1
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McElroy CA, Ihms EC, Kumar Yadav D, Holmquist ML, Wadhwa V, Wysocki VH, Gollnick P, Foster MP. Solution structure, dynamics and tetrahedral assembly of Anti-TRAP, a homo-trimeric triskelion-shaped regulator of tryptophan biosynthesis in Bacillus subtilis. J Struct Biol X 2024; 10:100103. [PMID: 39035014 PMCID: PMC11255114 DOI: 10.1016/j.yjsbx.2024.100103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 05/08/2024] [Accepted: 06/10/2024] [Indexed: 07/23/2024] Open
Abstract
Cellular production of tryptophan is metabolically expensive and tightly regulated. The small Bacillus subtilis zinc binding Anti-TRAP protein (AT), which is the product of the yczA/rtpA gene, is upregulated in response to accumulating levels of uncharged tRNATrp through a T-box antitermination mechanism. AT binds to the undecameric axially symmetric ring-shaped protein TRAP (trp RNA Binding Attenuation Protein), thereby preventing it from binding to the trp leader RNA. This reverses the inhibitory effect of TRAP on transcription and translation of the trp operon. AT principally adopts two symmetric oligomeric states, a trimer (AT3) featuring three-fold axial symmetry or a dodecamer (AT12) comprising a tetrahedral assembly of trimers, whereas only the trimeric form binds and inhibits TRAP. We apply native mass spectrometry (nMS) and small-angle x-ray scattering (SAXS), together with analytical ultracentrifugation (AUC) to monitor the pH and concentration-dependent equilibrium between the trimeric and dodecameric structural forms of AT. In addition, we use solution nuclear magnetic resonance (NMR) spectroscopy to determine the solution structure of AT3, while heteronuclear 15N relaxation measurements on both oligomeric forms of AT provide insights into the dynamic properties of binding-active AT3 and binding-inactive AT12, with implications for TRAP binding and inhibition.
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Affiliation(s)
- Craig A. McElroy
- Ohio State Biochemistry Program, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Elihu C. Ihms
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Program, USA
| | - Deepak Kumar Yadav
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Melody L. Holmquist
- Ohio State Biochemistry Program, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vibhuti Wadhwa
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- National Resource for Native MS-Guided Structural Biology, USA
| | - Paul Gollnick
- Department of Biological Sciences, State University of New York, Buffalo, NY 14260, USA
| | - Mark P. Foster
- Ohio State Biochemistry Program, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Program, USA
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2
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Diana D, Pirone L, Russo L, D'Abrosca G, Madheswaran M, Benfante R, Di Lascio S, Caldinelli L, Fornasari D, Acconcia C, Corvino A, Ventserova N, Pollegioni L, Isernia C, Di Gaetano S, Malgieri G, Pedone EM, Fattorusso R. Structural characterization of PHOX2B and its DNA interaction shed light on the molecular basis of the +7Ala variant pathogenicity in CCHS. Chem Sci 2024; 15:8858-8872. [PMID: 38873078 PMCID: PMC11168103 DOI: 10.1039/d3sc06427a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/12/2024] [Indexed: 06/15/2024] Open
Abstract
An expansion of poly-alanine up to +13 residues in the C-terminus of the transcription factor PHOX2B underlies the onset of congenital central hypoventilation syndrome (CCHS). Recent studies demonstrated that the alanine tract expansion influences PHOX2B folding and activity. Therefore, structural information on PHOX2B is an important target for obtaining clues to elucidate the insurgence of the alanine expansion-related syndrome and also for defining a viable therapy. Here we report by NMR spectroscopy the structural characterization of the homeodomain (HD) of PHOX2B and HD + C-terminus PHOX2B protein, free and in the presence of the target DNA. The obtained structural data are then exploited to obtain a structural model of the PHOX2B-DNA interaction. In addition, the variant +7Ala, responsible for one of the most frequent forms of the syndrome, was analysed, showing different conformational proprieties in solution and a strong propensity to aggregation. Our data suggest that the elongated poly-alanine tract would be related to disease onset through a loss-of-function mechanism. Overall, this study paves the way for the future rational design of therapeutic drugs, suggesting as a possible therapeutic route the use of specific anti-aggregating molecules capable of preventing variant aggregation and possibly restoring the DNA-binding activity of PHOX2B.
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Affiliation(s)
- Donatella Diana
- CNR - Institute of Biostructures and Bioimaging Via Pietro Castellino 111 80131 Naples Italy
| | - Luciano Pirone
- CNR - Institute of Biostructures and Bioimaging Via Pietro Castellino 111 80131 Naples Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies - University of Campania "Luigi Vanvitelli" Via Vivaldi 43 81100 Caserta Italy
| | - Gianluca D'Abrosca
- Department of Clinical and Experimental Medicine - University of Foggia Viale Luigi Pinto 71122 Foggia Italy
| | - Manoj Madheswaran
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies - University of Campania "Luigi Vanvitelli" Via Vivaldi 43 81100 Caserta Italy
| | - Roberta Benfante
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano Milan Italy
- CNR - Institute of Neuroscience Vedano Al Lambro (MB) Italy
- NeuroMi - Milan Center for Neuroscience, University of Milano Bicocca Milan Italy
| | - Simona Di Lascio
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano Milan Italy
| | - Laura Caldinelli
- Department of Biotechnology and Life Sciences, University of Insubria Via J.H. Dunant 3 21100 Varese Italy
| | - Diego Fornasari
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano Milan Italy
| | - Clementina Acconcia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies - University of Campania "Luigi Vanvitelli" Via Vivaldi 43 81100 Caserta Italy
| | - Andrea Corvino
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies - University of Campania "Luigi Vanvitelli" Via Vivaldi 43 81100 Caserta Italy
| | - Nataliia Ventserova
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies - University of Campania "Luigi Vanvitelli" Via Vivaldi 43 81100 Caserta Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria Via J.H. Dunant 3 21100 Varese Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies - University of Campania "Luigi Vanvitelli" Via Vivaldi 43 81100 Caserta Italy
| | - Sonia Di Gaetano
- CNR - Institute of Biostructures and Bioimaging Via Pietro Castellino 111 80131 Naples Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies - University of Campania "Luigi Vanvitelli" Via Vivaldi 43 81100 Caserta Italy
| | - Emilia M Pedone
- CNR - Institute of Biostructures and Bioimaging Via Pietro Castellino 111 80131 Naples Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies - University of Campania "Luigi Vanvitelli" Via Vivaldi 43 81100 Caserta Italy
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3
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Daffern N, Johansson KE, Baumer ZT, Robertson NR, Woojuh J, Bedewitz MA, Davis Z, Wheeldon I, Cutler SR, Lindorff-Larsen K, Whitehead TA. GMMA Can Stabilize Proteins Across Different Functional Constraints. J Mol Biol 2024; 436:168586. [PMID: 38663544 DOI: 10.1016/j.jmb.2024.168586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024]
Abstract
Stabilizing proteins without otherwise hampering their function is a central task in protein engineering and design. PYR1 is a plant hormone receptor that has been engineered to bind diverse small molecule ligands. We sought a set of generalized mutations that would provide stability without affecting functionality for PYR1 variants with diverse ligand-binding capabilities. To do this we used a global multi-mutant analysis (GMMA) approach, which can identify substitutions that have stabilizing effects and do not lower function. GMMA has the added benefit of finding substitutions that are stabilizing in different sequence contexts and we hypothesized that applying GMMA to PYR1 with different functionalities would identify this set of generalized mutations. Indeed, conducting FACS and deep sequencing of libraries for PYR1 variants with two different functionalities and applying a GMMA analysis identified 5 substitutions that, when inserted into four PYR1 variants that each bind a unique ligand, provided an increase of 2-6 °C in thermal inactivation temperature and no decrease in functionality.
