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Abdullah SJ, Yan BTS, Palanivelu N, Dhanabal VB, Bifani JP, Bhattacharjya S. Outer-Membrane Permeabilization, LPS Transport Inhibition: Activity, Interactions, and Structures of Thanatin Derived Antimicrobial Peptides. Int J Mol Sci 2024; 25:2122. [PMID: 38396798 PMCID: PMC10888688 DOI: 10.3390/ijms25042122] [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: 01/11/2024] [Revised: 01/30/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Currently, viable antibiotics available to mitigate infections caused by drug-resistant Gram-negative bacteria are highly limited. Thanatin, a 21-residue-long insect-derived antimicrobial peptide (AMP), is a promising lead molecule for the potential development of novel antibiotics. Thanatin is extremely potent, particularly against the Enterobacter group of Gram-negative pathogens, e.g., E. coli and K. pneumoniae. As a mode of action, cationic thanatin efficiently permeabilizes the LPS-outer membrane and binds to the periplasmic protein LptAm to inhibit outer membrane biogenesis. Here, we have utilized N-terminal truncated 16- and 14-residue peptide fragments of thanatin and investigated structure, activity, and selectivity with correlating modes of action. A designed 16-residue peptide containing D-Lys (dk) named VF16 (V1PIIYCNRRT-dk-KCQRF16) demonstrated killing activity in Gram-negative bacteria. The VF16 peptide did not show any detectable toxicity to the HEK 293T cell line and kidney cell line Hep G2. As a mode of action, VF16 interacted with LPS, permeabilizing the outer membrane and binding to LptAm with high affinity. Atomic-resolution structures of VF16 in complex with LPS revealed cationic and aromatic surfaces involved in outer membrane interactions and permeabilization. Further, analyses of an inactive 14-residue native thanatin peptide (IM14: IIYCNRRTGKCQRM) delineated the requirement of the β-sheet structure in activity and target interactions. Taken together, this work would pave the way for the designing of short analogs of thanatin-based antimicrobials.
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Affiliation(s)
- Swaleeha Jaan Abdullah
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; (S.J.A.); (N.P.)
| | - Bernice Tan Siu Yan
- A*Star Infectious Diseases Labs, 8A Biomedical Grove, Immunos, Singapore 138648, Singapore
| | - Nithya Palanivelu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; (S.J.A.); (N.P.)
| | - Vidhya Bharathi Dhanabal
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; (S.J.A.); (N.P.)
| | - Juan Pablo Bifani
- A*Star Infectious Diseases Labs, 8A Biomedical Grove, Immunos, Singapore 138648, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; (S.J.A.); (N.P.)
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Uceda AB, Frau J, Vilanova B, Adrover M. Tyrosine Nitroxidation Does Not Affect the Ability of α-Synuclein to Bind Anionic Micelles, but It Diminishes Its Ability to Bind and Assemble Synaptic-like Vesicles. Antioxidants (Basel) 2023; 12:1310. [PMID: 37372040 DOI: 10.3390/antiox12061310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023] Open
Abstract
Parkinson's disease (PD) is characterized by dopaminergic neuron degeneration and the accumulation of neuronal inclusions known as Lewy bodies, which are formed by aggregated and post-translationally modified α-synuclein (αS). Oxidative modifications such as the formation of 3-nitrotyrosine (3-NT) or di-tyrosine are found in αS deposits, and they could be promoted by the oxidative stress typical of PD brains. Many studies have tried to elucidate the molecular mechanism correlating nitroxidation, αS aggregation, and PD. However, it is unclear how nitroxidation affects the physiological function of αS. To clarify this matter, we synthetized an αS with its Tyr residues replaced by 3-NT. Its study revealed that Tyr nitroxidation had no effect on either the affinity of αS towards anionic micelles nor the overall structure of the micelle-bound αS, which retained its α-helical folding. Nevertheless, we observed that nitroxidation of Y39 lengthened the disordered stretch bridging the two consecutive α-helices. Conversely, the affinity of αS towards synaptic-like vesicles diminished as a result of Tyr nitroxidation. Additionally, we also proved that nitroxidation precluded αS from performing its physiological function as a catalyst of the clustering and the fusion of synaptic vesicles. Our findings represent a step forward towards the completion of the puzzle that must explain the molecular mechanism behind the link between αS-nitroxidation and PD.
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Affiliation(s)
- Ana Belén Uceda
- Health Research Institute of the Balearic Islands (IdISBa), E-07120 Palma de Mallorca, Spain
- Departament de Química, Universitat de les Illes Balears, Ctra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - Juan Frau
- Health Research Institute of the Balearic Islands (IdISBa), E-07120 Palma de Mallorca, Spain
- Departament de Química, Universitat de les Illes Balears, Ctra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - Bartolomé Vilanova
- Health Research Institute of the Balearic Islands (IdISBa), E-07120 Palma de Mallorca, Spain
- Departament de Química, Universitat de les Illes Balears, Ctra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - Miquel Adrover
- Health Research Institute of the Balearic Islands (IdISBa), E-07120 Palma de Mallorca, Spain
- Departament de Química, Universitat de les Illes Balears, Ctra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
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3
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Uceda AB, Frau J, Vilanova B, Adrover M. On the effect of methionine oxidation on the interplay between α-synuclein and synaptic-like vesicles. Int J Biol Macromol 2023; 229:92-104. [PMID: 36584779 DOI: 10.1016/j.ijbiomac.2022.12.262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022]
Abstract
Human alpha-synuclein (αS) is an intrinsically disordered protein highly expressed in dopaminergic neurons. Its amyloid aggregates are the major component of Lewy bodies, which are considered a hallmark of Parkinson's disease (PD). αS has four different Met, which are particularly sensitive to oxidation, as most of them are found as Met sulfoxide (MetO) in the αS deposits. Consequently, researchers have invested mounting efforts trying to elucidate the molecular mechanisms underlying the links between oxidative stress, αS aggregation and PD. However, it has not been described yet the effect of Met oxidation on the physiological function of αS. Trying to shed light on this aspect, we have here studied a synthetic αS that displayed all its Met replaced by MetO moieties (αS-MetO). Our study has allowed to prove that MetO diminishes the affinity of αS towards anionic micelles (SDS), although the micelle-bound fraction of αS-MetO still adopts an α-helical folding resembling that of the lipid-bound αS. MetO also diminishes the affinity of αS towards synaptic-like vesicles, and its hindering effect is much more pronounced than that displayed on the αS-micelle affinity. Additionally, we have also demonstrated that MetO impairs the physiological function of αS as a catalyst of the clustering and the fusion of synaptic vesicles (SVs). Our findings provide a new understanding on how Met oxidation affects one of the most relevant biological functions attributed to αS that is to bind and cluster SVs along the neurotransmission.
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Affiliation(s)
- Ana Belén Uceda
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Departament de Química, Universitat de les Illes Balears, Ctra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - Juan Frau
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Departament de Química, Universitat de les Illes Balears, Ctra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - Bartolomé Vilanova
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Departament de Química, Universitat de les Illes Balears, Ctra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - Miquel Adrover
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Departament de Química, Universitat de les Illes Balears, Ctra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain.
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Gogoi CR, Rahman A, Saikia B, Baruah A. Protein Dihedral Angle Prediction: The State of the Art. ChemistrySelect 2023. [DOI: 10.1002/slct.202203427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
| | - Aziza Rahman
- Department of Chemistry Dibrugarh University Dibrugarh Assam India
| | - Bondeepa Saikia
- Department of Chemistry Dibrugarh University Dibrugarh Assam India
| | - Anupaul Baruah
- Department of Chemistry Dibrugarh University Dibrugarh Assam India
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Tomiyama R, So M, Yamaguchi K, Miyanoiri Y, Sakurai K. The residual structure of acid-denatured β 2 -microglobulin is relevant to an ordered fibril morphology. Protein Sci 2023; 32:e4487. [PMID: 36321362 PMCID: PMC9793977 DOI: 10.1002/pro.4487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/15/2022] [Accepted: 10/29/2022] [Indexed: 11/09/2022]
Abstract
β2 -Microglobulin (β2m) forms amyloid fibrils in vitro under acidic conditions. Under these conditions, the residual structure of acid-denatured β2m is relevant to seeding and fibril extension processes. Disulfide (SS) bond-oxidized β2m has been shown to form rigid, ordered fibrils, whereas SS bond-reduced β2m forms curvy, less-ordered fibrils. These findings suggest that the presence of an SS bond affects the residual structure of the monomer, which subsequently influences the fibril morphology. To clarify this process, we herein performed NMR experiments. The results obtained revealed that oxidized β2m contained a residual structure throughout the molecule, including the N- and C-termini, whereas the residual structure of the reduced form was localized and other regions had a random coil structure. The range of the residual structure in the oxidized form was wider than that of the fibril core. These results indicate that acid-denatured β2m has variable conformations. Most conformations in the ensemble cannot participate in fibril formation because their core residues are hidden by residual structures. However, when hydrophobic residues are exposed, polypeptides competently form an ordered fibril. This conformational selection phase may be needed for the ordered assembly of amyloid fibrils.
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Affiliation(s)
- Ryosuke Tomiyama
- Graduate School of Biology‐oriented Science and TechnologyKindai UniversityWakayamaJapan
| | - Masatomo So
- Institute for Protein ResearchOsaka UniversityOsakaJapan,Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
| | - Keiichi Yamaguchi
- Global Center for Medical Engineering and InformaticsOsaka UniversitySuitaJapan
| | | | - Kazumasa Sakurai
- Graduate School of Biology‐oriented Science and TechnologyKindai UniversityWakayamaJapan,High Pressure Protein Research Center, Institute of Advanced TechnologyKindai UniversityWakayamaJapan
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Sinha S, Dhanabal VB, Manivannen VL, Cappiello F, Tan SM, Bhattacharjya S. Ultra-Short Cyclized β-Boomerang Peptides: Structures, Interactions with Lipopolysaccharide, Antibiotic Potentiator and Wound Healing. Int J Mol Sci 2022; 24:ijms24010263. [PMID: 36613707 PMCID: PMC9820106 DOI: 10.3390/ijms24010263] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Many antibiotics are ineffective in killing Gram-negative bacteria due to the permeability barrier of the outer-membrane LPS. Infections caused by multi-drug-resistant Gram-negative pathogens require new antibiotics, which are often difficult to develop. Antibiotic potentiators disrupt outer-membrane LPS and can assist the entry of large-scaffold antibiotics to the bacterial targets. In this work, we designed a backbone-cyclized ultra-short, six-amino-acid-long (WKRKRY) peptide, termed cWY6 from LPS binding motif of β-boomerang bactericidal peptides. The cWY6 peptide does not exhibit any antimicrobial activity; however, it is able to permeabilize the LPS outer membrane. Our results demonstrate the antibiotic potentiator activity in the designed cWY6 peptide for several conventional antibiotics (vancomycin, rifampicin, erythromycin, novobiocin and azithromycin). Remarkably, the short cWY6 peptide exhibits wound-healing activity in in vitro assays. NMR, computational docking and biophysical studies describe the atomic-resolution structure of the peptide in complex with LPS and mode of action in disrupting the outer membrane. The dual activities of cWY6 peptide hold high promise for further translation to therapeutics.
