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Vila JA. Analysis of proteins in the light of mutations. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:255-265. [PMID: 38955858 DOI: 10.1007/s00249-024-01714-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 05/23/2024] [Accepted: 06/18/2024] [Indexed: 07/04/2024]
Abstract
Proteins have evolved through mutations-amino acid substitutions-since life appeared on Earth, some 109 years ago. The study of these phenomena has been of particular significance because of their impact on protein stability, function, and structure. This study offers a new viewpoint on how the most recent findings in these areas can be used to explore the impact of mutations on protein sequence, stability, and evolvability. Preliminary results indicate that: (1) mutations can be viewed as sensitive probes to identify 'typos' in the amino-acid sequence, and also to assess the resistance of naturally occurring proteins to unwanted sequence alterations; (2) the presence of 'typos' in the amino acid sequence, rather than being an evolutionary obstacle, could promote faster evolvability and, in turn, increase the likelihood of higher protein stability; (3) the mutation site is far more important than the substituted amino acid in terms of the marginal stability changes of the protein, and (4) the unpredictability of protein evolution at the molecular level-by mutations-exists even in the absence of epistasis effects. Finally, the Darwinian concept of evolution "descent with modification" and experimental evidence endorse one of the results of this study, which suggests that some regions of any protein sequence are susceptible to mutations while others are not. This work contributes to our general understanding of protein responses to mutations and may spur significant progress in our efforts to develop methods to accurately forecast changes in protein stability, their propensity for metamorphism, and their ability to evolve.
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Affiliation(s)
- Jorge A Vila
- IMASL-CONICET, Universidad Nacional de San Luis, Ejército de los Andes 950, 5700, San Luis, Argentina.
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2
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Kao CF, Tsai MH, Carillo KJ, Tzou DL, Chang W. Structural and functional analysis of vaccinia viral fusion complex component protein A28 through NMR and molecular dynamic simulations. PLoS Pathog 2023; 19:e1011500. [PMID: 37948471 PMCID: PMC10664964 DOI: 10.1371/journal.ppat.1011500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 11/22/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Host cell entry of vaccinia virus (a poxvirus) proceeds through multiple steps that involve many viral proteins to mediate cell infection. Upon binding to cells, vaccinia virus membrane fuses with host membranes via a viral entry fusion protein complex comprising 11 proteins: A16, A21, A28, F9, G3, G9, H2, J5, L1, L5 and O3. Despite vaccinia virus having two infectious forms, mature and enveloped, that have different membrane layers, both forms require an identical viral entry fusion complex for membrane fusion. Components of the poxvirus entry fusion complex that have been structurally assessed to date share no known homology with all other type I, II and III viral fusion proteins, and the large number of fusion protein components renders it a unique system to investigate poxvirus-mediated membrane fusion. Here, we determined the NMR structure of a truncated version of vaccinia A28 protein. We also expressed a soluble H2 protein and showed that A28 interacts with H2 protein at a 1:1 ratio in vitro. Furthermore, we performed extensive in vitro alanine mutagenesis to identify A28 protein residues that are critical for H2 binding, entry fusion complex formation, and virus-mediated membrane fusion. Finally, we used molecular dynamic simulations to model full-length A28-H2 subcomplex in membranes. In summary, we characterized vaccinia virus A28 protein and determined residues important in its interaction with H2 protein and membrane components. We also provide a structural model of the A28-H2 protein interaction to illustrate how it forms a 1:1 subcomplex on a modeled membrane.
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Affiliation(s)
- Chi-Fei Kao
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Min-Hsin Tsai
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | | | - Der-Lii Tzou
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Wen Chang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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3
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Günsel U, Klöpfer K, Häusler E, Hitzenberger M, Bölter B, Sperl LE, Zacharias M, Soll J, Hagn F. Structural basis of metabolite transport by the chloroplast outer envelope channel OEP21. Nat Struct Mol Biol 2023:10.1038/s41594-023-00984-y. [PMID: 37156968 DOI: 10.1038/s41594-023-00984-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/31/2023] [Indexed: 05/10/2023]
Abstract
Triose phosphates (TPs) are the primary products of photosynthetic CO2 fixation in chloroplasts, which need to be exported into the cytosol across the chloroplast inner envelope (IE) and outer envelope (OE) membranes to sustain plant growth. While transport across the IE is well understood, the mode of action of the transporters in the OE remains unclear. Here we present the high-resolution nuclear magnetic resonance (NMR) structure of the outer envelope protein 21 (OEP21) from garden pea, the main exit pore for TPs in C3 plants. OEP21 is a cone-shaped β-barrel pore with a highly positively charged interior that enables binding and translocation of negatively charged metabolites in a competitive manner, up to a size of ~1 kDa. ATP stabilizes the channel and keeps it in an open state. Despite the broad substrate selectivity of OEP21, these results suggest that control of metabolite transport across the OE might be possible.
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Affiliation(s)
- Umut Günsel
- Bavarian NMR Center (BNMRZ), Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
- Institute of Structural Biology, Helmholtz Munich, Neuherberg, Germany
| | - Kai Klöpfer
- Bavarian NMR Center (BNMRZ), Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Elisabeth Häusler
- Institute of Structural Biology, Helmholtz Munich, Neuherberg, Germany
| | - Manuel Hitzenberger
- Lehrstuhl für Theoretische Biophysik (T38), Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Bettina Bölter
- Biozentrum, LMU München, Department of Biology, Planegg-Martinsried, Germany
| | - Laura E Sperl
- Bavarian NMR Center (BNMRZ), Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Martin Zacharias
- Lehrstuhl für Theoretische Biophysik (T38), Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Jürgen Soll
- Biozentrum, LMU München, Department of Biology, Planegg-Martinsried, Germany
| | - Franz Hagn
- Bavarian NMR Center (BNMRZ), Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany.