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Affiliation(s)
- Nicolas Daffern
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80305, USA
| | - Kristoffer E Johansson
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zachary T Baumer
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80305, USA
| | | | - Janty Woojuh
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Matthew A Bedewitz
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80305, USA
| | - Zoë Davis
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80305, USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, USA; Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Sean R Cutler
- Department of Botany and Plant Sciences, University of California, Riverside, USA; Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA; Center for Plant Cell Biology, University of California, Riverside, Riverside, CA, USA
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80305, USA.
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4
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Mohanty P, Phan TM, Mittal J. Transient interdomain interactions modulate the monomeric structural ensemble and oligomerization landscape of Huntingtin Exon 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592468. [PMID: 38766024 PMCID: PMC11100600 DOI: 10.1101/2024.05.03.592468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Polyglutamine expansion (≥ 36 residues) within the N-terminal exon-1 of Huntingtin (Httex1) leads to Huntington's disease, a neurogenerative condition marked by the presence of intranuclear Htt inclusions. Notably, the polyglutamine tract in Httex1 is flanked by an N-terminal coiled-coil domain - N17 (17 amino acids), which undergoes self-association to promote the formation of soluble Httex1 oligomers and brings the aggregation-prone polyQ tracts in close spatial proximity. However, the mechanisms underlying the subsequent conversion of soluble oligomers into insoluble β-rich aggregates with increasing polyQ length, remain unclear. Current knowledge suggests that expansion of the polyQ tract increases its helicity, and this favors its oligomerization and aggregation. In addition, studies utilizing conformation-specific antibodies and a stable coiled-coil heterotetrametric system fused to polyQ indicate that domain "cross-talk" (i.e., interdomain interactions) may be necessary to efficiently promote the emergence of toxic conformations (in monomers and oligomers) and fibrillar aggregation. Here, we performed extensive atomistic molecular dynamics (MD) simulations (aggregate time ∼ 0.7 ms) of N17-polyQ fragments to uncover the interplay between structural transformation and domain "cross-talk" on the monomeric structural ensemble and oligomerization landscape of Httex1. Our simulation ensembles of N17-polyQ monomers validated against 13 C NMR chemical shifts indicated that in addition to elevated α-helicity, polyQ expansion also favors transient, interdomain (N17-polyQ) interactions which result in the emergence of β-conformations. Further, interdomain interactions decreased the overall stability of N17-mediated dimers by counteracting the stabilizing effect of increased α-helicity and promoted a heterogenous oligomerization landscape on the sub-microsecond timescale. Overall, our study uncovers the significance of domain "cross-talk" in modulating the monomeric conformational ensemble and oligomerization landscape of Httex1 to favor the formation of amyloid aggregates.
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5
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Edholm F, Nandy A, Reinhardt CR, Kastner DW, Kulik HJ. Protein3D: Enabling analysis and extraction of metal-containing sites from the Protein Data Bank with molSimplify. J Comput Chem 2024; 45:352-361. [PMID: 37873926 DOI: 10.1002/jcc.27242] [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: 08/09/2023] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 10/25/2023]
Abstract
Metalloenzymes catalyze a wide range of chemical transformations, with the active site residues playing a key role in modulating chemical reactivity and selectivity. Unlike smaller synthetic catalysts, a metalloenzyme active site is embedded in a larger protein, which makes interrogation of electronic properties and geometric features with quantum mechanical calculations challenging. Here we implement the ability to fetch crystallographic structures from the Protein Data Bank and analyze the metal binding sites in the program molSimplify. We show the usefulness of the newly created protein3D class to extract the local environment around non-heme iron enzymes containing a two histidine motif and prepare 372 structures for quantum mechanical calculations. Our implementation of protein3D serves to expand the range of systems molSimplify can be used to analyze and will enable high-throughput study of metal-containing active sites in proteins.
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Affiliation(s)
- Freya Edholm
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Aditya Nandy
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Clorice R Reinhardt
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - David W Kastner
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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6
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Galano‐Frutos JJ, Sancho J. Energy, water, and protein folding: A molecular dynamics-based quantitative inventory of molecular interactions and forces that make proteins stable. Protein Sci 2024; 33:e4905. [PMID: 38284492 PMCID: PMC10804899 DOI: 10.1002/pro.4905] [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: 06/21/2023] [Revised: 12/12/2023] [Accepted: 01/05/2024] [Indexed: 01/30/2024]
Abstract
Protein folding energetics can be determined experimentally on a case-by-case basis but it is not understood in sufficient detail to provide deep control in protein design. The fundamentals of protein stability have been outlined by calorimetry, protein engineering, and biophysical modeling, but these approaches still face great difficulty in elucidating the specific contributions of the intervening molecules and physical interactions. Recently, we have shown that the enthalpy and heat capacity changes associated to the protein folding reaction can be calculated within experimental error using molecular dynamics simulations of native protein structures and their corresponding unfolded ensembles. Analyzing in depth molecular dynamics simulations of four model proteins (CI2, barnase, SNase, and apoflavodoxin), we dissect here the energy contributions to ΔH (a key component of protein stability) made by the molecular players (polypeptide and solvent molecules) and physical interactions (electrostatic, van der Waals, and bonded) involved. Although the proteins analyzed differ in length, isoelectric point and fold class, their folding energetics is governed by the same quantitative pattern. Relative to the unfolded ensemble, the native conformations are enthalpically stabilized by comparable contributions from protein-protein and solvent-solvent interactions, and almost equally destabilized by interactions between protein and solvent molecules. The native protein surface seems to interact better with water than the unfolded one, but this is outweighed by the unfolded surface being larger. From the perspective of physical interactions, the native conformations are stabilized by van de Waals and Coulomb interactions and destabilized by conformational strain arising from bonded interactions. Also common to the four proteins, the sign of the heat capacity change is set by interactions between protein and solvent molecules or, from the alternative perspective, by Coulomb interactions.
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Affiliation(s)
- Juan José Galano‐Frutos
- Biocomputation and Complex Systems Physics Institute (BIFI)‐Joint Unit GBsC‐CSICUniversity of ZaragozaZaragozaSpain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de CienciasUniversity of ZaragozaZaragozaSpain
| | - Javier Sancho
- Biocomputation and Complex Systems Physics Institute (BIFI)‐Joint Unit GBsC‐CSICUniversity of ZaragozaZaragozaSpain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de CienciasUniversity of ZaragozaZaragozaSpain
- Aragon Health Research Institute (IIS Aragón)ZaragozaSpain
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7
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Galano-Frutos JJ, Nerín-Fonz F, Sancho J. Calculation of Protein Folding Thermodynamics Using Molecular Dynamics Simulations. J Chem Inf Model 2023; 63:7791-7806. [PMID: 37955428 PMCID: PMC10751793 DOI: 10.1021/acs.jcim.3c01107] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023]
Abstract
Despite advances in artificial intelligence methods, protein folding remains in many ways an enigma to be solved. Accurate computation of protein folding energetics could help drive fields such as protein and drug design and genetic interpretation. However, the challenge of calculating the state functions governing protein folding from first-principles remains unaddressed. We present here a simple approach that allows us to accurately calculate the energetics of protein folding. It is based on computing the energy of the folded and unfolded states at different temperatures using molecular dynamics simulations. From this, two essential quantities (ΔH and ΔCp) are obtained and used to calculate the conformational stability of the protein (ΔG). With this approach, we have successfully calculated the energetics of two- and three-state proteins, representatives of the major structural classes, as well as small stability differences (ΔΔG) due to changes in solution conditions or variations in an amino acid residue.