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Affiliation(s)
- Sheetal Sinha
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore
- Interdisciplinary Graduate School, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Vidhya Bharathi Dhanabal
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Veronica Lavanya Manivannen
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Floriana Cappiello
- Department of Biochemical Sciences, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Suet-Mien Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- Correspondence:
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7
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Kenyon M, Maguire S, Rueda Pujol A, O'Shea F, McManus R. The genetic backbone of ankylosing spondylitis: how knowledge of genetic susceptibility informs our understanding and management of disease. Rheumatol Int 2022; 42:2085-2095. [PMID: 35939079 PMCID: PMC9548471 DOI: 10.1007/s00296-022-05174-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 07/20/2022] [Indexed: 11/25/2022]
Abstract
Ankylosing spondylitis (AS) is a seronegative, chronic inflammatory arthritis with high genetic burden. A strong association with HLA-B27 has long been established, but to date its contribution to disease aetiology remains unresolved. Recent insights through genome wide studies reveal an increasing array of immunogenetic risk variants extraneous to the HLA complex in AS cohorts. These genetic traits build a complex profile of disease causality, highlighting several molecular pathways associated with the condition. This and other evidence strongly implicates T-cell-driven pathology, revolving around the T helper 17 cell subset as an important contributor to disease. This prominence of the T helper 17 cell subset has presented the opportunity for therapeutic intervention through inhibition of interleukins 17 and 23 which drive T helper 17 activity. While targeting of interleukin 17 has proven effective, this success has not been replicated with interleukin 23 inhibition in AS patients. Evidence points to significant genetic diversity between AS patients which may, in part, explain the observed refractoriness among a proportion of patients. In this review we discuss the impact of genetics on our understanding of AS and its relationship with closely linked pathologies. We further explore how genetics can be used in the development of therapeutics and as a tool to assist in the diagnosis and management of patients. This evidence indicates that genetic profiling should play a role in the clinician’s choice of therapy as part of a precision medicine strategy towards disease management.
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Affiliation(s)
- Marcus Kenyon
- Department of Clinical Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland.
| | - Sinead Maguire
- Department of Rheumatology, St James' Hospital, Dublin, Ireland
| | - Anna Rueda Pujol
- Department of Clinical Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Finbar O'Shea
- Department of Rheumatology, St James' Hospital, Dublin, Ireland
| | - Ross McManus
- Department of Clinical Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
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Uceda AB, Frau J, Vilanova B, Adrover M. Glycation of α-synuclein hampers its binding to synaptic-like vesicles and its driving effect on their fusion. Cell Mol Life Sci 2022; 79:342. [PMID: 35662377 PMCID: PMC9167179 DOI: 10.1007/s00018-022-04373-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/08/2022] [Accepted: 05/11/2022] [Indexed: 12/24/2022]
Abstract
Parkinson's disease (PD) is one of the most prevalent neurodegenerative disorders affecting the worldwide population. One of its hallmarks is the intraneuronal accumulation of insoluble Lewy bodies (LBs), which cause the death of dopaminergic neurons. α-Synuclein (αS) is the main component of these LBs and in them, it commonly contains non-enzymatic post-translational modifications, such as those resulting from its reaction with reactive carbonyl species arising as side products of the intraneuronal glycolysis (mainly methylglyoxal). Consequently, lysines of the αS found in LBs of diabetic individuals are usually carboxyethylated. A precise comprehension of the effect of Nε-(carboxyethyl)lysine (CEL) on the aggregation of αS and on its physiological function becomes crucial to fully understand the molecular mechanisms underlying the development of diabetes-induced PD. Consequently, we have here used a synthetic αS where all its Lys have been replaced by CEL moieties (αS-CEL), and we have studied how these modifications could impact on the neurotransmission mechanism. This study allows us to describe how the non-enzymatic glycosylation (glycation) affects the function of a protein like αS, involved in the pathogenesis of PD. CEL decreases the ability of αS to bind micelles, although the micelle-bound fraction of αS-CEL still displays an α-helical fold resembling that of the lipid-bound αS. However, CEL completely abolishes the affinity of αS towards synaptic-like vesicles and, consequently, it hampers its physiological function as a catalyst of the clustering and the fusion of the synaptic vesicles.
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Affiliation(s)
- Ana Belén Uceda
- Departament de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Universitat de les Illes Balears, Ed. Mateu Orfila i Rotger, Ctra. Valldemossa km 7.5, 07122, Palma, Spain
| | - Juan Frau
- Departament de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Universitat de les Illes Balears, Ed. Mateu Orfila i Rotger, Ctra. Valldemossa km 7.5, 07122, Palma, Spain
| | - Bartolomé Vilanova
- Departament de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Universitat de les Illes Balears, Ed. Mateu Orfila i Rotger, Ctra. Valldemossa km 7.5, 07122, Palma, Spain
| | - Miquel Adrover
- Departament de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Universitat de les Illes Balears, Ed. Mateu Orfila i Rotger, Ctra. Valldemossa km 7.5, 07122, Palma, Spain.
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Sinha S, Bhattacharjya S. NMR Structure and Localization of the Host Defense Peptide ThanatinM21F in Zwitterionic Dodecylphosphocholine Micelle: Implications in Antimicrobial and Hemolytic Activity. J Membr Biol 2022; 255:151-160. [PMID: 35257227 DOI: 10.1007/s00232-022-00223-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/19/2022] [Indexed: 11/25/2022]
Abstract
Non-hemolytic antimicrobial peptides (AMPs) are vital lead molecules for the designing and development of peptide-based antibiotics. Thanatin a 21-amino acid long single disulfide bonded AMP is known to be highly non-hemolytic with a limited toxicity to human cells and model animals. Thanatin demonstrates a potent antibacterial activity against multidrug-resistant Gram-negative pathogens. A single mutated variant of thanatin replaced last residue Met21 to Phe or thanatin M21F has recently been found to be more active compared to the native peptide. In order to gain mechanistic insights toward bacterial cell lysis versus non-hemolysis, here, we report atomic resolution structure and mode insertion of thanatinM21F reconstituted into zwitterionic detergent micelle by use of solution NMR spectroscopy. The 3D structure of thanatinM21F in DPC micelle is defined by an anti-parallel β-sheet between residues I9-F21 with a central cationic loop, residues N12-R14. PRE NMR studies revealed hydrophobic core residues of thanatinM21F are deeply inserted in the DPC micelle, while residues at the extended N-terminal half of the peptide are appeared to be mostly surface localized. Marked structural differences of thanatin and thanatinM21F in negatively charged LPS and DPC micelle could be correlated with non-hemolytic and antibacterial activity.
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Affiliation(s)
- Sheetal Sinha
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- Interdisciplinary Graduate School, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore, 637141, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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10
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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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Sinha S, Dhanabal VB, Sperandeo P, Polissi A, Bhattacharjya S. Linking dual mode of action of host defense antimicrobial peptide thanatin: Structures, lipopolysaccharide and LptA m binding of designed analogs. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183839. [PMID: 34915021 DOI: 10.1016/j.bbamem.2021.183839] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 12/02/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
At present, antibiotics options to cure infections caused by drug resistant Gram-negative pathogens are highly inadequate. LPS outer membrane, proteins involved in LPS transport and biosynthesis pathways are vital targets. Thanatin, an insect derived 21-residue long antimicrobial peptide may be exploited for the development of effective antibiotics against Gram-negative bacteria. As a mode of bacterial cell killing, thanatin disrupts LPS outer membrane and inhibits LPS transport by binding to the periplasmic protein LptAm. Here, we report structure-activity correlation of thanatin and analogs for the purpose of rational design. These analogs of thanatin are investigated, by NMR, ITC and fluorescence, to correlate structure, antibacterial activity and binding with LPS and LptAm, a truncated monomeric variant. Our results demonstrate that an analog thanatin M21F exhibits superior antibacterial activity. In LPS interaction analyses, thanatin M21F demonstrate high affinity binding to outer membrane LPS. The atomic resolution structure of thanatin M21F in LPS micelle reveals four stranded β-sheet structure in a dimeric topology whereby the sidechain of aromatic residues Y10, F21 sustained mutual packing at the interface. Strikingly, LptAm binding affinity of thanatin M21F has been significantly increased with an estimated Kd ~ 0.73 nM vs 13 nM for thanatin. Further, atomic resolution structures and interactions of Ala based thanatin analogs define plausible correlations with antibacterial activity and LPS, LptAm interactions. Taken together, the current work provides a frame-work for the designing of thanatin based potent antimicrobial peptides for the treatment of drug resistance Gram-negative bacteria.
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Affiliation(s)
- Sheetal Sinha
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; Interdisciplinary Graduate School, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore; Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore
| | - Vidhya Bharathi Dhanabal
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Paola Sperandeo
- Dept. of Pharmacological and Biomolecular Sciences, University of Milano, Via Balzaretti 9, 20133 Milano, Italy
| | - Alessandra Polissi
- Dept. of Pharmacological and Biomolecular Sciences, University of Milano, Via Balzaretti 9, 20133 Milano, Italy
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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12
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Lopez K, Pinheiro S, Zamora WJ. Multiple linear regression models for predicting the n‑octanol/water partition coefficients in the SAMPL7 blind challenge. J Comput Aided Mol Des 2021; 35:923-931. [PMID: 34251523 PMCID: PMC8273033 DOI: 10.1007/s10822-021-00409-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 07/05/2021] [Indexed: 01/19/2023]
Abstract
A multiple linear regression model called MLR-3 is used for predicting the experimental n-octanol/water partition coefficient (log PN) of 22 N-sulfonamides proposed by the organizers of the SAMPL7 blind challenge. The MLR-3 method was trained with 82 molecules including drug-like sulfonamides and small organic molecules, which resembled the main functional groups present in the challenge dataset. Our model, submitted as "TFE-MLR", presented a root-mean-square error of 0.58 and mean absolute error of 0.41 in log P units, accomplishing the highest accuracy, among empirical methods and also in all submissions based on the ranked ones. Overall, the results support the appropriateness of multiple linear regression approach MLR-3 for computing the n-octanol/water partition coefficient in sulfonamide-bearing compounds. In this context, the outstanding performance of empirical methodologies, where 75% of the ranked submissions achieved root-mean-square errors < 1 log P units, support the suitability of these strategies for obtaining accurate and fast predictions of physicochemical properties as partition coefficients of bioorganic compounds.