- Institute of Structural Biology, Helmholtz Munich, Neuherberg, Germany.
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4
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A redox switch regulates the assembly and anti-CRISPR activity of AcrIIC1. Nat Commun 2022; 13:7071. [PMID: 36400778 PMCID: PMC9674691 DOI: 10.1038/s41467-022-34551-8] [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: 04/07/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
Anti-CRISPRs (Acrs) are natural inhibitors of bacteria's CRISPR-Cas systems, and have been developed as a safeguard to reduce the off-target effects of CRISPR gene-editing technology. Acrs can directly bind to CRISPR-Cas complexes and inhibit their activities. However, whether this process is under regulation in diverse eukaryotic cellular environments is poorly understood. In this work, we report the discovery of a redox switch for NmeAcrIIC1, which regulates NmeAcrIIC1's monomer-dimer interconversion and inhibitory activity on Cas9. Further structural studies reveal that a pair of conserved cysteines mediates the formation of inactive NmeAcrIIC1 dimer and directs the redox cycle. The redox switch also applies to the other two AcrIIC1 orthologs. Moreover, by replacing the redox-sensitive cysteines, we generated a robust AcrIIC1 variant that maintains potent inhibitory activity under various redox conditions. Our results reveal a redox-dependent regulation mechanism of Acr, and shed light on the design of superior Acr for CRISPR-Cas systems.
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Martin-Malpartida P, Arrastia-Casado S, Farrera-Sinfreu J, Lucas R, Fischer H, Fischer B, Eaton DC, Tzotzos S, Macias MJ. Conformational ensemble of the TNF-derived peptide solnatide in solution. Comput Struct Biotechnol J 2022; 20:2082-2090. [PMID: 35601958 PMCID: PMC9079168 DOI: 10.1016/j.csbj.2022.04.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 12/12/2022] Open
Abstract
Tumor necrosis factor (TNF) is a homotrimer that has two spatially distinct binding regions, three lectin-like domains (LLD) at the TIP of the protein and three basolaterally located receptor-binding sites, the latter of which are responsible for the inflammatory and cell death-inducing properties of the cytokine. Solnatide (a.k.a. TIP peptide, AP301) is a 17-mer cyclic peptide that mimics the LLD of human TNF which activates the amiloride-sensitive epithelial sodium channel (ENaC) and, as such, recapitulates the capacity of TNF to enhance alveolar fluid clearance, as demonstrated in numerous preclinical studies. TNF and solnatide interact with glycoproteins and these interactions are necessary for their trypanolytic and ENaC-activating activities. In view of the crucial role of ENaC in lung liquid clearance, solnatide is currently being evaluated as a novel therapeutic agent to treat pulmonary edema in patients with moderate-to-severe acute respiratory distress syndrome (ARDS), as well as severe COVID-19 patients with ARDS. To facilitate the description of the functional properties of solnatide in detail, as well as to further target-docking studies, we have analyzed its folding properties by NMR. In solution, solnatide populates a set of conformations characterized by a small hydrophobic core and two electrostatically charged poles. Using the structural information determined here and also that available for the ENaC protein, we propose a model to describe solnatide interaction with the C-terminal domain of the ENaCα subunit. This model may serve to guide future experiments to validate specific interactions with ENaCα and the design of new solnatide analogs with unexplored functionalities.
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Key Words
- AP301 peptide
- ARDS, Acute Respiratory Distress Syndrome
- AlphaFold applications
- Alveolar fluid clearance
- Amiloride-sensitive epithelial sodium channel
- Amphipathic helix
- ENaC
- ENaC, Amiloride-sensitive Epithelial Sodium/Channel
- HPLC, High Performance Liquid Chromatography
- HSQC, Heteronuclear Single Quantum Coherence
- LLD, Lectin-Like Domains
- MARCKS, Myristoylated Alanine-Rich C Kinase Substrate
- NMR, Nuclear Magnetic Resonance
- NOESY, Nuclear Overhauser Effect Spectroscopy
- PIP2, Phosphatidylinositol Bisphosphate
- Peptide NMR
- Pulmonary edema
- Solnatide structure
- TIP peptide
- TM, Transmembrane Regions
- TNF, Tumor Necrosis Factor
- TOCSY, Total Correlation Spectroscopy
- Tumor necrosis factor
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Affiliation(s)
- Pau Martin-Malpartida
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | | | | | - Rudolf Lucas
- Vascular Biology Center, Dept of Pharmacology and Toxicology, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Hendrik Fischer
- APEPTICO Forschung und Entwicklung GmbH, Mariahilferstraße 136, 1150 Vienna, Austria
| | - Bernhard Fischer
- APEPTICO Forschung und Entwicklung GmbH, Mariahilferstraße 136, 1150 Vienna, Austria
| | - Douglas C. Eaton
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Susan Tzotzos
- APEPTICO Forschung und Entwicklung GmbH, Mariahilferstraße 136, 1150 Vienna, Austria
| | - Maria J. Macias
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona 08010, Spain
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Skvortsova P, Valiullina Y, Baranova N, Faizullin D, Zuev Y, Ermakova E. Spectroscopic study of antimicrobial peptides: Structure and functional activity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 264:120273. [PMID: 34425316 DOI: 10.1016/j.saa.2021.120273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/21/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
Amphibians are a natural source of a large number of peptides with a wide range of functional activities. Here, a complex of spectroscopic methods including NMR-, FTIR-, CD-, and UV-spectroscopy was applied to characterize the structure and functional activity of megin-1, a peptide isolated from amphibian skin. The three-dimensional structure of two forms of the peptide was determined using solution NMR spectroscopy. Thermodynamic characteristics of the process of peptide transformation from linear to cyclic form were obtained. Antibacterial and antimycotic properties of the peptide, as well as its protease inhibitory activities, were analyzed.