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Affiliation(s)
- Juan J. Galano-Frutos
- Department
of Biochemistry, Molecular and Cell Biology, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Biocomputation
and Complex Systems Physics Institute (BIFI), Joint Unit GBs-CSIC, University of Zaragoza, 50018 Zaragoza, Spain
| | - Francho Nerín-Fonz
- Department
of Biochemistry, Molecular and Cell Biology, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
| | - Javier Sancho
- Department
of Biochemistry, Molecular and Cell Biology, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Biocomputation
and Complex Systems Physics Institute (BIFI), Joint Unit GBs-CSIC, University of Zaragoza, 50018 Zaragoza, Spain
- Aragon
Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
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8
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López‐Pérez E, de Gómez‐Puyou MT, Nuñez CJ, Zapién DM, Guardado SA, Beltrán HI, Pérez‐Hernández G. Ordered-domain unfolding of thermophilic isolated β subunit ATP synthase. Protein Sci 2023; 32:e4689. [PMID: 37252686 PMCID: PMC10273367 DOI: 10.1002/pro.4689] [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: 10/13/2022] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 05/31/2023]
Abstract
The flexibility of the ATP synthase's β subunit promotes its role in the ATP synthase rotational mechanism, but its domains stability remains unknown. A reversible thermal unfolding of the isolated β subunit (Tβ) of the ATP synthase from Bacillus thermophilus PS3, tracked through circular dichroism and molecular dynamics, indicated that Tβ shape transits from an ellipsoid to a molten globule through an ordered unfolding of its domains, preserving the β-sheet residual structure at high temperature. We determined that part of the stability origin of Tβ is due to a transversal hydrophobic array that crosses the β-barrel formed at the N-terminal domain and the Rossman fold of the nucleotide-binding domain (NBD), while the helix bundle of the C-terminal domain is the less stable due to the lack of hydrophobic residues, and thus the more flexible to trigger the rotational mechanism of the ATP synthase.
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Affiliation(s)
- Edgar López‐Pérez
- Unidad Cuajimalpa, Departamento de Ciencias NaturalesUniversidad Autónoma MetropolitanaCiudad de MéxicoMexico
| | - Marietta Tuena de Gómez‐Puyou
- Departamento de Bioquímica y Biología EstructuralInstituto de Fisiología Celular, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Concepción José Nuñez
- Departamento de Bioquímica y Biología EstructuralInstituto de Fisiología Celular, Universidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Denise Martínez Zapién
- Unidad Cuajimalpa, Departamento de Ciencias NaturalesUniversidad Autónoma MetropolitanaCiudad de MéxicoMexico
| | - Salomón Alas Guardado
- Unidad Cuajimalpa, Departamento de Ciencias NaturalesUniversidad Autónoma MetropolitanaCiudad de MéxicoMexico
| | - Hiram Isaac Beltrán
- División de Ciencias Básicas e Ingeniería, Departamento de Ciencias BásicasUniversidad Autónoma Metropolitana, Unidad AzcapotzalcoCiudad de MéxicoMexico
| | - Gerardo Pérez‐Hernández
- Unidad Cuajimalpa, Departamento de Ciencias NaturalesUniversidad Autónoma MetropolitanaCiudad de MéxicoMexico
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9
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McElroy C, Ihms E, Yadav DK, Holmquist M, Wadwha V, Wysocki V, Gollnick P, Foster M. Solution structure, dynamics and tetrahedral assembly of Anti-TRAP, a homo-trimeric triskelion-shaped regulator of tryptophan biosynthesis in Bacillus subtilis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.29.547145. [PMID: 37425951 PMCID: PMC10327191 DOI: 10.1101/2023.06.29.547145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Cellular production of tryptophan is metabolically expensive and tightly regulated. The small Bacillus subtilis zinc binding Anti-TRAP protein (AT), which is the product of the yczA/rtpA gene, is upregulated in response to accumulating levels of uncharged tRNATrp through a T-box antitermination mechanism. AT binds to the undecameric ring-shaped protein TRAP (trp RNA Binding Attenuation Protein), thereby preventing it from binding to the trp leader RNA. This reverses the inhibitory effect of TRAP on transcription and translation of the trp operon. AT principally adopts two symmetric oligomeric states, a trimer (AT3) featuring a three-helix bundle, or a dodecamer (AT12) comprising a tetrahedral assembly of trimers, whereas only the trimeric form has been shown to bind and inhibit TRAP. We demonstrate the utility of native mass spectrometry (nMS) and small-angle x-ray scattering (SAXS), together with analytical ultracentrifugation (AUC) for monitoring the pH and concentration-dependent equilibrium between the trimeric and dodecameric structural forms of AT. In addition, we report the use of solution nuclear magnetic resonance (NMR) spectroscopy to determine the solution structure of AT3, while heteronuclear 15N relaxation measurements on both oligomeric forms of AT provide insights into the dynamic properties of binding-active AT3 and binding-inactive AT12, with implications for TRAP inhibition.
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Affiliation(s)
- Craig McElroy
- Ohio State Biochemistry Program
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Elihu Ihms
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- Biophysics Program
| | - Deepak Kumar Yadav
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Melody Holmquist
- Ohio State Biochemistry Program
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Vibhuti Wadwha
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Vicki Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- National Resource for Native MS-Guided Structural Biology
| | - Paul Gollnick
- Department of Biological Sciences, State University of New York, Buffalo NY 14260
| | - Mark Foster
- Ohio State Biochemistry Program
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- Biophysics Program
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10
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Santambrogio C, Ponzini E, Grandori R. Native mass spectrometry for the investigation of protein structural (dis)order. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140828. [PMID: 35926718 DOI: 10.1016/j.bbapap.2022.140828] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/24/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
A central challenge in structural biology is represented by dynamic and heterogeneous systems, as typically represented by proteins in solution, with the extreme case of intrinsically disordered proteins (IDPs) [1-3]. These proteins lack a specific three-dimensional structure and have poorly organized secondary structure. For these reasons, they escape structural characterization by conventional biophysical methods. The investigation of these systems requires description of conformational ensembles, rather than of unique, defined structures or bundles of largely superimposable structures. Mass spectrometry (MS) has become a central tool in this field, offering a variety of complementary approaches to generate structural information on either folded or disordered proteins [4-6]. Two main categories of methods can be recognized. On one side, conformation-dependent reactions (such as cross-linking, covalent labeling, H/D exchange) are exploited to label molecules in solution, followed by the characterization of the labeling products by denaturing MS [7-11]. On the other side, non-denaturing ("native") MS can be used to directly explore the different conformational components in terms of geometry and structural compactness [12-16]. All these approaches have in common the capability to conjugate protein structure investigation with the peculiar analytical power of MS measurements, offering the possibility of assessing species distributions for folding and binding equilibria and the combination of both. These methods can be combined with characterization of noncovalent complexes [17, 18] and post-translational modifications [19-23]. This review focuses on the application of native MS to protein structure and dynamics investigation, with a general methodological section, followed by examples on specific proteins from our laboratory.