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Affiliation(s)
- Kenneth Lopez
- School of Chemistry, University of Costa Rica, San Pedro, San José, Costa Rica
| | - Silvana Pinheiro
- Institute of Exact and Natural Sciences, Federal University of Pará, Belém, Pará, 66075-110, Brazil
| | - William J Zamora
- School of Chemistry, University of Costa Rica, San Pedro, San José, Costa Rica.
- Advanced Computing Lab (CNCA), National High Technology Center (CeNAT-CONARE), Pavas, San José, Costa Rica.
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13
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Wesch N, Löhr F, Rogova N, Dötsch V, Rogov VV. A Concerted Action of UBA5 C-Terminal Unstructured Regions Is Important for Transfer of Activated UFM1 to UFC1. Int J Mol Sci 2021; 22:ijms22147390. [PMID: 34299007 PMCID: PMC8304084 DOI: 10.3390/ijms22147390] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/22/2022] Open
Abstract
Ubiquitin fold modifier 1 (UFM1) is a member of the ubiquitin-like protein family. UFM1 undergoes a cascade of enzymatic reactions including activation by UBA5 (E1), transfer to UFC1 (E2) and selective conjugation to a number of target proteins via UFL1 (E3) enzymes. Despite the importance of ufmylation in a variety of cellular processes and its role in the pathogenicity of many human diseases, the molecular mechanisms of the ufmylation cascade remains unclear. In this study we focused on the biophysical and biochemical characterization of the interaction between UBA5 and UFC1. We explored the hypothesis that the unstructured C-terminal region of UBA5 serves as a regulatory region, controlling cellular localization of the elements of the ufmylation cascade and effective interaction between them. We found that the last 20 residues in UBA5 are pivotal for binding to UFC1 and can accelerate the transfer of UFM1 to UFC1. We solved the structure of a complex of UFC1 and a peptide spanning the last 20 residues of UBA5 by NMR spectroscopy. This structure in combination with additional NMR titration and isothermal titration calorimetry experiments revealed the mechanism of interaction and confirmed the importance of the C-terminal unstructured region in UBA5 for the ufmylation cascade.
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Affiliation(s)
- Nicole Wesch
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany; (N.W.); (F.L.); (N.R.)
| | - Frank Löhr
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany; (N.W.); (F.L.); (N.R.)
| | - Natalia Rogova
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany; (N.W.); (F.L.); (N.R.)
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany; (N.W.); (F.L.); (N.R.)
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany
- Correspondence: (V.D.); (V.V.R.)
| | - Vladimir V. Rogov
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany; (N.W.); (F.L.); (N.R.)
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany
- Correspondence: (V.D.); (V.V.R.)
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14
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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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15
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Zhang K, Abdallah K, Ajmera P, Finos K, Looka A, Mekhael J, Frank AT. CS-Annotate: A Tool for Using NMR Chemical Shifts to Annotate RNA Structure. J Chem Inf Model 2021; 61:1545-1549. [PMID: 33797909 DOI: 10.1021/acs.jcim.1c00006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Here, we introduce CS-Annotate, a tool that uses assigned NMR chemical shifts to annotate structural features in RNA. At its core, CS-Annotate is a deployment of a multitask deep learning model that simultaneously classifies the solvent exposure, base-stacking and -pairing status, and conformation of individual RNA residues from their chemical shift fingerprint. Here, we briefly describe how we trained and tested the classifier and demonstrate its application to a model RNA system. CS-Annotate can be accessed via the SMALTR (Structure-based MAchine Learning Tools for RNA) Science Gateway (smaltr.org).
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Affiliation(s)
- Kexin Zhang
- Chemistry Department, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Kyrillos Abdallah
- Biophysics Program, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Pujan Ajmera
- Biophysics Program, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Kyle Finos
- Biophysics Program, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Andrew Looka
- Biophysics Program, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Joseph Mekhael
- Biophysics Program, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Aaron T Frank
- Biophysics Program, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
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16
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Dermouche S, Chagot ME, Manival X, Quinternet M. Optimizing the First TPR Domain of the Human SPAG1 Protein Provides Insight into the HSP70 and HSP90 Binding Properties. Biochemistry 2021; 60:2349-2363. [PMID: 33739091 DOI: 10.1021/acs.biochem.1c00052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tetratricopeptide repeat domains, or TPR domains, are protein domains that mediate protein:protein interaction. As they allow contacts between proteins, they are of particular interest in transient steps of the assembly process of macromolecular complexes, such as the ribosome or the dynein arms. In this study, we focused on the first TPR domain of the human SPAG1 protein. SPAG1 is a multidomain protein that is important for ciliogenesis whose known mutations are linked to primary ciliary dyskinesia syndrome. It can interact with the chaperones RUVBL1/2, HSP70, and HSP90. Using protein sequence optimization in combination with structural and biophysical approaches, we analyzed, with atomistic precision, how the C-terminal tails of HSPs bind a variant form of SPAG1-TPR1 that mimics the wild-type domain. We discuss our results with regard to other complex three-dimensional structures with the aim of highlighting the motifs in the TPR sequences that could drive the positioning of the HSP peptides. These data could be important for the druggability of TPR regulators.
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Affiliation(s)
- Sana Dermouche
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | | | - Xavier Manival
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | - Marc Quinternet
- Université de Lorraine, CNRS, INSERM, IBSLor, F-54000 Nancy, France
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17
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Lawrence C, Grishaev A. Chemical shifts-based similarity restraints improve accuracy of RNA structures determined via NMR. RNA (NEW YORK, N.Y.) 2020; 26:2051-2061. [PMID: 32917774 PMCID: PMC7668244 DOI: 10.1261/rna.074617.119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 08/19/2020] [Indexed: 06/01/2023]
Abstract
Determination of structure of RNA via NMR is complicated in large part by the lack of a precise parameterization linking the observed chemical shifts to the underlying geometric parameters. In contrast to proteins, where numerous high-resolution crystal structures serve as coordinate templates for this mapping, such models are rarely available for smaller oligonucleotides accessible via NMR, or they exhibit crystal packing and counter-ion binding artifacts that prevent their use for the chemical shifts analysis. On the other hand, NMR-determined structures of RNA often are not solved at the density of restraints required to precisely define the variable degrees of freedom. In this study we sidestep the problems of direct parameterization of the RNA chemical shifts/structure relationship and examine the effects of imposing local fragmental coordinate similarity restraints based on similarities of the experimental secondary ribose 13C/1H chemical shifts instead. The effect of such chemical shift similarity (CSS) restraints on the structural accuracy is assessed via residual dipolar coupling (RDC)-based cross-validation. Improvements in the coordinate accuracy are observed for all of the six RNA constructs considered here as test cases, which argues for routine inclusion of these terms during NMR-based oligonucleotide structure determination. Such accuracy improvements are expected to facilitate derivation of the chemical shift/structure relationships for RNA.
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Affiliation(s)
- Chad Lawrence
- Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, USA
| | - Alexander Grishaev
- Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, USA
- Biomolecular Measurement Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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18
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Sinha S, Ng WJ, Bhattacharjya S. NMR structure and localization of the host defense antimicrobial peptide thanatin in zwitterionic dodecylphosphocholine micelle: Implications in antimicrobial activity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183432. [PMID: 32781154 DOI: 10.1016/j.bbamem.2020.183432] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/11/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023]
Abstract
Antimicrobial peptides (AMPs) are potentially vital as the next generation of antibiotics against multidrug resistant bacterial pathogens. Thanatin, an insect derived pathogen inducible 21-residue long antimicrobial peptide, demonstrates antimicrobial activity toward broad range of pathogens. Thanatin is an excellent candidate for antibiotics development due to potent in vivo activity in animal model and low toxicity to human cells. Recent studies indicated mode of action of thanatin could be intriguing and may comprise bacterial membrane permeabilization and interactions with periplasmic proteins. In order to better understand selectivity and membrane disruption, here, we determined 3-D structure of the thanatin in zwitterionic DPC-d38 micelle by NMR spectroscopy. The depth of insertion of thanatin into micelle structure was investigated by spin labelled doxyl lipids, 5-DSA and 16-DSA. DPC-bound structure of thanatin is defined by a β-hairpin structure and an extended and turn conformations, for residues G1-I8, at the N-terminus. The β-hairpin structure is delineated by two antiparallel β-strands, residues I9-C11 and residues K17-R20, which is connected by loop consisted of residues N12-G16. There are cross β-strands sidechain-sidechain packing interactions among hydrophobic and aromatic residues. Spin labelled lipid studies revealed a set of spatially proximal residues V6, I8, Q19, R20 and M21 may be deeply inserted into the hydrophobic core of the DPC micelle. While, residues including those at the turn/loop are merely surface localized. The atomic resolution structure and orientation of thanatin in zwitterionic DPC micelle may be utilized for understating mode of action in lipid membrane and further development of non-toxic analogs.
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Affiliation(s)
- Sheetal Sinha
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; Interdisciplinary Graduate School, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore; Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore
| | - Wun Jern Ng
- Environmental Bio-Innovation Group (EBiG), School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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19
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Structural biology of human GPCR drugs and endogenous ligands - insights from NMR spectroscopy. Methods 2020; 180:79-88. [PMID: 32911074 DOI: 10.1016/j.ymeth.2020.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/30/2020] [Accepted: 08/31/2020] [Indexed: 12/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs) represent the largest class of "druggable" proteins in the human genome. For more than a decade, crystal structures and, more recently, cryoEM structures of GPCR complexes have provided unprecedented insight into GPCR drug binding and cell signaling. Nevertheless, structure determination of receptors in complexes with weakly binding molecules or complex polypeptides remains especially challenging, including for hormones, many of which have so far eluded researchers. Nuclear magnetic resonance (NMR) spectroscopy has emerged as a promising approach to determine structures of ligands bound to their receptors and to provide insights into the dynamics of GPCR-bound drugs. The capability to investigate compounds with weak binding affinities has also been leveraged in NMR applications to identify novel lead compounds in drug screening campaigns. We review recent structural biology studies of GPCR ligands by NMR, highlighting new methodologies enabling studies of GPCRs with native sequences and in native-like membrane environments that provide insights into important drugs and endogenous ligands.
