/14/2022] Open
Abstract
The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I′, II′ and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0.
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Affiliation(s)
- Noor E Hafsa
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada
| | - David Arndt
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada
| | - David S Wishart
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada
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45
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Kumar AV, Ali RFM, Cao Y, Krishnan VV. Application of data mining tools for classification of protein structural class from residue based averaged NMR chemical shifts. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1545-52. [PMID: 25758094 DOI: 10.1016/j.bbapap.2015.02.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/25/2015] [Indexed: 10/23/2022]
Abstract
The number of protein sequences deriving from genome sequencing projects is outpacing our knowledge about the function of these proteins. With the gap between experimentally characterized and uncharacterized proteins continuing to widen, it is necessary to develop new computational methods and tools for protein structural information that is directly related to function. Nuclear magnetic resonance (NMR) provides powerful means to determine three-dimensional structures of proteins in the solution state. However, translation of the NMR spectral parameters to even low-resolution structural information such as protein class requires multiple time consuming steps. In this paper, we present an unorthodox method to predict the protein structural class directly by using the residue's averaged chemical shifts (ACS) based on machine learning algorithms. Experimental chemical shift information from 1491 proteins obtained from Biological Magnetic Resonance Bank (BMRB) and their respective protein structural classes derived from structural classification of proteins (SCOP) were used to construct a data set with 119 attributes and 5 different classes. Twenty four different classification schemes were evaluated using several performance measures. Overall the residue based ACS values can predict the protein structural classes with 80% accuracy measured by Matthew correlation coefficient. Specifically protein classes defined by mixed αβ or small proteins are classified with >90% correlation. Our results indicate that this NMR-based method can be utilized as a low-resolution tool for protein structural class identification without any prior chemical shift assignments.
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Affiliation(s)
- Arun V Kumar
- Department of Computer Science, California State University, Fresno, CA 93740, United States
| | - Rehana F M Ali
- Department of Computer Science, California State University, Fresno, CA 93740, United States
| | - Yu Cao
- Department of Computer Science, California State University, Fresno, CA 93740, United States
| | - V V Krishnan
- Department of Chemistry, California State University, Fresno, CA 93740, United States; Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, CA 95616, United States.
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Senior L, Crump MP, Williams C, Booth PJ, Mann S, Perriman AW, Curnow P. Structure and function of the silicifying peptide R5. J Mater Chem B 2015; 3:2607-2614. [DOI: 10.1039/c4tb01679c] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first detailed description of the structure and function of the silicifying peptide R5.
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Affiliation(s)
- Laura Senior
- School of Biochemistry
- University of Bristol
- UK
- Bristol Centre for Functional Nanomaterials
- University of Bristol
| | | | | | | | | | - Adam W. Perriman
- School of Cellular and Molecular Medicine
- University of Bristol
- UK
| | - Paul Curnow
- School of Biochemistry
- University of Bristol
- UK
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