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Affiliation(s)
- Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
| | - Erika Ponzini
- Materials Science Department, University of Milano-Bicocca, Via R. Cozzi 55, 20125 Milan, Italy; COMiB Research Center, University of Milano-Bicocca, Via R. Cozzi 55, 20125 Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
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11
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Kellerman MAW, Almeida T, Rudd TR, Matejtschuk P, Dalby PA. NMR Reveals Functionally Relevant Thermally Induced Structural Changes within the Native Ensemble of G-CSF. Mol Pharm 2022; 19:3242-3255. [PMID: 35948076 PMCID: PMC9449972 DOI: 10.1021/acs.molpharmaceut.2c00398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Structure–function relationships in proteins refer
to a
trade-off between stability and bioactivity, molded by evolution of
the molecule. Identifying which protein amino acid residues jeopardize
global or local stability for the benefit of bioactivity would reveal
residues pivotal to this structure–function trade-off. Here,
we use 15N–1H heteronuclear single quantum
coherence (HSQC) nuclear magnetic resonance (NMR) spectroscopy to
probe the microenvironment and dynamics of residues in granulocyte
colony-stimulating factor (G-CSF) through thermal perturbation. From
this analysis, we identified four residues (G4, A6, T133, and Q134)
that we classed as significant to global stability, given that they
all experienced large environmental and dynamic changes and were closely
correlated to each other in their NMR characteristics. Additionally,
we observe that roughly four structural clusters are subject to localized
conformational changes or partial unfolding prior to global unfolding
at higher temperature. Combining NMR observables with structure relaxation
methods reveals that these structural clusters concentrate around
loop AB (binding site III inclusive). This loop has been previously
implicated in conformational changes that result in an aggregation
prone state of G-CSF. Residues H43, V48, and S63 appear to be pivotal
to an opening motion of loop AB, a change that is possibly also important
for function. Hence, we present here an approach to profiling residues
in order to highlight their potential roles in the two vital characteristics
of proteins: stability and bioactivity.
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Affiliation(s)
- Mark-Adam W Kellerman
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Teresa Almeida
- Medicines & Healthcare Products Regulatory Agency, National Institute for Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom
| | - Timothy R Rudd
- Medicines & Healthcare Products Regulatory Agency, National Institute for Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom.,Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, United Kingdom
| | - Paul Matejtschuk
- Medicines & Healthcare Products Regulatory Agency, National Institute for Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom
| | - Paul A Dalby
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, United Kingdom
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12
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Palomino-Hernandez O, Santambrogio C, Rossetti G, Fernandez CO, Grandori R, Carloni P. Molecular Dynamics-Assisted Interpretation of Experimentally Determined Intrinsically Disordered Protein Conformational Components: The Case of Human α-Synuclein. J Phys Chem B 2022; 126:3632-3639. [PMID: 35543707 DOI: 10.1021/acs.jpcb.1c10954] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Mass spectrometry and single molecule force microscopy are two experimental approaches able to provide structural information on intrinsically disordered proteins (IDPs). These techniques allow the dissection of conformational ensembles in their main components, although at a low-resolution level. In this work, we interpret the results emerging from these experimental approaches on human alpha synuclein (AS) by analyzing a previously published 73 μs-long molecular-dynamics (MD) simulation of the protein in explicit solvent. We further compare MD-based predictions of single molecule Förster resonance energy transfer (smFRET) data of AS in solution with experimental data. The combined theoretical and experimental data provide a description of AS main conformational ensemble, shedding light into its intramolecular interactions and overall structural compactness. This analysis could be easily transferred to other IDPs.
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Affiliation(s)
- Oscar Palomino-Hernandez
- Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany.,Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, 52425 Aachen, Germany.,Computation-Based Science and Technology Research Center, The Cyprus Institute, 2121 Nicosia, Cyprus.,Institute of Life Science, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, 20126 Milan, Italy
| | - Giulia Rossetti
- Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany.,Department of Neurology, University Hospital Aachen, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany.,Jülich Supercomputing Center (JSC), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Claudio O Fernandez
- Max Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR, UNR-MPI-NAT). Partner Laboratory of the Max Planck Institute for Biophysical Chemistry (MPI-NAT, MPG). Centro de Estudios Interdisciplinarios, Universidad Nacional de Rosario, Rosario, Argentina S2002LRK Rosario, Argentina
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, 20126 Milan, Italy
| | - Paolo Carloni
- Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany.,Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, 52425 Aachen, Germany.,Institute for Neuroscience and Medicine (INM-11) Forschungszentrum Jülich, 52425 Jülich, Germany
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13
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García-Cebollada H, López A, Sancho J. Protposer: the web server that readily proposes protein stabilizing mutations with high PPV. Comput Struct Biotechnol J 2022; 20:2415-2433. [PMID: 35664235 PMCID: PMC9133766 DOI: 10.1016/j.csbj.2022.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/05/2022] [Accepted: 05/05/2022] [Indexed: 01/23/2023] Open
Abstract
Protein stability is a requisite for most biotechnological and medical applications of proteins. As natural proteins tend to suffer from a low conformational stability ex vivo, great efforts have been devoted toward increasing their stability through rational design and engineering of appropriate mutations. Unfortunately, even the best currently used predictors fail to compute the stability of protein variants with sufficient accuracy and their usefulness as tools to guide the rational stabilisation of proteins is limited. We present here Protposer, a protein stabilising tool based on a different approach. Instead of quantifying changes in stability, Protposer uses structure- and sequence-based screening modules to nominate candidate mutations for subsequent evaluation by a logistic regression model, carefully trained to avoid overfitting. Thus, Protposer analyses PDB files in search for stabilization opportunities and provides a ranked list of promising mutations with their estimated success rates (eSR), their probabilities of being stabilising by at least 0.5 kcal/mol. The agreement between eSRs and actual positive predictive values (PPV) on external datasets of mutations is excellent. When Protposer is used with its Optimal kappa selection threshold, its PPV is above 0.7. Even with less stringent thresholds, Protposer largely outperforms FoldX, Rosetta and PoPMusiC. Indicating the PDB file of the protein suffices to obtain a ranked list of mutations, their eSRs and hints on the likely source of the stabilization expected. Protposer is a distinct, straightforward and highly successful tool to design protein stabilising mutations, and it is freely available for academic use at http://webapps.bifi.es/the-protposer.
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14
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PirePred: An Accurate Online Consensus Tool to Interpret Newborn Screening-Related Genetic Variants in Structural Context. J Mol Diagn 2022; 24:406-425. [PMID: 35143952 DOI: 10.1016/j.jmoldx.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/30/2021] [Accepted: 01/05/2022] [Indexed: 11/20/2022] Open
Abstract
PirePred is a genetic interpretation tool used for a variety of medical conditions investigated in newborn screening programs. The PirePred server retrieves, analyzes, and displays in real time genetic and structural data on 58 genes/proteins associated with medical conditions frequently investigated in the newborn. PirePred analyzes the predictions generated by 15 pathogenicity predictors and applies an optimized majority vote algorithm to classify any possible nonsynonymous single-nucleotide variant as pathogenic, benign, or of uncertain significance. PirePred predictions for variants of clear clinical significance are better than those of any of the individual predictors considered (based on accuracy, sensitivity, and negative predictive value) or are among the best ones (for positive predictive value and Matthews correlation coefficient). PirePred predictions also outperform the comparable in silico predictions offered as supporting evidence, according to American College of Medical Genetics and Genomics guidelines, by VarSome and Franklin. Also, PirePred has very high prediction coverage. To facilitate the molecular interpretation of the missense, nonsense, and frameshift variants in ClinVar, the changing amino acid residue is displayed in its structural context, which is analyzed to provide functional clues. PirePred is an accurate, robust, and easy-to-use tool for clinicians involved in neonatal screening programs and for researchers of related diseases. The server is freely accessible and provides a user-friendly gateway into the structural/functional consequences of genetic variants at the protein level.