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20
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Ratha BN, Kar RK, Bednarikova Z, Gazova Z, Kotler SA, Raha S, De S, Maiti NC, Bhunia A. Molecular Details of a Salt Bridge and Its Role in Insulin Fibrillation by NMR and Raman Spectroscopic Analysis. J Phys Chem B 2020; 124:1125-1136. [PMID: 31958230 DOI: 10.1021/acs.jpcb.9b10349] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Insulin, a simple polypeptide hormone with huge biological importance, has long been known to self-assemble in vitro and form amyloid-like fibrillar aggregates. Utilizing high-resolution NMR, Raman spectroscopy, and computational analysis, we demonstrate that the fluctuation of the carboxyl terminal (C-ter) residues of the insulin B-chain plays a key role in the growth phase of insulin aggregation. By comparing the insulin sourced from bovine, human, and the modified glargine (GI), we observed reduced aggregation propensity in the GI variant, resulting from two additional Arg residues at its C-ter. NMR analysis showed atomic contacts and residue-specific interactions, particularly the salt bridge and H-bond formed among the C-ter residues Arg31B, Lys29B, and Glu4A. These inter-residue interactions were reflected in strong nuclear Overhauser effects among Arg31BδH-Glu4AδH and Lys29BδHs-Glu4AδH in GI, as well as the associated downfield chemical shift of several A-chain amino terminal (N-ter) residues. The two additional Arg residues of GI, Arg31B and Arg32B, enhanced the stability of the GI native structure by strengthening the Arg31B, Lys29B, and Glu4A salt bridge, thus reducing extensive thermal distortion and fluctuation of the terminal residues. The high stability of the salt bridge retards tertiary collapse, a crucial biochemical event for oligomerization and subsequent fibril formation. Circular dichroism and Raman spectroscopic measurement also suggest slow structural distortion in the early phase of the aggregation of GI because of the restricted mobility of the C-ter residues as explained by NMR. In addition, the structural and dynamic parameters derived from molecular dynamics simulations of insulin variants highlight the role of residue-specific contacts in aggregation and amyloid-like fibril formation.
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Affiliation(s)
- Bhisma N Ratha
- Department of Biophysics , Bose Institute , P-1/12 CIT Scheme VII (M) , Kolkata 700054 , India
| | - Rajiv K Kar
- Department of Biophysics , Bose Institute , P-1/12 CIT Scheme VII (M) , Kolkata 700054 , India
| | - Zuzana Bednarikova
- Department of Biophysics , Institute of Experimental Physics Slovak Academy of Sciences , Kosice 040 01 , Slovakia
| | - Zuzana Gazova
- Department of Biophysics , Institute of Experimental Physics Slovak Academy of Sciences , Kosice 040 01 , Slovakia
| | - Samuel A Kotler
- National Center for Advancing Translational Sciences , National Institutes of Health , Rockville , Maryland 20850 , United States
| | - Sreyan Raha
- Department of Physics , Bose Institute , 93/1 APC Road , Kolkata 700009 , India
| | - Soumya De
- School of Bioscience , IIT Kharagpur , Kharagpur 721302 , India
| | - Nakul C Maiti
- Division Structural Biology and Bioinformatics , CSIR-Indian Institute of Chemical Biology , Kolkata 700032 , India
| | - Anirban Bhunia
- Department of Biophysics , Bose Institute , P-1/12 CIT Scheme VII (M) , Kolkata 700054 , India
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21
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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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22
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Cannon JF. Novel phosphorylation-dependent regulation in an unstructured protein. Proteins 2019; 88:366-384. [PMID: 31512287 DOI: 10.1002/prot.25812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/15/2019] [Accepted: 09/04/2019] [Indexed: 12/15/2022]
Abstract
This work explores how phosphorylation of an unstructured protein region in inhibitor-2 (I2) regulates protein phosphatase-1 (PP1) enzyme activity using molecular dynamics (MD). Free I2 is largely unstructured; however, when bound to PP1, three segments adopt a stable structure. In particular, an I2 helix (i-helix) blocks the PP1 active site and inhibits phosphatase activity. I2 phosphorylation in the PP1-I2 complex activates phosphatase activity without I2 dissociation. The I2 Thr74 regulatory phosphorylation site is in an unstructured domain in PP1-I2. PP1-I2 MD demonstrated that I2 phosphorylation promotes early steps of PP1-I2 activation in explicit solvent models. Moreover, phosphorylation-dependent activation occurred in PP1-I2 complexes derived from I2 orthologs with diverse sequences from human, yeast, worm, and protozoa. This system allowed exploration of features of the 73-residue unstructured human I2 domain critical for phosphorylation-dependent activation. These studies revealed that components of I2 unstructured domain are strategically positioned for phosphorylation responsiveness including a transient α-helix. There was no evidence that electrostatic interactions of I2 phosphothreonine74 influenced PP1-I2 activation. Instead, phosphorylation altered the conformation of residues around Thr74. Phosphorylation uncurled the distance between I2 residues Glu71 to Tyr76 to promote PP1-I2 activation, whereas reduced distances reduced activation. This I2 residue Glu71 to Tyr76 distance distribution, independently from Thr74 phosphorylation, controls I2 i-helix displacement from the PP1 active site leading to PP1-I2 activation.
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Affiliation(s)
- John F Cannon
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri
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23
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PaleAle 5.0: prediction of protein relative solvent accessibility by deep learning. Amino Acids 2019; 51:1289-1296. [PMID: 31388850 DOI: 10.1007/s00726-019-02767-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/29/2019] [Indexed: 10/26/2022]
Abstract
Predicting the three-dimensional structure of proteins is a long-standing challenge of computational biology, as the structure (or lack of a rigid structure) is well known to determine a protein's function. Predicting relative solvent accessibility (RSA) of amino acids within a protein is a significant step towards resolving the protein structure prediction challenge especially in cases in which structural information about a protein is not available by homology transfer. Today, arguably the core of the most powerful prediction methods for predicting RSA and other structural features of proteins is some form of deep learning, and all the state-of-the-art protein structure prediction tools rely on some machine learning algorithm. In this article we present a deep neural network architecture composed of stacks of bidirectional recurrent neural networks and convolutional layers which is capable of mining information from long-range interactions within a protein sequence and apply it to the prediction of protein RSA using a novel encoding method that we shall call "clipped". The final system we present, PaleAle 5.0, which is available as a public server, predicts RSA into two, three and four classes at an accuracy exceeding 80% in two classes, surpassing the performances of all the other predictors we have benchmarked.
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24
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Binding properties of the quaternary assembly protein SPAG1. Biochem J 2019; 476:1679-1694. [PMID: 31118266 DOI: 10.1042/bcj20190198] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/09/2019] [Accepted: 05/22/2019] [Indexed: 12/12/2022]
Abstract
In cells, many constituents are able to assemble resulting in large macromolecular machineries possessing very specific biological and physiological functions, e.g. ribosome, spliceosome and proteasome. Assembly of such entities is commonly mediated by transient protein factors. SPAG1 is a multidomain protein, known to participate in the assembly of both the inner and outer dynein arms. These arms are required for the function of sensitive and motile cells. Together with RUVBL1, RUVBL2 and PIH1D2, SPAG1 is a key element of R2SP, a protein complex assisting the quaternary assembly of specific protein clients in a tissue-specific manner and associating with heat shock proteins (HSPs) and regulators. In this study, we have investigated the role of TPR domains of SPAG1 in the recruitment of HSP chaperones by combining biochemical assays, ITC, NMR spectroscopy and molecular dynamics (MD) simulations. First, we propose that only two, out of the three TPR domains, are able to recruit the protein chaperones HSP70 and HSP90. We then focused on one of these TPR domains and elucidated its 3D structure using NMR spectroscopy. Relying on an NMR-driven docking approach and MD simulations, we deciphered its binding interface with the C-terminal tails of both HSP70 and HSP90. Finally, we addressed the biological function of SPAG1 and specifically demonstrated that a SPAG1 sub-fragment, containing a putative P-loop motif, cannot efficiently bind and hydrolyze GTP in vitro Our data challenge the interpretation of SPAG1 possessing GTPase activity. We propose instead that SPAG1 regulates nucleotide hydrolysis activity of the HSP and RUVBL1/2 partners.
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25
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Richard T, Petit E, Pouységu L, Monti JP, Bondon A, Sylla T, Mérillon JM, Quideau S, Da Costa G. Impact of polyphenols on receptor-ligand interactions by NMR: the case of neurotensin (NT)-neurotensin receptor fragment (NTS1) complex. J Biomol Struct Dyn 2019; 38:1467-1478. [PMID: 31046599 DOI: 10.1080/07391102.2019.1608863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Ligand-receptor interactions can be implicated in many pathological events such as chronic neurodegenerative diseases. Thus, the discovery of molecules disrupting this type of interactions could be an interesting therapeutic approach. Polyphenols are well known for their affinity for proteins and several studies have characterized these direct interactions. But studying the direct influence of multi-therapeutic drugs on a ligand-receptor complex relevant to a neurodegenerative disorder is a challenging issue. Solution NMR, molecular modeling and iterative calculations were used to obtain information about the interaction between a phenolic compound, α-glucogallin (α-2) and a ligand/fragment receptor complex neurotensin (NT) and its receptor NTS1. The α-2 was shown to bind to NT and a peptidic fragment of its NTS1 receptor, independently. Although the formation of the corresponding ligand-receptor complex did not seem to be affected, this experimental modeling protocol will enable the evaluation of other anti-amyloidogenic compounds such as blockers of NT-NTS1 binding. These types of studies help in understanding the specificity and influence in binding and can provide information to develop new molecules with a putative pharmacological interest.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tristan Richard
- Université de Bordeaux, ISVV, EA 4577, USC 1366 INRA, Unité de Recherche OEnologie, Villenave d'Ornon, France
| | - Eva Petit
- Université de Toulouse, Institut National Polytechnique de Toulouse, Ecole d'Ingénieurs de Purpan, Unité Propre Physiologie, Pathologie et Génétique Végétales (PPGV), Toulouse, France
| | | | - Jean-Pierre Monti
- Université de Bordeaux, Laboratoire de Physique et Biophysique, Bordeaux, France
| | - Arnaud Bondon
- Université de Rennes, CNRS, ISCR - UMR 6226, Rennes, France
| | - Tahiri Sylla
- Université de Bordeaux, ISM (CNRS-UMR 5255), Talence, France
| | - Jean-Michel Mérillon
- Université de Bordeaux, ISVV, EA 4577, USC 1366 INRA, Unité de Recherche OEnologie, Villenave d'Ornon, France
| | | | - Grégory Da Costa
- Université de Bordeaux, ISVV, EA 4577, USC 1366 INRA, Unité de Recherche OEnologie, Villenave d'Ornon, France
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26
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Agrawal P, Patiyal S, Kumar R, Kumar V, Singh H, Raghav PK, Raghava GPS. ccPDB 2.0: an updated version of datasets created and compiled from Protein Data Bank. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019; 2019:5298333. [PMID: 30689843 PMCID: PMC6343045 DOI: 10.1093/database/bay142] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 12/09/2018] [Indexed: 12/20/2022]
Abstract
ccPDB 2.0 (http://webs.iiitd.edu.in/raghava/ccpdb) is an updated version of the manually curated database ccPDB that maintains datasets required for developing methods to predict the structure and function of proteins. The number of datasets compiled from literature increased from 45 to 141 in ccPDB 2.0. Similarly, the number of protein structures used for creating datasets also increased from ~74 000 to ~137 000 (PDB March 2018 release). ccPDB 2.0 provides the same web services and flexible tools which were present in the previous version of the database. In the updated version, links of the number of methods developed in the past few years have also been incorporated. This updated resource is built on responsive templates which is compatible with smartphones (mobile, iPhone, iPad, tablets etc.) and large screen gadgets. In summary, ccPDB 2.0 is a user-friendly web-based platform that provides comprehensive as well as updated information about datasets.