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Affiliation(s)
- Polina Skvortsova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, Russian Federation
| | - Yuliya Valiullina
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, Russian Federation
| | - Natalia Baranova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, Russian Federation
| | - Dzhigangir Faizullin
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, Russian Federation
| | - Yuriy Zuev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, Russian Federation
| | - Elena Ermakova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, Russian Federation.
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7
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Wiedemann C, Kumar A, Lang A, Ohlenschläger O. Cysteines and Disulfide Bonds as Structure-Forming Units: Insights From Different Domains of Life and the Potential for Characterization by NMR. Front Chem 2020; 8:280. [PMID: 32391319 PMCID: PMC7191308 DOI: 10.3389/fchem.2020.00280] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/23/2020] [Indexed: 12/22/2022] Open
Abstract
Disulfide bridges establish a fundamental element in the molecular architecture of proteins and peptides which are involved e.g., in basic biological processes or acting as toxins. NMR spectroscopy is one method to characterize the structure of bioactive compounds including cystine-containing molecules. Although the disulfide bridge itself is invisible in NMR, constraints obtained via the neighboring NMR-active nuclei allow to define the underlying conformation and thereby to resolve their functional background. In this mini-review we present shortly the impact of cysteine and disulfide bonds in the proteasome from different domains of life and give a condensed overview of recent NMR applications for the characterization of disulfide-bond containing biomolecules including advantages and limitations of the different approaches.
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Affiliation(s)
- Christoph Wiedemann
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Amit Kumar
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Andras Lang
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
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8
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Ambadipudi S, Reddy JG, Biernat J, Mandelkow E, Zweckstetter M. Residue-specific identification of phase separation hot spots of Alzheimer's-related protein tau. Chem Sci 2019; 10:6503-6507. [PMID: 31341602 PMCID: PMC6610569 DOI: 10.1039/c9sc00531e] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/22/2019] [Indexed: 12/30/2022] Open
Abstract
Visualizing liquid–liquid phase separation by NMR spectroscopy: LLPS of the Alzheimer's-related protein tau involves aggregation-prone hexapeptides and activity regulating KXGS motifs.
Liquid–liquid phase separation (LLPS) of proteins enables the formation of non-membrane-bound organelles in cells and is associated with cancer and neurodegeneration. Little is known however about the structure and dynamics of proteins in LLPS conditions, because of the polymorphic nature of liquid-like protein droplets. Using carbon-detected NMR experiments we here show that the conversion of the aggregation-prone repeat region of the Alzheimer's-related protein tau from the dispersed monomeric state to phase-separated liquid-like droplets involves tau's aggregation-prone hexapeptides and regulatory KXGS motifs. Droplet dissolution in presence of 1,6-hexanediol revealed that chemical shift perturbations in the hexapeptide motifs are temperature driven, while those in KXGS motifs report on phase separation. Residue-specific secondary structure analysis further indicated that tau's repeat region exists in extended conformation in the dispersed state and attains transient β-hairpin propensity upon LLPS. Taken together our work shows that NMR spectroscopy can provide high-resolution insights into LLPS-induced changes in intrinsically disordered proteins.
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Affiliation(s)
- Susmitha Ambadipudi
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) , Von-Siebold-Str. 3a , 37075 Göttingen , Germany .
| | - Jithender G Reddy
- Max-Planck-Institut für Biophysikalische Chemie , Am Fassberg 11 , 37077 Göttingen , Germany.,NMR & Structural Chemistry Division , CSIR-Indian Institute of Chemical Technology , Hyderabad , 500007 , India
| | - Jacek Biernat
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) , Ludwig-Erhard-Allee 2 , 53175 Bonn , Germany
| | - Eckhard Mandelkow
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) , Ludwig-Erhard-Allee 2 , 53175 Bonn , Germany.,CAESAR Research Center, Bonn , MPI for Metabolism Research , Hamburg Outstation , 22607 Hamburg , Germany
| | - Markus Zweckstetter
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) , Von-Siebold-Str. 3a , 37075 Göttingen , Germany . .,Max-Planck-Institut für Biophysikalische Chemie , Am Fassberg 11 , 37077 Göttingen , Germany
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9
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Antimicrobial alumina nanobiostructures of disulfide- and triazole-linked peptides: Synthesis, characterization, membrane interactions and biological activity. Colloids Surf B Biointerfaces 2019; 177:94-104. [DOI: 10.1016/j.colsurfb.2019.01.052] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 11/18/2022]
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10
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Lee W, Bahrami A, Dashti HT, Eghbalnia HR, Tonelli M, Westler WM, Markley JL. I-PINE web server: an integrative probabilistic NMR assignment system for proteins. JOURNAL OF BIOMOLECULAR NMR 2019; 73:213-222. [PMID: 31165321 PMCID: PMC6579641 DOI: 10.1007/s10858-019-00255-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/21/2019] [Indexed: 05/12/2023]
Abstract
Various methods for understanding the structural and dynamic properties of proteins rely on the analysis of their NMR chemical shifts. These methods require the initial assignment of NMR signals to particular atoms in the sequence of the protein, a step that can be very time-consuming. The probabilistic interaction network of evidence (PINE) algorithm for automated assignment of backbone and side chain chemical shifts utilizes a Bayesian probabilistic network model that analyzes sequence data and peak lists from multiple NMR experiments. PINE, which is one of the most popular and reliable automated chemical shift assignment algorithms, has been available to the protein NMR community for longer than a decade. We announce here a new web server version of PINE, called Integrative PINE (I-PINE), which supports more types of NMR experiments than PINE (including three-dimensional nuclear Overhauser enhancement and four-dimensional J-coupling experiments) along with more comprehensive visualization of chemical shift based analysis of protein structure and dynamics. The I-PINE server is freely accessible at http://i-pine.nmrfam.wisc.edu . Help pages and tutorial including browser capability are available at: http://i-pine.nmrfam.wisc.edu/instruction.html . Sample data that can be used for testing the web server are available at: http://i-pine.nmrfam.wisc.edu/examples.html .