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15
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Karlsson E, Sorgenfrei FA, Andersson E, Dogan J, Jemth P, Chi CN. The dynamic properties of a nuclear coactivator binding domain are evolutionarily conserved. Commun Biol 2022; 5:286. [PMID: 35354917 PMCID: PMC8967867 DOI: 10.1038/s42003-022-03217-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 03/02/2022] [Indexed: 12/21/2022] Open
Abstract
Evolution of proteins is constrained by their structure and function. While there is a consensus that the plasticity of intrinsically disordered proteins relaxes the structural constraints on evolution there is a paucity of data on the molecular details of these processes. The Nuclear Coactivator Binding Domain (NCBD) from CREB-binding protein is a protein interaction domain, which contains a hydrophobic core but is not behaving as a typical globular domain, and has been described as 'molten-globule like'. The highly dynamic properties of NCBD makes it an interesting model system for evolutionary structure-function investigation of intrinsically disordered proteins. We have here compared the structure and biophysical properties of an ancient version of NCBD present in a bilaterian animal ancestor living around 600 million years ago with extant human NCBD. Using a combination of NMR spectroscopy, circular dichroism and kinetics we show that although NCBD has increased its thermodynamic stability, it has retained its dynamic biophysical properties in the ligand-free state in the evolutionary lineage leading from the last common bilaterian ancestor to humans. Our findings suggest that the dynamic properties of NCBD have been maintained by purifying selection and thus are important for its function, which includes mediating several distinct protein-protein interactions.
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Affiliation(s)
- Elin Karlsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden
| | - Frieda A Sorgenfrei
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden.,acib GmbH, Krenngasse 37, 8010 Graz c/o University of Graz, Institute of Chemistry, NAWI Graz, BioTechMed Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden
| | - Jakob Dogan
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden.
| | - Celestine N Chi
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden. .,Department of Pharmaceutical Biosciences, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden.
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16
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Laura Darriba M, Castro CP, Coria LM, Bruno L, Laura Cerutti M, Otero LH, Chemes LB, Rasia RM, Klinke S, Cassataro J, Pasquevich KA. A disordered region retains the full protease inhibitor activity and the capacity to induce CD8+ T cells in vivo of the oral vaccine adjuvant U-Omp19. Comput Struct Biotechnol J 2022; 20:5098-5114. [PMID: 36187929 PMCID: PMC9486555 DOI: 10.1016/j.csbj.2022.08.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 01/18/2023] Open
Affiliation(s)
- M. Laura Darriba
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Celeste Pueblas Castro
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Lorena M. Coria
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Laura Bruno
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - M. Laura Cerutti
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Lisandro H. Otero
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Lucía B. Chemes
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Rodolfo M. Rasia
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Santa Fe, Argentina and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Juliana Cassataro
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Karina A. Pasquevich
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
- Corresponding author.
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17
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Ribeiro SS, Castro TG, Gomes CM, Marcos JC. Hofmeister effects on protein stability are dependent on the nature of the unfolded state. Phys Chem Chem Phys 2021; 23:25210-25225. [PMID: 34730580 DOI: 10.1039/d1cp02477a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interpretation of a salt's effect on protein stability traditionally discriminates low concentration regimes (<0.3 M), dominated by electrostatic forces, and high concentration regimes, generally described by ion-specific Hofmeister effects. However, increased theoretical and experimental studies have highlighted observations of the Hofmeister phenomena at concentration ranges as low as 0.001 M. Reasonable quantitative predictions of such observations have been successfully achieved throughout the inclusion of ion dispersion forces in classical electrostatic theories. This molecular description is also on the basis of quantitative estimates obtained resorting to surface/bulk solvent partition models developed for ion-specific Hofmeister effects. However, the latter are limited by the availability of reliable structures representative of the unfolded state. Here, we use myoglobin as a model to explore how ion-dependency on the nature of the unfolded state affects protein stability, combining spectroscopic techniques with molecular dynamic simulations. To this end, the thermal and chemical stability of myoglobin was assessed in the presence of three different salts (NaCl, (NH4)2SO4 and Na2SO4), at physiologically relevant concentrations (0-0.3 M). We observed mild destabilization of the native state induced by each ion, attributed to unfavorable neutralization and hydrogen-bonding with the protein side-chains. Both effects, combined with binding of Na+, Cl- and SO42- to the thermally unfolded state, resulted in an overall destabilization of the protein. Contrastingly, ion binding was hindered in the chemically unfolded conformation, due to occupation of the binding sites by urea molecules. Such mechanistic action led to a lower degree of destabilization, promoting surface tension effects that stabilized myoglobin according to the Hofmeister series. Therefore, we demonstrate that Hofmeister effects on protein stability are modulated by the heterogeneous physico-chemical nature of the unfolded state. Altogether, our findings evidence the need to characterize the structure of the unfolded state when attempting to dissect the molecular mechanisms underlying the effects of salts on protein stability.
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Affiliation(s)
- Sara S Ribeiro
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Tarsila G Castro
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Cláudio M Gomes
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências and Departamento de Química e Bioquímica, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - João C Marcos
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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18
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Russo L, Mascanzoni F, Farina B, Dolga AM, Monti A, Caporale A, Culmsee C, Fattorusso R, Ruvo M, Doti N. Design, Optimization, and Structural Characterization of an Apoptosis-Inducing Factor Peptide Targeting Human Cyclophilin A to Inhibit Apoptosis Inducing Factor-Mediated Cell Death. J Med Chem 2021; 64:11445-11459. [PMID: 34338510 DOI: 10.1021/acs.jmedchem.1c00777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Blocking the interaction between the apoptosis-inducing factor (AIF) and cyclophilin A (CypA) by the AIF fragment AIF(370-394) is protective against glutamate-induced neuronal cell death and brain injury in mice. Starting from AIF(370-394), we report the generation of the disulfide-bridged and shorter variant AIF(381-389) and its structural characterization by nuclear magnetic resonance (NMR) in the free and CypA-bound state. AIF(381-389) in both the free and bound states assumes a β-hairpin conformation similar to that of the fragment in the AIF protein and shows a highly reduced conformational flexibility. This peptide displays a similar in vitro affinity for CypA, an improved antiapoptotic activity in cells and an enhanced proteolytic stability compared to the parent peptide. The NMR-based 3D model of the AIF(381-389)/CypA complex provides a better understanding of the binding hot spots on both the peptide and the protein and can be exploited to design AIF/CypA inhibitors with improved pharmacokinetic and pharmacodynamics features.