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Affiliation(s)
- Piyush Agrawal
- Bioinformatics Center, CSIR-Institute of Microbial Technology, India.,Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Industrial Estate, Phase III, New Delhi, India
| | - Sumeet Patiyal
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Industrial Estate, Phase III, New Delhi, India
| | - Rajesh Kumar
- Bioinformatics Center, CSIR-Institute of Microbial Technology, India.,Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Industrial Estate, Phase III, New Delhi, India
| | - Vinod Kumar
- Bioinformatics Center, CSIR-Institute of Microbial Technology, India.,Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Industrial Estate, Phase III, New Delhi, India
| | - Harinder Singh
- J. Craig Venter Institute 9605 Medical Center Drive, Suite 150 Rockville, MD, USA
| | - Pawan Kumar Raghav
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Industrial Estate, Phase III, New Delhi, India
| | - Gajendra P S Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Industrial Estate, Phase III, New Delhi, India
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Carabet LA, Rennie PS, Cherkasov A. Therapeutic Inhibition of Myc in Cancer. Structural Bases and Computer-Aided Drug Discovery Approaches. Int J Mol Sci 2018; 20:E120. [PMID: 30597997 PMCID: PMC6337544 DOI: 10.3390/ijms20010120] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/08/2018] [Accepted: 12/21/2018] [Indexed: 12/23/2022] Open
Abstract
Myc (avian myelocytomatosis viral oncogene homolog) represents one of the most sought after drug targets in cancer. Myc transcription factor is an essential regulator of cell growth, but in most cancers it is overexpressed and associated with treatment-resistance and lethal outcomes. Over 40 years of research and drug development efforts did not yield a clinically useful Myc inhibitor. Drugging the "undruggable" is problematic, as Myc inactivation may negatively impact its physiological functions. Moreover, Myc is a disordered protein that lacks effective binding pockets on its surface. It is well established that the Myc function is dependent on dimerization with its obligate partner, Max (Myc associated factor X), which together form a functional DNA-binding domain to activate genomic targets. Herein, we provide an overview of the knowledge accumulated to date on Myc regulation and function, its critical role in cancer, and summarize various strategies that are employed to tackle Myc-driven malignant transformation. We focus on important structure-function relationships of Myc with its interactome, elaborating structural determinants of Myc-Max dimer formation and DNA recognition exploited for therapeutic inhibition. Chronological development of small-molecule Myc-Max prototype inhibitors and corresponding binding sites are comprehensively reviewed and particular emphasis is placed on modern computational drug design methods. On the outlook, technological advancements may soon provide the so long-awaited Myc-Max clinical candidate.
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Affiliation(s)
- Lavinia A Carabet
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada.
| | - Paul S Rennie
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada.
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada.
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Armstrong DA, Kaas Q, Rosengren KJ. Prediction of disulfide dihedral angles using chemical shifts. Chem Sci 2018; 9:6548-6556. [PMID: 30310586 PMCID: PMC6115640 DOI: 10.1039/c8sc01423j] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/02/2018] [Indexed: 01/02/2023] Open
Abstract
Cystine residues result from the formation of disulfide bonds between pairs of cysteine residues. This cross linking of the backbone is essential for the structure and activity of peptides and proteins. The conformation of a cystine side chain can be described using five dihedral angles, χ1, χ2, χ3, χ2', and χ1', with cystines favouring certain combinations of these angles. 2D NMR spectroscopy is ideally suited for structure determination of disulfide-rich peptides, because of their small size and constrained nature. However, only limited information of the cystine side chain conformation can be determined by NMR spectroscopy, leading to ambiguity in the deduced 3D structures. Resolving accurate structures is important as disulfide-rich peptides have proven to be promising drug candidates in a number of fields, either as bioactive leads or scaffolds. Using a database of NMR chemical shifts combined with crystallographic structures, we have developed a method called DISH that uses support vector machines to predict the dihedral angles of cysteine side chains. It is able to successfully predict χ2 angles with 91% accuracy, and has improved performance over existing prediction methods for χ1 angles, with 87% accuracy. For 81% of cysteine residues, DISH successfully predicted both the χ1 and χ2 angles. By revisiting published solution structures of peptides determined using NMR spectroscopy, we assessed the impact of additional cystine dihedral restraints on the quality of 3D models. DISH improved the resolution and accuracy, highlighting the potential for improving the understanding of structure-activity relationships and rational development of peptide drugs.
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Affiliation(s)
- David A Armstrong
- The University of Queensland , Faculty of Medicine , School of Biomedical Sciences , Brisbane , Australia . ;
| | - Quentin Kaas
- The University of Queensland , Institute for Molecular Biosciences , Brisbane , Australia
| | - K Johan Rosengren
- The University of Queensland , Faculty of Medicine , School of Biomedical Sciences , Brisbane , Australia . ;
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29
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A new insight into identification of in silico analysis of natural compounds targeting GPR120. ACTA ACUST UNITED AC 2018; 7:8. [PMID: 29780684 PMCID: PMC5951878 DOI: 10.1007/s13721-018-0166-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 04/06/2018] [Accepted: 04/07/2018] [Indexed: 01/08/2023]
Abstract
G-protein coupled receptor (GPR120) is an omega-3 fatty acid receptor that inhibits macrophage-induced tissue inflammation. Recent studies revealed GPR120 promotes colorectal carcinoma through modulation of VEGF, IL-8, PGE2, and NF-kB expression. However, three-dimensional structure of GPR120 is not yet available in Protein Data Bank (PDB). In the present study, we focused on a 3-D structural model of GPR120 has been constructed using homology modeling techniques. The structural quality of the predicted GPR120 model was verified using Procheck, Whatif, ProSA, and Verify 3D. After this chemical database of natural compounds have been constructed and screened for its druggability using molinspiration server. Molecular docking studies of natural compounds on GPR120 model revealed that silibinin (− 6.87 kcal/mol), withanolide (− 6.19 kcal/mol), limonene (− 6.17 kcal/mol), and cervical (− 6.15 kcal/mol) have shown good docking interactions with active site residues of the target. Active site residues of Arg280, Asp275, and Gly122 showed hydrogen-bonding interactions with predicted compounds. Based on these in silico findings, we proposed that virtual screening of natural compounds against of GPR120 is a novel approach to find potential anti-colorectal cancer therapeutics.
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30
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Miears HL, Gruber DR, Horvath NM, Antos JM, Young J, Sigurjonsson JP, Klem ML, Rosenkranz EA, Okon M, McKnight CJ, Vugmeyster L, Smirnov SL. Plant Villin Headpiece Domain Demonstrates a Novel Surface Charge Pattern and High Affinity for F-Actin. Biochemistry 2018; 57:1690-1701. [PMID: 29444403 DOI: 10.1021/acs.biochem.7b00856] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plants utilize multiple isoforms of villin, an F-actin regulating protein with an N-terminal gelsolin-like core and a distinct C-terminal headpiece domain. Unlike their vertebrate homologues, plant villins have a much longer linker polypeptide connecting the core and headpiece. Moreover, the linker-headpiece connection region in plant villins lacks sequence homology to the vertebrate villin sequences. It is unknown to what extent the plant villin headpiece structure and function resemble those of the well-studied vertebrate counterparts. Here we present the first solution NMR structure and backbone dynamics characterization of a headpiece from plants, villin isoform 4 from Arabidopsis thaliana. The villin 4 headpiece is a 63-residue domain (V4HP63) that adopts a typical headpiece fold with an aromatics core and a tryptophan-centered hydrophobic cap within its C-terminal subdomain. However, V4HP63 has a distinct N-terminal subdomain fold as well as a novel, high mobility loop due to the insertion of serine residue in the canonical sequence that follows the variable length loop in headpiece sequences. The domain binds actin filaments with micromolar affinity, like the vertebrate analogues. However, the V4HP63 surface charge pattern is novel and lacks certain features previously thought necessary for high-affinity F-actin binding. Utilizing the updated criteria for strong F-actin binding, we predict that the headpiece domains of all other villin isoforms in A. thaliana have high affinity for F-actin.