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Affiliation(s)
- Woonghee Lee
- National Magnetic Resonance Facility at Madison, and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Arash Bahrami
- National Magnetic Resonance Facility at Madison, and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
- NetSeer, Inc, 555 Ellis Street, Suite B, Mountain View, CA, 94043, USA
| | - Hesam T Dashti
- National Magnetic Resonance Facility at Madison, and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02215, USA
| | - Hamid R Eghbalnia
- National Magnetic Resonance Facility at Madison, and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - William M Westler
- National Magnetic Resonance Facility at Madison, and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - John L Markley
- National Magnetic Resonance Facility at Madison, and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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Abstract
Nuclear magnetic resonance (NMR) spectroscopy is perhaps the most widely used technology from the undergraduate teaching labs in organic chemistry to advanced research for the determination of three-dimensional structure as well as dynamics of biomolecular systems... The NMR spectrum of a molecule under a given experimental condition is unique, providing both quantitative and structural information. In particular, the quantitative nature of NMR spectroscopy offers the ability to follow a reaction pathway of the given molecule in a dynamic process under well-defined experimental conditions. To highlight the use of NMR when determining the molecular thermodynamic parameters, a review of three distinct applications developed from our laboratory is presented. These applications include the thermodynamic parameters of (a) molecular oxidation from time-dependent kinetics, (b) intramolecular rotation, and (c) intermolecular exchange. An experimental overview and the method of data analysis are provided so that these applications can be adopted in a range of molecular systems.
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12
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Vila JA, Arnautova YA. 13C Chemical Shifts in Proteins: A Rich Source of Encoded Structural Information. SPRINGER SERIES ON BIO- AND NEUROSYSTEMS 2019. [PMCID: PMC7123919 DOI: 10.1007/978-3-319-95843-9_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Despite the formidable progress in Nuclear Magnetic Resonance (NMR) spectroscopy, quality assessment of NMR-derived structures remains as an important problem. Thus, validation of protein structures is essential for the spectroscopists, since it could enable them to detect structural flaws and potentially guide their efforts in further refinement. Moreover, availability of accurate and efficient validation tools would help molecular biologists and computational chemists to evaluate quality of available experimental structures and to select a protein model which is the most suitable for a given scientific problem. The 13Cα nuclei are ubiquitous in proteins, moreover, their shieldings are easily obtainable from NMR experiments and represent a rich source of encoded structural information that makes 13Cα chemical shifts an attractive candidate for use in computational methods aimed at determination and validation of protein structures. In this chapter, the basis of a novel methodology of computing, at the quantum chemical level of theory, the 13Cα shielding for the amino acid residues in proteins is described. We also identify and examine the main factors affecting the 13Cα-shielding computation. Finally, we illustrate how the information encoded in the 13C chemical shifts can be used for a number of applications, viz., from protein structure prediction of both α-helical and β-sheet conformations, to determination of the fraction of the tautomeric forms of the imidazole ring of histidine in proteins as a function of pH or to accurate detection of structural flaws, at a residue-level, in NMR-determined protein models.
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In-Depth Glyco-Peptidomics Approach Reveals Unexpected Diversity of Glycosylated Peptides and Atypical Post-Translational Modifications in Dendroaspis angusticeps Snake Venom. Int J Mol Sci 2017; 18:ijms18112453. [PMID: 29156586 PMCID: PMC5713420 DOI: 10.3390/ijms18112453] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 11/08/2017] [Accepted: 11/09/2017] [Indexed: 11/16/2022] Open
Abstract
Animal venoms represent a valuable source of bioactive peptides that can be derived into useful pharmacological tools, or even innovative drugs. In this way, the venom of Dendroaspis angusticeps (DA), the Eastern Green Mamba, has been intensively studied during recent years. It mainly contains hundreds of large toxins from 6 to 9 kDa, each displaying several disulfide bridges. These toxins are the main target of venom-based studies due to their valuable activities obtained by selectively targeting membrane receptors, such as ion channels or G-protein coupled receptors. This study aims to demonstrate that the knowledge of venom composition is still limited and that animal venoms contain unexpected diversity and surprises. A previous study has shown that Dendroaspis angusticeps venom contains not only a cocktail of classical toxins, but also small glycosylated peptides. Following this work, a deep exploration of DA glycopeptidome by a dual nano liquid chromatography coupled to electrospray ionization mass spectrometry (nanoLC-ESI-MS) and Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) analyses was initiated. This study reveals unsuspected structural diversity of compounds such as 221 glycopeptides, displaying different glycan structures. Sequence alignments underline structural similarities with natriuretic peptides already characterized in Elapidae venoms. Finally, the presence of an S-cysteinylation and hydroxylation of proline on four glycopeptides, never described to date in snake venoms, is also revealed by proteomics and affined by nuclear magnetic resonance (NMR) experiments.