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Affiliation(s)
- Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "L. Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Fabiola Mascanzoni
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone, 16, 80134 Napoli, Italy
| | - Biancamaria Farina
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone, 16, 80134 Napoli, Italy
| | - Amalia Mihaela Dolga
- Institute of Pharmacology and Clinical Pharmacy, University of Marburg, 35043 Marburg, Germany.,Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), Research School of Behavioural and Cognitive Neurosciences (BCN), Department of Molecular Pharmacology, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Alessandra Monti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone, 16, 80134 Napoli, Italy
| | - Andrea Caporale
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone, 16, 80134 Napoli, Italy
| | - Carsten Culmsee
- Institute of Pharmacology and Clinical Pharmacy, University of Marburg, 35043 Marburg, Germany
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "L. Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Menotti Ruvo
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone, 16, 80134 Napoli, Italy
| | - Nunzianna Doti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone, 16, 80134 Napoli, Italy
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19
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Koirala M, Shashikala HBM, Jeffries J, Wu B, Loftus SK, Zippin JH, Alexov E. Computational Investigation of the pH Dependence of Stability of Melanosome Proteins: Implication for Melanosome formation and Disease. Int J Mol Sci 2021; 22:ijms22158273. [PMID: 34361043 PMCID: PMC8347052 DOI: 10.3390/ijms22158273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 11/16/2022] Open
Abstract
Intravesicular pH plays a crucial role in melanosome maturation and function. Melanosomal pH changes during maturation from very acidic in the early stages to neutral in late stages. Neutral pH is critical for providing optimal conditions for the rate-limiting, pH-sensitive melanin-synthesizing enzyme tyrosinase (TYR). This dramatic change in pH is thought to result from the activity of several proteins that control melanosomal pH. Here, we computationally investigated the pH-dependent stability of several melanosomal membrane proteins and compared them to the pH dependence of the stability of TYR. We confirmed that the pH optimum of TYR is neutral, and we also found that proteins that are negative regulators of melanosomal pH are predicted to function optimally at neutral pH. In contrast, positive pH regulators were predicted to have an acidic pH optimum. We propose a competitive mechanism among positive and negative regulators that results in pH equilibrium. Our findings are consistent with previous work that demonstrated a correlation between the pH optima of stability and activity, and they are consistent with the expected activity of positive and negative regulators of melanosomal pH. Furthermore, our data suggest that disease-causing variants impact the pH dependence of melanosomal proteins; this is particularly prominent for the OCA2 protein. In conclusion, melanosomal pH appears to affect the activity of multiple melanosomal proteins.
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Affiliation(s)
- Mahesh Koirala
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (M.K.); (H.B.M.S.); (J.J.); (B.W.)
| | - H. B. Mihiri Shashikala
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (M.K.); (H.B.M.S.); (J.J.); (B.W.)
| | - Jacob Jeffries
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (M.K.); (H.B.M.S.); (J.J.); (B.W.)
| | - Bohua Wu
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (M.K.); (H.B.M.S.); (J.J.); (B.W.)
| | - Stacie K. Loftus
- Genetic Disease Research Branch, National Human Genome Research Branch, National Institutes of Health, Bethesda, MD 22066, USA;
| | - Jonathan H. Zippin
- Department of Dermatology, Weill Cornell Medical College, New York, NY 10021, USA;
| | - Emil Alexov
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (M.K.); (H.B.M.S.); (J.J.); (B.W.)
- Correspondence:
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20
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POT1 stability and binding measured by fluorescence thermal shift assays. PLoS One 2021; 16:e0245675. [PMID: 33784306 PMCID: PMC8009405 DOI: 10.1371/journal.pone.0245675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/03/2021] [Indexed: 11/19/2022] Open
Abstract
The protein POT1 (Protection of Telomeres 1) is an integral part of the shelterin complex that protects the ends of human chromosomes from degradation or end fusions. It is the only component of shelterin that binds single-stranded DNA. We describe here the application of two separate fluorescent thermal shift assays (FTSA) that provide quantitative biophysical characterization of POT1 stability and its interactions. The first assay uses Sypro Orange™ and monitors the thermal stability of POT1 and its binding under a variety of conditions. This assay is useful for the quality control of POT1 preparations, for biophysical characterization of its DNA binding and, potentially, as an efficient screening tool for binding of small molecule drug candidates. The second assay uses a FRET-labeled human telomeric G-quadruplex structure that reveals the effects of POT1 binding on thermal stability from the DNA frame of reference. These complementary assays provide efficient biophysical approaches for the quantitative characterization of multiple aspects of POT1 structure and function. The results from these assays provide thermodynamics details of POT1 folding, the sequence selectivity of its DNA binding and the thermodynamic profile for its binding to its preferred DNA binding sequence. Most significantly, results from these assays elucidate two mechanisms for the inhibition of POT1 -DNA interactions. The first is by competitive inhibition at the POT1 DNA binding site. The second is indirect and is by stabilization of G-quadruplex formation within the normal POT1 single-stranded DNA sequence to prevent POT1 binding.
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21
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Kaplan AR, Olson R, Alexandrescu AT. Protein yoga: Conformational versatility of the Hemolysin II C-terminal domain detailed by NMR structures for multiple states. Protein Sci 2021; 30:990-1005. [PMID: 33733504 DOI: 10.1002/pro.4066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/10/2021] [Accepted: 03/13/2021] [Indexed: 11/05/2022]
Abstract
The C-terminal domain of Bacillus cereus hemolysin II (HlyIIC), stabilizes the trans-membrane-pore formed by the HlyII toxin and may aid in target cell recognition. Initial efforts to determine the NMR structure of HlyIIC were hampered by cis/trans isomerization about the single proline at position 405 that leads to doubling of NMR resonances. We used the mutant P405M-HlyIIC that eliminates the cis proline to determine the NMR structure of the domain, which revealed a novel fold. Here, we extend earlier studies to the NMR structure determination of the cis and trans states of WT-HlyIIC that exist simultaneously in solution. The primary structural differences between the cis and trans states are in the loop that contains P405, and structurally adjacent loops. Thermodynamic linkage analysis shows that at 25 C the cis proline, which already has a large fraction of 20% in the unfolded protein, increases to 50% in the folded state due to coupling with the global stability of the domain. The P405M or P405A substitutions eliminate heterogeneity due to proline isomerization but lead to the formation of a new dimeric species. The NMR structure of the dimer shows that it is formed through domain-swapping of strand β5, the last segment of secondary structure following P405. The presence of P405 in WT-HlyIIC strongly disfavors the dimer compared to the P405M-HlyIIC or P405A-HlyIIC mutants. The WT proline may thus act as a "gatekeeper," warding off aggregative misfolding.
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Affiliation(s)
- Anne R Kaplan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Rich Olson
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut, USA
| | - Andrei T Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
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22
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Guseman AJ, Whitley MJ, González JJ, Rathi N, Ambarian M, Gronenborn AM. Assessing the Structures and Interactions of γD-Crystallin Deamidation Variants. Structure 2020; 29:284-291.e3. [PMID: 33264606 DOI: 10.1016/j.str.2020.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 10/12/2020] [Accepted: 11/06/2020] [Indexed: 11/25/2022]
Abstract
Cataracts involve the deposition of the crystallin proteins in the vertebrate eye lens, causing opacification and blindness. They are associated with either genetic mutation or protein damage that accumulates over the lifetime of the organism. Deamidation of Asn residues in several different crystallins has been observed and is frequently invoked as a cause of cataract. Here, we investigated the properties of Asp variants, deamidation products of γD-crystallin, by solution NMR, X-ray crystallography, and other biophysical techniques. No substantive structural or stability changes were noted for all seven Asn to Asp γD-crystallins. Importantly, no changes in diffusion interaction behavior could be detected. Our combined experimental results demonstrate that introduction of single Asp residues on the surface of γD-crystallin by deamidation is unlikely to be the driver of cataract formation in the eye lens.
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Affiliation(s)
- Alex J Guseman
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA
| | - Matthew J Whitley
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA
| | - Jeremy J González
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA
| | - Nityam Rathi
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA
| | - Mikayla Ambarian
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA.