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Affiliation(s)
- Heather L Miears
- Department of Chemistry , Western Washington University , 516 High Street , Bellingham , Washington 98225-9150 , United States
| | - David R Gruber
- Department of Chemistry , Western Washington University , 516 High Street , Bellingham , Washington 98225-9150 , United States
| | - Nicholas M Horvath
- Department of Chemistry , Western Washington University , 516 High Street , Bellingham , Washington 98225-9150 , United States
| | - John M Antos
- Department of Chemistry , Western Washington University , 516 High Street , Bellingham , Washington 98225-9150 , United States
| | - Jeff Young
- Department of Biology , Western Washington University , 516 High Street , Bellingham , Washington 98225-9160 , United States
| | - Johann P Sigurjonsson
- Department of Chemistry , Western Washington University , 516 High Street , Bellingham , Washington 98225-9150 , United States
| | - Maya L Klem
- Department of Chemistry , Western Washington University , 516 High Street , Bellingham , Washington 98225-9150 , United States
| | - Erin A Rosenkranz
- Department of Chemistry , Western Washington University , 516 High Street , Bellingham , Washington 98225-9150 , United States
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories , University of British Columbia , Vancouver , British Columbia V6T 1Z3 , Canada
| | - C James McKnight
- Department of Physiology and Biophysics , Boston University School of Medicine , 700 Albany Street , Boston , Massachusetts 02118-2526 , United States
| | - Liliya Vugmeyster
- Department of Chemistry , University of Colorado at Denver , Denver , Colorado 80204 , United States
| | - Serge L Smirnov
- Department of Chemistry , Western Washington University , 516 High Street , Bellingham , Washington 98225-9150 , United States
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31
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The molecular basis of subtype selectivity of human kinin G-protein-coupled receptors. Nat Chem Biol 2018; 14:284-290. [PMID: 29334381 DOI: 10.1038/nchembio.2551] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 11/21/2017] [Indexed: 12/16/2022]
Abstract
G-protein-coupled receptors (GPCRs) are the most important signal transducers in higher eukaryotes. Despite considerable progress, the molecular basis of subtype-specific ligand selectivity, especially for peptide receptors, remains unknown. Here, by integrating DNP-enhanced solid-state NMR spectroscopy with advanced molecular modeling and docking, the mechanism of the subtype selectivity of human bradykinin receptors for their peptide agonists has been resolved. The conserved middle segments of the bound peptides show distinct conformations that result in different presentations of their N and C termini toward their receptors. Analysis of the peptide-receptor interfaces reveals that the charged N-terminal residues of the peptides are mainly selected through electrostatic interactions, whereas the C-terminal segments are recognized via both conformations and interactions. The detailed molecular picture obtained by this approach opens a new gateway for exploring the complex conformational and chemical space of peptides and peptide analogs for designing GPCR subtype-selective biochemical tools and drugs.
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32
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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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33
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Loffredo MR, Ghosh A, Harmouche N, Casciaro B, Luca V, Bortolotti A, Cappiello F, Stella L, Bhunia A, Bechinger B, Mangoni ML. Membrane perturbing activities and structural properties of the frog-skin derived peptide Esculentin-1a(1-21)NH2 and its Diastereomer Esc(1-21)-1c: Correlation with their antipseudomonal and cytotoxic activity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2327-2339. [DOI: 10.1016/j.bbamem.2017.09.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/21/2017] [Accepted: 09/08/2017] [Indexed: 01/21/2023]
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34
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Kingsley CN, Antanasijevic A, Palka-Hamblin H, Durst M, Ramirez B, Lavie A, Caffrey M. Probing the metastable state of influenza hemagglutinin. J Biol Chem 2017; 292:21590-21597. [PMID: 29127198 DOI: 10.1074/jbc.m117.815043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/05/2017] [Indexed: 12/24/2022] Open
Abstract
Viral entry into host cells is mediated by membrane proteins in a metastable state that transition to a more stable state upon a stimulus. For example, in the influenza envelope protein hemagglutinin (HA), the low pH in the endosome triggers a transition from the metastable prefusion conformation to the stable fusion conformation. To identify probes that interfere with HA function, here we screened a library of H7 HA peptides for inhibition of H7 HA-mediated entry. We discovered a peptide, PEP87 (WSYNAELLVAMENQHTI), that inhibited H7 and H5 HA-mediated entry. PEP87 corresponds to a highly conserved helical region of the HA2 subunit of HA that self-interacts in the neutral pH conformation. Mutagenesis experiments indicated that PEP87 binds to its native region in the HA trimer. We also found that PEP87 is unstructured in isolation but tends to form a helix as evidenced by CD and NMR studies. Fluorescence, chemical cross-linking, and saturation transfer difference NMR data suggested that PEP87 binds to the neutral pH conformation of HA and disrupts the HA structure without affecting its oligomerization state. Together, this work provides support for a model in which PEP87 disrupts HA function by displacing native interactions of the neutral pH conformation. Moreover, our observations indicate that the HA prefusion structure (and perhaps the metastable states of other viral entry proteins) is more dynamic with transient motions being larger than generally appreciated. These findings also suggest that the ensemble of prefusion structures presents many potential sites for targeting in therapeutic interventions.
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Affiliation(s)
- Carolyn N Kingsley
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
| | - Aleksandar Antanasijevic
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
| | - Helena Palka-Hamblin
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
| | - Matthew Durst
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
| | - Benjamin Ramirez
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
| | - Arnon Lavie
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
| | - Michael Caffrey
- From the Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607
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35
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Roganowicz MD, Komurlu S, Mukherjee S, Plewka J, Alam SL, Skorupka KA, Wan Y, Dawidowski D, Cafiso DS, Ganser-Pornillos BK, Campbell EM, Pornillos O. TRIM5α SPRY/coiled-coil interactions optimize avid retroviral capsid recognition. PLoS Pathog 2017; 13:e1006686. [PMID: 29040325 PMCID: PMC5667893 DOI: 10.1371/journal.ppat.1006686] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 11/02/2017] [Accepted: 10/10/2017] [Indexed: 12/30/2022] Open
Abstract
Restriction factors are important components of intrinsic cellular defense mechanisms against viral pathogens. TRIM5α is a restriction factor that intercepts the incoming capsid cores of retroviruses such as HIV and provides an effective species-specific barrier to retroviral infection. The TRIM5α SPRY domain directly binds the capsid with only very weak, millimolar-level affinity, and productive capsid recognition therefore requires both TRIM5α dimerization and assembly of the dimers into a multivalent hexagonal lattice to promote avid binding. Here, we explore the important unresolved question of whether the SPRY domains are flexibly linked to the TRIM lattice or more precisely positioned to maximize avidity. Biochemical and biophysical experiments indicate that the linker segment connecting the SPRY domain to the coiled-coil domain adopts an α-helical fold, and that this helical portion mediates interactions between the two domains. Targeted mutations were generated to disrupt the putative packing interface without affecting dimerization or higher-order assembly, and we identified mutant proteins that were nevertheless deficient in capsid binding in vitro and restriction activity in cells. Our studies therefore support a model wherein substantial avidity gains during assembly-mediated capsid recognition by TRIM5α come in part from tailored spacing of tethered recognition domains.
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Affiliation(s)
- Marcin D. Roganowicz
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Sevnur Komurlu
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Santanu Mukherjee
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Jacek Plewka
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Steven L. Alam
- Department of Biochemistry, University of Utah, Salt Lake City, Utah, United States of America
| | - Katarzyna A. Skorupka
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Yueping Wan
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Damian Dawidowski
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, United States of America
| | - David S. Cafiso
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, United States of America
| | - Barbie K. Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Edward M. Campbell
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
- * E-mail:
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36
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Ghosh A, Bhattacharyya D, Bhunia A. Structural insights of a self-assembling 9-residue peptide from the C-terminal tail of the SARS corona virus E-protein in DPC and SDS micelles: A combined high and low resolution spectroscopic study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:335-346. [PMID: 29038024 PMCID: PMC7094419 DOI: 10.1016/j.bbamem.2017.10.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 10/09/2017] [Accepted: 10/11/2017] [Indexed: 12/25/2022]
Abstract
In recent years, several studies based on the interaction of self-assembling short peptides derived from viroporins with model membranes, have improved our understanding of the molecular mechanism of corona virus (CoV) infection under physiological conditions. In this study, we have characterized the mechanism of membrane interaction of a short, 9-residue peptide TK9 (T55VYVYSRVK63) that had been derived from the carboxyl terminal of the Severe Acute Respiratory Syndrome (SARS) corona virus (SARS CoV) envelope (E) protein. The peptide has been studied for its physical changes in the presence of both zwitterionic DPC and negatively charged SDS model membrane micelles, respectively, with the help of a battery of biophysical techniques including two-dimensional solution state NMR spectroscopy. Interestingly, in both micellar environments, TK9 adopted an alpha helical conformation; however, the helical propensities were much higher in the case of DPC compared to those of SDS micelle, suggesting that TK9 has more specificity towards eukaryotic cell membrane than the bacterial cell membrane. The orientation of the peptide TK9 also varies in the different micellar environments. The peptide's affinity was further manifested by its pronounced membrane disruption ability towards the mammalian compared to the bacterial membrane mimic. Collectively, the in-depth structural information on the interaction of TK9 with different membrane environments explains the host specificity and membrane orientation owing to subsequent membrane disruption implicated in the viral pathogenesis.
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Affiliation(s)
- Anirban Ghosh
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Dipita Bhattacharyya
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India.
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Loquet A, Tolchard J, Berbon M, Martinez D, Habenstein B. Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy. J Vis Exp 2017:55779. [PMID: 28994783 PMCID: PMC5752270 DOI: 10.3791/55779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Supramolecular protein assemblies play fundamental roles in biological processes ranging from host-pathogen interaction, viral infection to the propagation of neurodegenerative disorders. Such assemblies consist in multiple protein subunits organized in a non-covalent way to form large macromolecular objects that can execute a variety of cellular functions or cause detrimental consequences. Atomic insights into the assembly mechanisms and the functioning of those macromolecular assemblies remain often scarce since their inherent insolubility and non-crystallinity often drastically reduces the quality of the data obtained from most techniques used in structural biology, such as X-ray crystallography and solution Nuclear Magnetic Resonance (NMR). We here present magic-angle spinning solid-state NMR spectroscopy (SSNMR) as a powerful method to investigate structures of macromolecular assemblies at atomic resolution. SSNMR can reveal atomic details on the assembled complex without size and solubility limitations. The protocol presented here describes the essential steps from the production of 13C/15N isotope-labeled macromolecular protein assemblies to the acquisition of standard SSNMR spectra and their analysis and interpretation. As an example, we show the pipeline of a SSNMR structural analysis of a filamentous protein assembly.