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Structural Analysis of Human Cofilin 2/Filamentous Actin Assemblies: Atomic-Resolution Insights from Magic Angle Spinning NMR Spectroscopy. Sci Rep 2017; 7:44506. [PMID: 28303963 PMCID: PMC5355874 DOI: 10.1038/srep44506] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/08/2017] [Indexed: 01/22/2023] Open
Abstract
Cellular actin dynamics is an essential element of numerous cellular processes, such as cell motility, cell division and endocytosis. Actin’s involvement in these processes is mediated by many actin-binding proteins, among which the cofilin family plays unique and essential role in accelerating actin treadmilling in filamentous actin (F-actin) in a nucleotide-state dependent manner. Cofilin preferentially interacts with older filaments by recognizing time-dependent changes in F-actin structure associated with the hydrolysis of ATP and release of inorganic phosphate (Pi) from the nucleotide cleft of actin. The structure of cofilin on F-actin and the details of the intermolecular interface remain poorly understood at atomic resolution. Here we report atomic-level characterization by magic angle spinning (MAS) NMR of the muscle isoform of human cofilin 2 (CFL2) bound to F-actin. We demonstrate that resonance assignments for the majority of atoms are readily accomplished and we derive the intermolecular interface between CFL2 and F-actin. The MAS NMR approach reported here establishes the foundation for atomic-resolution characterization of a broad range of actin-associated proteins bound to F-actin.
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15
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Dougherty RJ, Singh J, Krishnan V. Kinetics and thermodynamics of oxidation mediated reaction in l-cysteine and its methyl and ethyl esters in dimethyl sulfoxide-d6 by NMR spectroscopy. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.11.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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16
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Structural Characterization of Fibrils from Recombinant Human Islet Amyloid Polypeptide by Solid-State NMR: The Central FGAILS Segment Is Part of the β-Sheet Core. PLoS One 2016; 11:e0161243. [PMID: 27607147 PMCID: PMC5015977 DOI: 10.1371/journal.pone.0161243] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 08/02/2016] [Indexed: 11/19/2022] Open
Abstract
Amyloid deposits formed from islet amyloid polypeptide (IAPP) are a hallmark of type 2 diabetes mellitus and are known to be cytotoxic to pancreatic β-cells. The molecular structure of the fibrillar form of IAPP is subject of intense research, and to date, different models exist. We present results of solid-state NMR experiments on fibrils of recombinantly expressed and uniformly 13C, 15N-labeled human IAPP in the non-amidated, free acid form. Complete sequential resonance assignments and resulting constraints on secondary structure are shown. A single set of chemical shifts is found for most residues, which is indicative of a high degree of homogeneity. The core region comprises three to four β-sheets. We find that the central 23-FGAILS-28 segment, which is of critical importance for amyloid formation, is part of the core region and forms a β-strand in our sample preparation. The eight N-terminal amino acid residues of IAPP, forming a ring-like structure due to a disulfide bridge between residues C2 and C7, appear to be well defined but with an increased degree of flexibility. This study supports the elucidation of the structural basis of IAPP amyloid formation and highlights the extent of amyloid fibril polymorphism.
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17
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Wang CC, Lai WC, Chuang WJ. Predicting the redox state and secondary structure of cysteine residues using multi-dimensional classification analysis of NMR chemical shifts. JOURNAL OF BIOMOLECULAR NMR 2016; 66:55-68. [PMID: 27613298 DOI: 10.1007/s10858-016-0057-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/02/2016] [Indexed: 06/06/2023]
Abstract
A tool for predicting the redox state and secondary structure of cysteine residues using multi-dimensional analyses of different combinations of nuclear magnetic resonance (NMR) chemical shifts has been developed. A data set of cysteine [Formula: see text], (13)C(α), (13)C(β), (1)H(α), (1)H(N), and (15)N(H) chemical shifts was created, classified according to redox state and secondary structure, using a library of 540 re-referenced BioMagResBank (BMRB) entries. Multi-dimensional analyses of three, four, five, and six chemical shifts were used to derive rules for predicting the structural states of cysteine residues. The results from 60 BMRB entries containing 122 cysteines showed that four-dimensional analysis of the C(α), C(β), H(α), and N(H) chemical shifts had the highest prediction accuracy of 100 and 95.9 % for the redox state and secondary structure, respectively. The prediction of secondary structure using 3D, 5D, and 6D analyses had the accuracy of ~90 %, suggesting that H(N) and [Formula: see text] chemical shifts may be noisy and made the discrimination worse. A web server (6DCSi) was established to enable users to submit NMR chemical shifts, either in BMRB or key-in formats, for prediction. 6DCSi displays predictions using sets of 3, 4, 5, and 6 chemical shifts, which shows their consistency and allows users to draw their own conclusions. This web-based tool can be used to rapidly obtain structural information regarding cysteine residues directly from experimental NMR data.
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Affiliation(s)
- Ching-Cheng Wang
- Institute of Manufacturing Information and Systems, National Cheng Kung University College of Electrical Engineering and Computer Science, Tainan, 701, Taiwan
| | - Wen-Chung Lai
- Institute of Manufacturing Information and Systems, National Cheng Kung University College of Electrical Engineering and Computer Science, Tainan, 701, Taiwan
| | - Woei-Jer Chuang
- Department of Biochemistry and Molecular Biology, National Cheng Kung University College of Medicine, Tainan, 701, Taiwan.