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23
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Piñana M, Vila J, Maldonado C, Galano-Frutos JJ, Valls M, Sancho J, Nuvials FX, Andrés C, Martín-Gómez MT, Esperalba J, Codina MG, Pumarola T, Antón A. Insights into immune evasion of human metapneumovirus: novel 180- and 111-nucleotide duplications within viral G gene throughout 2014-2017 seasons in Barcelona, Spain. J Clin Virol 2020; 132:104590. [PMID: 32957052 PMCID: PMC7418790 DOI: 10.1016/j.jcv.2020.104590] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/24/2020] [Accepted: 08/10/2020] [Indexed: 11/30/2022]
Abstract
HMPV has a prevalence of 3%, affecting equally children and adults. 180- and 111-nucleotide duplications emerged, increasing in prevalence over seasons. G proteins w/ duplications protruded more from the membrane than w/o duplication. Viruses w/ duplications were more associated to LRTI in adults than w/o duplication. These facts suggest these duplications might enhance an immune evasion mechanism
Background Human metapneumovirus (HMPV) is an important aetiologic agent of respiratory tract infection (RTI). This study aimed to describe its genetic diversity and clinical impact in patients attended at a tertiary university hospital in Barcelona from the 2014-2015 to the 2016-2017 seasons, focusing on the emerging duplications in G gene and their structural properties. Methods Laboratory-confirmed HMPV were characterised based on partial-coding F and G gene sequences with MEGA.v6.0. Computational analysis of disorder propensity, aggregation propensity and glycosylation sites in viral G predicted protein sequence were carried out. Clinical data was retrospectively reviewed and further associated to virological features. Results HMPV prevalence was 3%. The 180- and 111-nucleotide duplications occurred in A2c lineage G protein increased in prevalence throughout the study, in addition to short genetic changes observed in other HMPV lineages. The A2c G protein without duplications was calculated to protrude over F protein in 23% of cases and increased to a 39% and a 46% with the 111- and 180-nucleotide duplications, respectively. Children did not seem to be more affected by these mutant viruses, but there was a strong association of these variants to LRTI in adults. Discussion HMPV presents a high genetic diversity in all lineages. Novel variants carrying duplications might present an evolutionary advantage due to an improved steric shielding, which would have been responsible for the reported increasing prevalence and the association to LRTI in adults.
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Affiliation(s)
- Maria Piñana
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Jorgina Vila
- Paediatric Hospitalization Unit, Paediatrics Department, Hospital Universitari Maternoinfantil Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Carolina Maldonado
- Intensive Care Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Juan José Galano-Frutos
- Biochemistry and Molecular and Cell Biology Department, Sciences Faculty, Universidad de Zaragoza, Zaragoza, Spain; Biocomputation and Complex Systems Physics Institute (BIFI). Joint Units BIFI-IQFR (CSIC) and GBs-CSIC, Universidad de Zaragoza, Zaragoza, Spain
| | - Maria Valls
- Paediatric Hospitalization Unit, Paediatrics Department, Hospital Universitari Maternoinfantil Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Javier Sancho
- Biochemistry and Molecular and Cell Biology Department, Sciences Faculty, Universidad de Zaragoza, Zaragoza, Spain; Biocomputation and Complex Systems Physics Institute (BIFI). Joint Units BIFI-IQFR (CSIC) and GBs-CSIC, Universidad de Zaragoza, Zaragoza, Spain; Aragon Health Research Institute (IIS Aragón), Zaragoza, Spain
| | - Francesc Xavier Nuvials
- Intensive Care Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Cristina Andrés
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - María Teresa Martín-Gómez
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Juliana Esperalba
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Maria Gema Codina
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Tomàs Pumarola
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain.
| | - Andrés Antón
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
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24
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Canepa J, Torgerson J, Kim DK, Lindahl E, Takahashi R, Whitelock K, Heying M, Wilkinson SP. Characterizing osmolyte chemical class hierarchies and functional group requirements for thermal stabilization of proteins. Biophys Chem 2020; 264:106410. [PMID: 32574923 DOI: 10.1016/j.bpc.2020.106410] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/25/2020] [Accepted: 05/31/2020] [Indexed: 12/20/2022]
Abstract
Osmolytes are naturally occurring organic compounds that protect cellular proteins and other macromolecules against various forms of stress including temperature extremes. While biological studies have correlated the accumulation of certain classes of osmolytes with specific forms of stress, including thermal stress, it remains unclear whether or not these observations reflect an intrinsic chemical class hierarchy amongst the osmolytes with respect to effects on protein stability. In addition, very little is known in regards to the molecular elements of the osmolytes themselves that are essential for their functions. In this study, we use differential scanning fluorimetry to quantify the thermal stabilizing effects of members from each of the three main classes of protecting osmolytes on two model protein systems, C-reactive protein and tumor necrosis factor alpha. Our data reveals the absence of a strict chemical class hierarchy amongst the osmolytes with respect to protein thermal stabilization, and indicates differential responses of these proteins to certain osmolytes. In the second part of this investigation we dissected the molecular elements of amino acid osmolytes required for thermal stabilization of myoglobin and C-reactive protein. We show that the complete amino acid zwitterion is required for thermal stabilization of myoglobin, whereas removal of the osmolyte amino group does not diminish stabilizing effects on C-reactive protein. These disparate responses of proteins to osmolytes and other small molecules are consistent with previous observations that osmolyte effects on protein stability are protein-specific. Moreover, the data reported in this study support the view that osmolyte effects cannot be fully explained by considering only the solvent accessibility of the polypeptide backbone in the native and denatured states, and corroborate the need for more complex models that take into account the entire protein fabric.
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Affiliation(s)
- J Canepa
- Department of Chemistry & Biochemistry, California Polytechnic State University, San Luis Obispo, CA, USA
| | - J Torgerson
- Department of Chemistry & Biochemistry, California Polytechnic State University, San Luis Obispo, CA, USA
| | - D K Kim
- Department of Chemistry & Biochemistry, California Polytechnic State University, San Luis Obispo, CA, USA
| | - E Lindahl
- Department of Chemistry & Biochemistry, California Polytechnic State University, San Luis Obispo, CA, USA
| | - R Takahashi
- Department of Chemistry & Biochemistry, California Polytechnic State University, San Luis Obispo, CA, USA
| | - K Whitelock
- Department of Chemistry & Biochemistry, California Polytechnic State University, San Luis Obispo, CA, USA
| | - M Heying
- Department of Chemistry & Biochemistry, California Polytechnic State University, San Luis Obispo, CA, USA
| | - S P Wilkinson
- Department of Chemistry & Biochemistry, California Polytechnic State University, San Luis Obispo, CA, USA.
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25
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Hull JJ, Perera OP, Wang MX. Molecular cloning and comparative analysis of transcripts encoding chemosensory proteins from two plant bugs, Lygus lineolaris and Lygus hesperus. INSECT SCIENCE 2020; 27:404-424. [PMID: 30549241 DOI: 10.1111/1744-7917.12656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 11/21/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Abstract
Chemosensory proteins (CSPs) are soluble carrier proteins typically characterized by a six-helix bundle structure joined by two disulfide bridges and a conserved Cys spacing pattern (C1-X6-8 -C2-X16-21 -C3-X2 -C4). CSPs are functionally diverse with reported roles in chemosensation, immunity, development, and resistance. To expand our molecular understanding of CSP function in plant bugs, we used recently developed transcriptomic resources for Lygus lineolaris and Lygus hesperus to identify 17 and 14 CSP-like sequences, respectively. The Lygus CSPs are orthologous and share significant sequence identity with previously annotated CSPs. Three of the CSPs are predicted to deviate from the typical CSP structure with either five or seven helical segments rather than six. The seven helix CSP is further differentiated by an atypical C3-X3 -C4 Cys spacing motif. Reverse transcriptase PCR-based profiling of CSP transcript abundance in adult L. lineolaris tissues revealed broad expression for most of the CSPs with antenna specific expression limited to a subset of the CSPs. Comparative sequence analyses and homology modeling suggest that variations in the amino acids that comprise the Lygus CSP binding pockets affect the size and nature of the ligands accommodated.