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Affiliation(s)
- Antoine Loquet
- Institute of Chemistry, Biology of Membranes, Nanoobjects, UMR5248 CNRS, Université de Bordeaux;
| | - James Tolchard
- Institute of Chemistry, Biology of Membranes, Nanoobjects, UMR5248 CNRS, Université de Bordeaux
| | - Melanie Berbon
- Institute of Chemistry, Biology of Membranes, Nanoobjects, UMR5248 CNRS, Université de Bordeaux
| | - Denis Martinez
- Institute of Chemistry, Biology of Membranes, Nanoobjects, UMR5248 CNRS, Université de Bordeaux
| | - Birgit Habenstein
- Institute of Chemistry, Biology of Membranes, Nanoobjects, UMR5248 CNRS, Université de Bordeaux;
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Dydecka A, Bloch S, Rizvi A, Perez S, Nejman-Falenczyk B, Topka G, Gasior T, Necel A, Wegrzyn G, Donaldson LW, Wegrzyn A. Bad Phages in Good Bacteria: Role of the Mysterious orf63 of λ and Shiga Toxin-Converting Φ24 B Bacteriophages. Front Microbiol 2017; 8:1618. [PMID: 28890713 PMCID: PMC5575149 DOI: 10.3389/fmicb.2017.01618] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 08/08/2017] [Indexed: 11/13/2022] Open
Abstract
Lambdoid bacteriophages form a group of viruses that shares a common schema of genome organization and lifecycle. Some of them can play crucial roles in creating the pathogenic profiles of Escherichia coli strains. For example, Shiga toxin-producing E. coli (STEC) acquired stx genes, encoding Shiga toxins, via lambdoid prophages (Stx phages). The results obtained so far present the evidence for the relation between the exo-xis region of the phage genome and lambdoid phage development, however molecular mechanisms of activities of the exo-xis genes' products are still unknown. In view of this, we decided to determine the influence of the uncharacterized open reading frame orf63 of the exo-xis region on lambdoid phages development using recombinant prophages, λ and Stx phage Φ24B. We have demonstrated that orf63 codes for a folded protein, thus, it is a functional gene. NMR spectroscopy and analytical gel filtration were used to extend this observation further. From backbone chemical shifts, Orf63 is oligomeric in solution, likely a trimer and consistent with its small size (63 aa.), is comprised of two helices, likely intertwined to form the oligomer. We observed that the deletion of phage orf63 does not impair the intracellular lambdoid phage lytic development, however delays the time and decreases the efficiency of prophage induction and in consequence results in increased survival of E. coli during phage lytic development. Additionally, the deletion of phage orf63 negatively influences expression of the major phage genes and open reading frames from the exo-xis region during prophage induction with hydrogen peroxide. We conclude, that lambdoid phage orf63 may have specific functions in the regulation of lambdoid phages development, especially at the stage of the lysis vs. lysogenization decision. Besides, orf63 probably participates in the regulation of the level of expression of essential phage genes and open reading frames from the exo-xis region during prophage induction.
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Affiliation(s)
- Aleksandra Dydecka
- Department of Molecular Biology, Faculty of Biology, University of GdanskGdansk, Poland
| | - Sylwia Bloch
- Department of Molecular Biology, Faculty of Biology, University of GdanskGdansk, Poland
| | - Ali Rizvi
- Department of Biology, York UniversityToronto, ON, Canada
| | - Shaili Perez
- Department of Biology, York UniversityToronto, ON, Canada
| | | | - Gracja Topka
- Department of Molecular Biology, Faculty of Biology, University of GdanskGdansk, Poland
| | - Tomasz Gasior
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsaw, Poland
| | - Agnieszka Necel
- Department of Molecular Biology, Faculty of Biology, University of GdanskGdansk, Poland
| | - Grzegorz Wegrzyn
- Department of Molecular Biology, Faculty of Biology, University of GdanskGdansk, Poland
| | | | - Alicja Wegrzyn
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsaw, Poland
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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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Ragunathan P, Sielaff H, Sundararaman L, Biuković G, Subramanian Manimekalai MS, Singh D, Kundu S, Wohland T, Frasch W, Dick T, Grüber G. The uniqueness of subunit α of mycobacterial F-ATP synthases: An evolutionary variant for niche adaptation. J Biol Chem 2017; 292:11262-11279. [PMID: 28495884 PMCID: PMC5500794 DOI: 10.1074/jbc.m117.784959] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/11/2017] [Indexed: 01/30/2023] Open
Abstract
The F1F0 -ATP (F-ATP) synthase is essential for growth of Mycobacterium tuberculosis, the causative agent of tuberculosis (TB). In addition to their synthase function most F-ATP synthases possess an ATP-hydrolase activity, which is coupled to proton-pumping activity. However, the mycobacterial enzyme lacks this reverse activity, but the reason for this deficiency is unclear. Here, we report that a Mycobacterium-specific, 36-amino acid long C-terminal domain in the nucleotide-binding subunit α (Mtα) of F-ATP synthase suppresses its ATPase activity and determined the mechanism of suppression. First, we employed vesicles to show that in intact membrane-embedded mycobacterial F-ATP synthases deletion of the C-terminal domain enabled ATPase and proton-pumping activity. We then generated a heterologous F-ATP synthase model system, which demonstrated that transfer of the mycobacterial C-terminal domain to a standard F-ATP synthase α subunit suppresses ATPase activity. Single-molecule rotation assays indicated that the introduction of this Mycobacterium-specific domain decreased the angular velocity of the power-stroke after ATP binding. Solution X-ray scattering data and NMR results revealed the solution shape of Mtα and the 3D structure of the subunit α C-terminal peptide 521PDEHVEALDEDKLAKEAVKV540 of M. tubercolosis (Mtα(521-540)), respectively. Together with cross-linking studies, the solution structural data lead to a model, in which Mtα(521-540) comes in close proximity with subunit γ residues 104-109, whose interaction may influence the rotation of the camshaft-like subunit γ. Finally, we propose that the unique segment Mtα(514-549), which is accessible at the C terminus of mycobacterial subunit α, is a promising drug epitope.
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Affiliation(s)
- Priya Ragunathan
- From the Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Hendrik Sielaff
- From the Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Lavanya Sundararaman
- From the Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Goran Biuković
- the Department of Microbiology and Immunology, National University of Singapore, Yong Loo Lin School of Medicine, 14 Medical Drive, Singapore 117599, Republic of Singapore
| | | | - Dhirendra Singh
- From the Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Subhashri Kundu
- the Department of Microbiology and Immunology, National University of Singapore, Yong Loo Lin School of Medicine, 14 Medical Drive, Singapore 117599, Republic of Singapore
| | - Thorsten Wohland
- the Departments of Biological Sciences and Chemistry and NUS Centre for Bioimaging Sciences (CBIS), National University of Singapore, 14 Science Drive 4, Singapore 117557, Republic of Singapore, and
| | - Wayne Frasch
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287
| | - Thomas Dick
- the Department of Microbiology and Immunology, National University of Singapore, Yong Loo Lin School of Medicine, 14 Medical Drive, Singapore 117599, Republic of Singapore
| | - Gerhard Grüber
- From the Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore,
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41
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Bacterial Filamentous Appendages Investigated by Solid-State NMR Spectroscopy. Methods Mol Biol 2017. [PMID: 28667627 DOI: 10.1007/978-1-4939-7033-9_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The assembly of filamentous appendages at the surface of bacteria is essential in many infection mechanisms. The extent of mechanical, dynamical, and functional properties of such appendages is very diverse, ranging from a structural scaffold of the pathogen-host cell interaction to cell motility, surface adhesion, or the export of virulence effectors. In particular, the architectures of several bacterial secretion systems have revealed the presence of filamentous architectures, known as pili, fimbriae, andneedles. At the macroscopic level, filamentous bacterial appendages appear as thin extracellular filaments of several nanometers in diameter and up to several microns in length. The structural characterization of these appendages at atomic-scale resolution represents an extremely challenging task because of their inherent noncrystallinity and very poor solubility. Here, we describe protocols based on recent advances in solid-state NMR spectroscopy to investigate the secondary structure, subunit-subunit protein interactions, symmetry parameters, and atomic architecture of bacterial filaments.
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42
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Ziarek JJ, Baptista D, Wagner G. Recent developments in solution nuclear magnetic resonance (NMR)-based molecular biology. J Mol Med (Berl) 2017. [PMID: 28643003 DOI: 10.1007/s00109-017-1560-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Visualizing post-translational modifications, conformations, and interaction surfaces of protein structures at atomic resolution underpins the development of novel therapeutics to combat disease. As computational resources expand, in silico calculations coupled with experimentally derived structures and functional assays have led to an explosion in structure-based drug design (SBDD) with several compounds in clinical trials. It is increasingly clear that "hidden" transition-state structures along activation trajectories can be harnessed to develop novel classes of allosteric inhibitors. The goal of this mini-review is to empower the clinical researcher with a general knowledge of the strengths and weaknesses of nuclear magnetic resonance (NMR) spectroscopy in molecular medicine. Although NMR can determine protein structures at atomic resolution, its unrivaled strength lies in sensing subtle changes in a nuclei's chemical environment as a result of intrinsic conformational dynamics, solution conditions, and binding interactions. These can be recorded at atomic resolution, without explicit structure determination, and then incorporated with static structures or molecular dynamics simulations to produce a complete biological picture.
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Affiliation(s)
- Joshua J Ziarek
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA, 02115, USA
| | - Diego Baptista
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA, 02115, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA, 02115, USA.
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43
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Vernhes E, Renouard M, Gilquin B, Cuniasse P, Durand D, England P, Hoos S, Huet A, Conway JF, Glukhov A, Ksenzenko V, Jacquet E, Nhiri N, Zinn-Justin S, Boulanger P. High affinity anchoring of the decoration protein pb10 onto the bacteriophage T5 capsid. Sci Rep 2017; 7:41662. [PMID: 28165000 PMCID: PMC5292684 DOI: 10.1038/srep41662] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 12/20/2016] [Indexed: 12/14/2022] Open
Abstract
Bacteriophage capsids constitute icosahedral shells of exceptional stability that protect the viral genome. Many capsids display on their surface decoration proteins whose structure and function remain largely unknown. The decoration protein pb10 of phage T5 binds at the centre of the 120 hexamers formed by the major capsid protein. Here we determined the 3D structure of pb10 and investigated its capsid-binding properties using NMR, SAXS, cryoEM and SPR. Pb10 consists of an α-helical capsid-binding domain and an Ig-like domain exposed to the solvent. It binds to the T5 capsid with a remarkably high affinity and its binding kinetics is characterized by a very slow dissociation rate. We propose that the conformational exchange events observed in the capsid-binding domain enable rearrangements upon binding that contribute to the quasi-irreversibility of the pb10-capsid interaction. Moreover we show that pb10 binding is a highly cooperative process, which favours immediate rebinding of newly dissociated pb10 to the 120 hexamers of the capsid protein. In extreme conditions, pb10 protects the phage from releasing its genome. We conclude that pb10 may function to reinforce the capsid thus favouring phage survival in harsh environments.