- Department of Biochemistry, National Cheng Kung University College of Medicine, Tainan, 701, Taiwan.
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18
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Takeda M, Miyanoiri Y, Terauchi T, Kainosho M. (13)C-NMR studies on disulfide bond isomerization in bovine pancreatic trypsin inhibitor (BPTI). JOURNAL OF BIOMOLECULAR NMR 2016; 66:37-53. [PMID: 27566173 DOI: 10.1007/s10858-016-0055-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/22/2016] [Indexed: 06/06/2023]
Abstract
Conformational isomerization of disulfide bonds is associated with the dynamics and thus the functional aspects of proteins. However, our understanding of the isomerization is limited by experimental difficulties in probing it. We explored the disulfide conformational isomerization of the Cys14-Cys38 disulfide bond in bovine pancreatic trypsin inhibitor (BPTI), by performing an NMR line-shape analysis of its Cys carbon peaks. In this approach, 1D (13)C spectra were recorded at small temperature intervals for BPTI samples selectively labeled with site-specifically (13)C-enriched Cys, and the recorded peaks were displayed in the order of the temperature after the spectral scales were normalized to a carbon peak. Over the profile of the line-shape, exchange broadening that altered with temperature was manifested for the carbon peaks of Cys14 and Cys38. The Cys14-Cys38 disulfide bond reportedly exists in equilibrium between a high-populated (M) and two low-populated states (m c14 and m c38). Consistent with the three-site exchange model, biphasic exchange broadening arising from the two processes was observed for the peak of the Cys14 α-carbon. As the exchange broadening is maximized when the exchange rate equals the chemical shift difference in Hz between equilibrating sites, semi-quantitative information that was useful for establishing conditions for (13)C relaxation dispersion experiments was obtained through the carbon line-shape profile. With respect to the m c38 isomerization, the (1)H-(13)C signals at the β-position of the minor state were resolved from the major peaks and detected by exchange experiments at a low temperature.
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Affiliation(s)
- Mitsuhiro Takeda
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
- Department of Structural BioImaging, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Yohei Miyanoiri
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Tsutomu Terauchi
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo, 192-0397, Japan
- SAIL Technologies Inc., 2008-2 Wada, Tama, Tokyo, 206-0001, Japan
| | - Masatsune Kainosho
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo, 192-0397, Japan.
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19
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Sumowski CV, Hanni M, Schweizer S, Ochsenfeld C. Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides. J Chem Theory Comput 2015; 10:122-33. [PMID: 26579896 DOI: 10.1021/ct400713t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates.
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Affiliation(s)
- Chris Vanessa Sumowski
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 Munich, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 Munich, Germany
| | - Matti Hanni
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 Munich, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 Munich, Germany
| | - Sabine Schweizer
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 Munich, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 Munich, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 Munich, Germany
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20
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Li Y, Ducasse R, Zirah S, Blond A, Goulard C, Lescop E, Giraud C, Hartke A, Guittet E, Pernodet JL, Rebuffat S. Characterization of Sviceucin from Streptomyces Provides Insight into Enzyme Exchangeability and Disulfide Bond Formation in Lasso Peptides. ACS Chem Biol 2015; 10:2641-9. [PMID: 26343290 DOI: 10.1021/acschembio.5b00584] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lasso peptides are bacterial ribosomally synthesized and post-translationally modified peptides. They have sparked increasing interest in peptide-based drug development because of their compact, interlocked structure, which offers superior stability and protein-binding capacity. Disulfide bond-containing lasso peptides are rare and exhibit highly sought-after activities. In an effort to expand the repertoire of such molecules, we heterologously expressed, in Streptomyces coelicolor, the gene cluster encoding sviceucin, a type I lasso peptide with two disulfide bridges originating from Streptomyces sviceus, which allowed it to be fully characterized. Sviceucin and its reduced forms were characterized by mass spectrometry and peptidase digestion. The three-dimensional structure of sviceucin was determined using NMR. Sviceucin displayed antimicrobial activity selectively against Gram-positive bacteria and inhibition of fsr quorum sensing in Enterococcus faecalis. This study adds sviceucin to the type I lasso peptide family as a new representative. Moreover, new clusters encoding disulfide-bond containing lasso peptides from Actinobacteria were identified by genome mining. Genetic and functional analyses revealed that the formation of disulfide bonds in sviceucin does not require a pathway-encoded thiol-disulfide oxidoreductase. Most importantly, we demonstrated the functional exchangeability of the sviceucin and microcin J25 (a non-disulfide-bridged lasso peptide) macrolactam synthetases in vitro, highlighting the potential of hybrid lasso synthetases in lasso peptide engineering.