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Affiliation(s)
- Emeline Vernhes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Madalena Renouard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Bernard Gilquin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Philippe Cuniasse
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Patrick England
- Institut Pasteur, Biophysique Moléculaire, Citech, UMR 3528, Paris, France
| | - Sylviane Hoos
- Institut Pasteur, Biophysique Moléculaire, Citech, UMR 3528, Paris, France
| | - Alexis Huet
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - James F. Conway
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Anatoly Glukhov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - Vladimir Ksenzenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, Univ Paris-Sud, Université Paris-Saclay, CNRS UPR 2301, Gif-sur-Yvette, France
| | - Naïma Nhiri
- Institut de Chimie des Substances Naturelles, Univ Paris-Sud, Université Paris-Saclay, CNRS UPR 2301, Gif-sur-Yvette, France
| | - Sophie Zinn-Justin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Pascale Boulanger
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
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44
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Rozbeský D, Adámek D, Pospíšilová E, Novák P, Chmelík J. Solution structure of the lymphocyte receptor Nkrp1a reveals a distinct conformation of the long loop region as compared to in the crystal structure. Proteins 2016; 84:1304-11. [PMID: 27238500 DOI: 10.1002/prot.25078] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 05/13/2016] [Accepted: 05/20/2016] [Indexed: 11/08/2022]
Abstract
Mouse Nkrp1a receptor is a C-type lectin-like receptor expressed on the surface of natural killer cells that play an important role against virally infected and tumor cells. The recently solved crystal structure of Nkrp1a raises questions about a long loop region which was uniquely extended from the central region in the crystal. To understand the functional significance of the loop, the solution structure of Nkrp1a using nuclear magnetic resonance (NMR) spectroscopy was determined. A notable difference between the crystal and NMR structure of Nkrp1a appears in the conformation of the long loop region. While the extended loop points away from the central core and mediates formation of a domain swapped dimer in the crystal, the solution structure is monomeric with the loop tightly anchored to the central region. The findings described the first solution structure in the Nkrp1 family and revealed intriguing similarities and differences to the crystal structure. Proteins 2016; 84:1304-1311. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Daniel Rozbeský
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - David Adámek
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Eliška Pospíšilová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Novák
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Josef Chmelík
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
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45
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Anamika, Spyracopoulos L. Molecular Basis for Phosphorylation-dependent SUMO Recognition by the DNA Repair Protein RAP80. J Biol Chem 2015; 291:4417-28. [PMID: 26719330 DOI: 10.1074/jbc.m115.705061] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Indexed: 01/04/2023] Open
Abstract
Recognition and repair of double-stranded DNA breaks (DSB) involves the targeted recruitment of BRCA tumor suppressors to damage foci through binding of both ubiquitin (Ub) and the Ub-like modifier SUMO. RAP80 is a component of the BRCA1 A complex, and plays a key role in the recruitment process through the binding of Lys(63)-linked poly-Ub chains by tandem Ub interacting motifs (UIM). RAP80 also contains a SUMO interacting motif (SIM) just upstream of the tandem UIMs that has been shown to specifically bind the SUMO-2 isoform. The RAP80 tandem UIMs and SIM function collectively for optimal recruitment of BRCA1 to DSBs, although the molecular basis of this process is not well understood. Using NMR spectroscopy, we demonstrate that the RAP80 SIM binds SUMO-2, and that both specificity and affinity are enhanced through phosphorylation of the canonical CK2 site within the SIM. The affinity increase results from an enhancement of electrostatic interactions between the phosphoserines of RAP80 and the SIM recognition module within SUMO-2. The NMR structure of the SUMO-2·phospho-RAP80 complex reveals that the molecular basis for SUMO-2 specificity is due to isoform-specific sequence differences in electrostatic SIM recognition modules.
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Affiliation(s)
- Anamika
- From the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Leo Spyracopoulos
- From the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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46
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Berjanskii M, Arndt D, Liang Y, Wishart DS. A robust algorithm for optimizing protein structures with NMR chemical shifts. JOURNAL OF BIOMOLECULAR NMR 2015; 63:255-264. [PMID: 26345175 DOI: 10.1007/s10858-015-9982-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/27/2015] [Indexed: 06/05/2023]
Abstract
Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts. However, there have been relatively few methods that allow these approximate models to be substantively refined or improved using the available NMR chemical shift data. Here, we present a novel method, called Chemical Shift driven Genetic Algorithm for biased Molecular Dynamics (CS-GAMDy), for the robust optimization of protein structures using experimental NMR chemical shifts. The method incorporates knowledge-based scoring functions and structural information derived from NMR chemical shifts via a unique combination of multi-objective MD biasing, a genetic algorithm, and the widely used XPLOR molecular modelling language. Using this approach, we demonstrate that CS-GAMDy is able to refine and/or fold models that are as much as 10 Å (RMSD) away from the correct structure using only NMR chemical shift data. CS-GAMDy is also able to refine of a wide range of approximate or mildly erroneous protein structures to more closely match the known/correct structure and the known/correct chemical shifts. We believe CS-GAMDy will allow protein models generated by sparse restraint or chemical-shift-only methods to achieve sufficiently high quality to be considered fully refined and "PDB worthy". The CS-GAMDy algorithm is explained in detail and its performance is compared over a range of refinement scenarios with several commonly used protein structure refinement protocols. The program has been designed to be easily installed and easily used and is available at http://www.gamdy.ca.
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Affiliation(s)
- Mark Berjanskii
- 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
| | - Yongjie Liang
- 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 2E9, Canada.
- National Research Council, National Institute for Nanotechnology (NINT), Edmonton, AB, T6G 2M9, Canada.
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47
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Follis AV, Llambi F, Merritt P, Chipuk JE, Green DR, Kriwacki RW. Pin1-Induced Proline Isomerization in Cytosolic p53 Mediates BAX Activation and Apoptosis. Mol Cell 2015; 59:677-84. [PMID: 26236013 PMCID: PMC4546541 DOI: 10.1016/j.molcel.2015.06.029] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 05/15/2015] [Accepted: 06/22/2015] [Indexed: 12/31/2022]
Abstract
The cytosolic fraction of the tumor suppressor p53 activates the apoptotic effector protein BAX to trigger apoptosis. Here we report that p53 activates BAX through a mechanism different from that associated with activation by BH3 only proteins (BIM and BID). We observed that cis-trans isomerization of proline 47 (Pro47) within p53, an inherently rare molecular event, was required for BAX activation. The prolyl isomerase Pin1 enhanced p53-dependent BAX activation by catalyzing cis-trans interconversion of p53 Pro47. Our results reveal a signaling mechanism whereby proline cis-trans isomerization in one protein triggers conformational and functional changes in a downstream signaling partner. Activation of BAX through the concerted action of cytosolic p53 and Pin1 may integrate cell stress signals to induce a direct apoptotic response.
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Affiliation(s)
- Ariele Viacava Follis
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Fabien Llambi
- Department of Immunology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Parker Merritt
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jerry E Chipuk
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA; Department of Dermatology, The Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, 920 Court Avenue, Memphis, TN 38163, USA.
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48
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de Paola I, Pirone L, Palmieri M, Balasco N, Esposito L, Russo L, Mazzà D, Di Marcotullio L, Di Gaetano S, Malgieri G, Vitagliano L, Pedone E, Zaccaro L. Cullin3-BTB interface: a novel target for stapled peptides. PLoS One 2015; 10:e0121149. [PMID: 25848797 PMCID: PMC4388676 DOI: 10.1371/journal.pone.0121149] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 02/06/2015] [Indexed: 12/21/2022] Open
Abstract
Cullin3 (Cul3), a key factor of protein ubiquitination, is able to interact with dozens of different proteins containing a BTB (Bric-a-brac, Tramtrack and Broad Complex) domain. We here targeted the Cul3–BTB interface by using the intriguing approach of stabilizing the α-helical conformation of Cul3-based peptides through the “stapling” with a hydrocarbon cross-linker. In particular, by combining theoretical and experimental techniques, we designed and characterized stapled Cul3-based peptides embedding the helix 2 of the protein (residues 49–68). Intriguingly, CD and NMR experiments demonstrate that these stapled peptides were able to adopt the helical structure that the fragment assumes in the parent protein. We also show that some of these peptides were able to bind to the BTB of the tetrameric KCTD11, a substrate adaptor involved in HDAC1 degradation, with high affinity (~ 300–600 nM). Cul3-derived staple peptides are also able to bind the BTB of the pentameric KCTD5. Interestingly, the affinity of these peptides is of the same order of magnitude of that reported for the interaction of full-length Cul3 with some BTB containing proteins. Moreover, present data indicate that stapling endows these peptides with an increased serum stability. Altogether, these findings indicate that the designed stapled peptides can efficiently mimic protein-protein interactions and are potentially able to modulate fundamental biological processes involving Cul3.
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Affiliation(s)
- Ivan de Paola
- Institute of Biostructures and Bioimaging, C.N.R., Napoli, Italy
| | | | | | - Nicole Balasco
- Institute of Biostructures and Bioimaging, C.N.R., Napoli, Italy
- Second University of Napoli, Caserta, Italy
| | - Luciana Esposito
- Institute of Biostructures and Bioimaging, C.N.R., Napoli, Italy
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), Napoli, Italy
| | | | - Daniela Mazzà
- Department of Molecular Medicine, La Sapienza University, Roma, Italy
| | | | - Sonia Di Gaetano
- Institute of Biostructures and Bioimaging, C.N.R., Napoli, Italy
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), Napoli, Italy
| | | | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, C.N.R., Napoli, Italy
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), Napoli, Italy
| | - Emilia Pedone
- Institute of Biostructures and Bioimaging, C.N.R., Napoli, Italy
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), Napoli, Italy
- * E-mail: (EP); (LZ)
| | - Laura Zaccaro
- Institute of Biostructures and Bioimaging, C.N.R., Napoli, Italy
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), Napoli, Italy
- * E-mail: (EP); (LZ)
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Abramov G, Morag O, Goldbourt A. Magic-angle spinning NMR of intact bacteriophages: insights into the capsid, DNA and their interface. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:80-90. [PMID: 25797007 DOI: 10.1016/j.jmr.2015.01.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 01/05/2015] [Accepted: 01/18/2015] [Indexed: 06/04/2023]
Abstract
Bacteriophages are viruses that infect bacteria. They are complex macromolecular assemblies, which are composed of multiple protein subunits that protect genomic material and deliver it to specific hosts. Various biophysical techniques have been used to characterize their structure in order to unravel phage morphogenesis. Yet, most bacteriophages are non-crystalline and have very high molecular weights, in the order of tens of MegaDaltons. Therefore, complete atomic-resolution characterization on such systems that encompass both capsid and DNA is scarce. In this perspective article we demonstrate how magic-angle spinning solid-state NMR has and is used to characterize in detail bacteriophage viruses, including filamentous and icosahedral phage. We discuss the process of sample preparation, spectral assignment of both capsid and DNA and the use of chemical shifts and dipolar couplings to probe the capsid-DNA interface, describe capsid structure and dynamics and extract structural differences between viruses.
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Affiliation(s)
- Gili Abramov
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
| | - Omry Morag
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
| | - Amir Goldbourt
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel.
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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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