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Affiliation(s)
- Yanyan Li
- Laboratory Molecules
of Communication and Adaptation of Microorganisms (MCAM, UMR 7245
CNRS-MNHN), Sorbonne Universités, Muséum National d’Histoire
Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, F-75005, Paris, France
| | - Rémi Ducasse
- Laboratory Molecules
of Communication and Adaptation of Microorganisms (MCAM, UMR 7245
CNRS-MNHN), Sorbonne Universités, Muséum National d’Histoire
Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, F-75005, Paris, France
| | - Séverine Zirah
- Laboratory Molecules
of Communication and Adaptation of Microorganisms (MCAM, UMR 7245
CNRS-MNHN), Sorbonne Universités, Muséum National d’Histoire
Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, F-75005, Paris, France
| | - Alain Blond
- Laboratory Molecules
of Communication and Adaptation of Microorganisms (MCAM, UMR 7245
CNRS-MNHN), Sorbonne Universités, Muséum National d’Histoire
Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, F-75005, Paris, France
| | - Christophe Goulard
- Laboratory Molecules
of Communication and Adaptation of Microorganisms (MCAM, UMR 7245
CNRS-MNHN), Sorbonne Universités, Muséum National d’Histoire
Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, F-75005, Paris, France
| | - Ewen Lescop
- Institut
de Chimie
des Substances Naturelles, Centre de Recherche de Gif, UPR 2301 CNRS
Université Paris-Sud, 1 avenue
de la Terrasse, F-91198 Gif-sur-Yvette, France
| | - Caroline Giraud
- Unité de
Recherche Risques Microbiens (U2RM)-Stress et Virulence (EA 4655),
Université de Caen-Basse Normandie, F-14032 Caen, France
| | - Axel Hartke
- Unité de
Recherche Risques Microbiens (U2RM)-Stress et Virulence (EA 4655),
Université de Caen-Basse Normandie, F-14032 Caen, France
| | - Eric Guittet
- Institut
de Chimie
des Substances Naturelles, Centre de Recherche de Gif, UPR 2301 CNRS
Université Paris-Sud, 1 avenue
de la Terrasse, F-91198 Gif-sur-Yvette, France
| | - Jean-Luc Pernodet
- Institute
for
Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris-Sud, Bât. 400, Université
Paris-Sud, F-91405 Orsay, France
| | - Sylvie Rebuffat
- Laboratory Molecules
of Communication and Adaptation of Microorganisms (MCAM, UMR 7245
CNRS-MNHN), Sorbonne Universités, Muséum National d’Histoire
Naturelle, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, F-75005, Paris, France
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21
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Váradi G, Tóth GK, Kele Z, Galgóczy L, Fizil Á, Batta G. Synthesis of PAF, an antifungal protein from P. chrysogenum, by native chemical ligation: native disulfide pattern and fold obtained upon oxidative refolding. Chemistry 2014; 19:12684-92. [PMID: 24175344 DOI: 10.1002/chem.201301098] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The folding of disulfide proteins is of considerable interest because knowledge of this may influence our present understanding of protein folding. However, sometimes even the disulfide pattern cannot be unequivocally determined by the available experimental techniques. For example, the structures of a few small antifungal proteins (PAF, AFP) have been disclosed recently using NMR spectroscopy but with some ambiguity in the actual disulfide pattern. For this reason, we carried out the chemical synthesis of PAF. Probing different approaches, the oxidative folding of the synthetic linear PAF yielded a folded protein that has identical structure and antifungal activity as the native PAF. In contrast, unfolded linear PAF was inactive, a result that may have implications concerning its redox state in the mode of action.
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22
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Vila JA, Arnautova YA. 13C Chemical Shifts in Proteins: A Rich Source of Encoded Structural Information. COMPUTATIONAL METHODS TO STUDY THE STRUCTURE AND DYNAMICS OF BIOMOLECULES AND BIOMOLECULAR PROCESSES 2014. [PMCID: PMC7121069 DOI: 10.1007/978-3-642-28554-7_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite the formidable progress in Nuclear Magnetic Resonance (NMR) spectroscopy, quality assessment of NMR-derived structures remains as an important problem. Thus, validation of protein structures is essential for the spectroscopists, since it could enable them to detect structural flaws and potentially guide their efforts in further refinement. Moreover, availability of accurate and efficient validation tools would help molecular biologists and computational chemists to evaluate quality of available experimental structures and to select a protein model which is the most suitable for a given scientific problem. The 13Cα nuclei are ubiquitous in proteins, moreover, their shieldings are easily obtainable from NMR experiments and represent a rich source of encoded structural information that makes 13Cα chemical shifts an attractive candidate for use in computational methods aimed at determination and validation of protein structures. In this chapter, the basis of a novel methodology of computing, at the quantum chemical level of theory, the 13Cα shielding for the amino acid residues in proteins is described. We also identify and examine the main factors affecting the 13Cα-shielding computation. Finally, we illustrate how the information encoded in the 13C chemical shifts can be used for a number of applications, viz., from protein structure prediction of both α-helical and β-sheet conformations, to determination of the fraction of the tautomeric forms of the imidazole ring of histidine in proteins as a function of pH or to accurate detection of structural flaws, at a residue-level, in NMR-determined protein models.
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23
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Kövér KE, Batta G. NMR investigation of disulfide containing peptides and proteins. AMINO ACIDS, PEPTIDES AND PROTEINS 2013:37-59. [DOI: 10.1039/9781849737081-00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
Peptides and proteins with disulfide bonds are abundant in all kingdoms and play essential role in many biological events. Because small disulfide-rich peptides (proteins) are usually difficult to crystallize, nuclear magnetic resonance (NMR) is by far one of the most powerful techniques for the determination of their solution structure. Besides the “static” three-dimensional structure, NMR has unique opportunities to acquire additional information about molecular dynamics and folding at atomic resolution. Nowadays it is becoming increasingly evident, that “excited”, “disordered” or “fuzzy” protein states may exhibit biological function and disulfide proteins are also promising targets for such studies. In this short two-three years overview those disulfide peptides and proteins were cited from the literature that were studied by NMR. Though we may have missed some, their structural diversity and complexity as well as their wide repertoire of biological functions is impressive. We emphasised especially antimicrobial peptides and peptide based toxins in addition to some biologically important other structures. Besides the general NMR methods we reviewed some contemporary techniques suitable for disclosing the peculiar properties of disulfide bonds. Interesting dynamics and folding studies of disulfide proteins were also mentioned. It is important to disclose the essential structure, dynamics, function aspects of disulfide proteins since this aids the design of new compounds with improved activity and reduced toxicity. Undoubtedly, NMR has the potential to accelerate the development of new disulfide peptides/proteins with pharmacological activity.
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24
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Rosato A, Tejero R, Montelione GT. Quality assessment of protein NMR structures. Curr Opin Struct Biol 2013; 23:715-24. [PMID: 24060334 DOI: 10.1016/j.sbi.2013.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 08/14/2013] [Indexed: 10/26/2022]
Abstract
Biomolecular NMR structures are now routinely used in biology, chemistry, and bioinformatics. Methods and metrics for assessing the accuracy and precision of protein NMR structures are beginning to be standardized across the biological NMR community. These include both knowledge-based assessment metrics, parameterized from the database of protein structures, and model versus data assessment metrics. On line servers are available that provide comprehensive protein structure quality assessment reports, and efforts are in progress by the world-wide Protein Data Bank (wwPDB) to develop a biomolecular NMR structure quality assessment pipeline as part of the structure deposition process. These quality assessment metrics and standards will aid NMR spectroscopists in determining more accurate structures, and increase the value and utility of these structures for the broad scientific community.
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Affiliation(s)
- Antonio Rosato
- Magnetic Resonance Center and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
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25
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Nowakowski M, Ruszczyńska-Bartnik K, Budzińska M, Jaremko Ł, Jaremko M, Zdanowski K, Bierzyński A, Ejchart A. Impact of Calcium Binding and Thionylation of S100A1 Protein on Its Nuclear Magnetic Resonance-Derived Structure and Backbone Dynamics. Biochemistry 2013; 52:1149-59. [DOI: 10.1021/bi3015407] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michał Nowakowski
- Institute of Biochemistry and
Biophysics, Polish Academy of Sciences,
Pawińskiego 5A, 02-106 Warsaw, Poland
| | | | - Monika Budzińska
- Institute of Biochemistry and
Biophysics, Polish Academy of Sciences,
Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Łukasz Jaremko
- Institute of Biochemistry and
Biophysics, Polish Academy of Sciences,
Pawińskiego 5A, 02-106 Warsaw, Poland
- Faculty of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland
| | - Mariusz Jaremko
- Institute of Biochemistry and
Biophysics, Polish Academy of Sciences,
Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Konrad Zdanowski
- Institute of Biochemistry and
Biophysics, Polish Academy of Sciences,
Pawińskiego 5A, 02-106 Warsaw, Poland
- Institute of Chemistry, University of Natural Sciences and Humanities, 3 Maja
54, 08-110 Siedlce, Poland
| | - Andrzej Bierzyński
- Institute of Biochemistry and
Biophysics, Polish Academy of Sciences,
Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Andrzej Ejchart
- Institute of Biochemistry and
Biophysics, Polish Academy of Sciences,
Pawińskiego 5A, 02-106 Warsaw, Poland
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26
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Solution NMR structure and dynamics of human apo-S100A1 protein. J Struct Biol 2011; 174:391-9. [DOI: 10.1016/j.jsb.2011.01.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 01/28/2011] [Accepted: 01/28/2011] [Indexed: 11/22/2022]
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27
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Vila JA, Serrano P, Wüthrich K, Scheraga HA. Sequential nearest-neighbor effects on computed 13Calpha chemical shifts. JOURNAL OF BIOMOLECULAR NMR 2010; 48:23-30. [PMID: 20644980 PMCID: PMC2970923 DOI: 10.1007/s10858-010-9435-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 06/30/2010] [Indexed: 05/11/2023]
Abstract
To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of (13)C(alpha) chemical shifts, we selected the structure of the nucleic acid binding (NAB) protein from the SARS coronavirus determined by NMR in solution (PDB id 2K87). NAB is a 116-residue alpha/beta protein, which contains 9 prolines and has 50% of its residues located in loops and turns. Overall, the results presented here show that sizeable nearest-neighbor effects are seen only for residues preceding proline, where Pro introduces an overestimation, on average, of 1.73 ppm in the computed (13)C(alpha) chemical shifts. A new ensemble of 20 conformers representing the NMR structure of the NAB, which was calculated with an input containing backbone torsion angle constraints derived from the theoretical (13)C(alpha) chemical shifts as supplementary data to the NOE distance constraints, exhibits very similar topology and comparable agreement with the NOE constraints as the published NMR structure. However, the two structures differ in the patterns of differences between observed and computed (13)C(alpha) chemical shifts, Delta(ca,i), for the individual residues along the sequence. This indicates that the Delta(ca,i)-values for the NAB protein are primarily a consequence of the limited sampling by the bundles of 20 conformers used, as in common practice, to represent the two NMR structures, rather than of local flaws in the structures.
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Affiliation(s)
- Jorge A. Vila
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301 USA
- Universidad Nacional de San Luis, Instituto de Matemática Aplicada San Luis, CONICET, Ejército de Los Andes, 950-5700 San Luis Argentina
| | - Pedro Serrano
- Department of Molecular Biology, The Scripps Research Institute, 10,550 North Torrey Pines Road, La Jolla, CA 92037 USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10,550 North Torrey Pines Road, La Jolla, CA 92037 USA
| | - Kurt Wüthrich
- Department of Molecular Biology, The Scripps Research Institute, 10,550 North Torrey Pines Road, La Jolla, CA 92037 USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10,550 North Torrey Pines Road, La Jolla, CA 92037 USA
| | - Harold A. Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301 USA
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