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Affiliation(s)
- J Joe Hull
- USDA-ARS Arid Land Agricultural Research Center, Maricopa, Arizona, USA
| | - Omaththage P Perera
- USDA-ARS, Southern Insect Management Research Unit, Stoneville, Mississippi, USA
| | - Mei-Xian Wang
- USDA-ARS Arid Land Agricultural Research Center, Maricopa, Arizona, USA
- College of Animal Sciences, Zhejiang University, Hangzhou, China
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26
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Fujiwara H, Shiga S, Makabe K. Cooperative unfolding of a single-layer β-sheet protein, CPAP G-box. Biochem Biophys Res Commun 2020; 526:105-109. [PMID: 32197835 DOI: 10.1016/j.bbrc.2020.03.056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/08/2020] [Indexed: 11/25/2022]
Abstract
CPAP is a centriolar protein and its C-terminal domain, G-box or TCP, has a very unique structure that comprises a single-layer β-sheet without hydrophobic core packing. Here we characterized its biophysical properties, including its stability against chemical denaturation. Interestingly, upon urea-induced equilibrium unfolding, the CPAP G-box showed cooperative unfolding behavior that is the hallmark of globular proteins. We analyzed the m-value, a measure of the cooperative transition, from the urea-induced unfolding and found that the estimated m-value from surface burial upon folding is consistent with the experimental value, supporting the two-state unfolding. Next, we constructed deletion mutants of the terminal β-strands and found that the mutants showed reduced stability. The unique structure and characteristics of CPAP G-box provides an interesting opportunity to observe how the core-less flat β-sheet protein can be folded in solution.
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Affiliation(s)
- Hideki Fujiwara
- Graduate School of Science and Engineering, Yamagata University, Jyonan 4-3-16, Yonezawa, Yamagata, 992-8510, Japan
| | - Shota Shiga
- Graduate School of Science and Engineering, Yamagata University, Jyonan 4-3-16, Yonezawa, Yamagata, 992-8510, Japan
| | - Koki Makabe
- Graduate School of Science and Engineering, Yamagata University, Jyonan 4-3-16, Yonezawa, Yamagata, 992-8510, Japan.
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27
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Chen Z, Kibler RD, Hunt A, Busch F, Pearl J, Jia M, VanAernum ZL, Wicky BIM, Dods G, Liao H, Wilken MS, Ciarlo C, Green S, El-Samad H, Stamatoyannopoulos J, Wysocki VH, Jewett MC, Boyken SE, Baker D. De novo design of protein logic gates. Science 2020; 368:78-84. [PMID: 32241946 DOI: 10.1126/science.aay2790] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 03/05/2020] [Indexed: 12/16/2022]
Abstract
The design of modular protein logic for regulating protein function at the posttranscriptional level is a challenge for synthetic biology. Here, we describe the design of two-input AND, OR, NAND, NOR, XNOR, and NOT gates built from de novo-designed proteins. These gates regulate the association of arbitrary protein units ranging from split enzymes to transcriptional machinery in vitro, in yeast and in primary human T cells, where they control the expression of the TIM3 gene related to T cell exhaustion. Designed binding interaction cooperativity, confirmed by native mass spectrometry, makes the gates largely insensitive to stoichiometric imbalances in the inputs, and the modularity of the approach enables ready extension to three-input OR, AND, and disjunctive normal form gates. The modularity and cooperativity of the control elements, coupled with the ability to de novo design an essentially unlimited number of protein components, should enable the design of sophisticated posttranslational control logic over a wide range of biological functions.
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Affiliation(s)
- Zibo Chen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Ryan D Kibler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Andrew Hunt
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Florian Busch
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Jocelynn Pearl
- Altius Institute for Biomedical Sciences, Seattle, WA 98195, USA
| | - Mengxuan Jia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Zachary L VanAernum
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Basile I M Wicky
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Galen Dods
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hanna Liao
- Altius Institute for Biomedical Sciences, Seattle, WA 98195, USA
| | - Matthew S Wilken
- Altius Institute for Biomedical Sciences, Seattle, WA 98195, USA
| | - Christie Ciarlo
- Altius Institute for Biomedical Sciences, Seattle, WA 98195, USA
| | - Shon Green
- Altius Institute for Biomedical Sciences, Seattle, WA 98195, USA
| | - Hana El-Samad
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.,Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - John Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, WA 98195, USA.,Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,Department of Medicine, Division of Oncology, University of Washington, Seattle, WA 98109, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Scott E Boyken
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. .,Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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28
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Galano-Frutos JJ, García-Cebollada H, Sancho J. Molecular dynamics simulations for genetic interpretation in protein coding regions: where we are, where to go and when. Brief Bioinform 2019; 22:3-19. [PMID: 31813950 DOI: 10.1093/bib/bbz146] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/22/2019] [Accepted: 10/25/2019] [Indexed: 12/18/2022] Open
Abstract
The increasing ease with which massive genetic information can be obtained from patients or healthy individuals has stimulated the development of interpretive bioinformatics tools as aids in clinical practice. Most such tools analyze evolutionary information and simple physical-chemical properties to predict whether replacement of one amino acid residue with another will be tolerated or cause disease. Those approaches achieve up to 80-85% accuracy as binary classifiers (neutral/pathogenic). As such accuracy is insufficient for medical decision to be based on, and it does not appear to be increasing, more precise methods, such as full-atom molecular dynamics (MD) simulations in explicit solvent, are also discussed. Then, to describe the goal of interpreting human genetic variations at large scale through MD simulations, we restrictively refer to all possible protein variants carrying single-amino-acid substitutions arising from single-nucleotide variations as the human variome. We calculate its size and develop a simple model that allows calculating the simulation time needed to have a 0.99 probability of observing unfolding events of any unstable variant. The knowledge of that time enables performing a binary classification of the variants (stable-potentially neutral/unstable-pathogenic). Our model indicates that the human variome cannot be simulated with present computing capabilities. However, if they continue to increase as per Moore's law, it could be simulated (at 65°C) spending only 3 years in the task if we started in 2031. The simulation of individual protein variomes is achievable in short times starting at present. International coordination seems appropriate to embark upon massive MD simulations of protein variants.
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Affiliation(s)
- Juan J Galano-Frutos
- Protein Folding and Molecular Design (ProtMol)' group at BIFI, University of Zaragoza
| | | | - Javier Sancho
- Protein Folding and Molecular Design (ProtMol)' group at BIFI, University of Zaragoza
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29
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Sekhon G, Singh R. Human aldose reductase unfolds through an intermediate. F1000Res 2019; 8:564. [PMID: 31723418 PMCID: PMC6844136 DOI: 10.12688/f1000research.18963.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/22/2019] [Indexed: 11/26/2022] Open
Abstract
Background: Human aldose reductase (hAR) is the first and rate-limiting enzyme of the polyol pathway. For the development of secondary complications of diabetes in chronic hyperglycemic conditions, one of the critical factors is the increased flux of glucose through the polyol pathway. Due to this clinical implication, hAR attracted considerable attention from the drug discovery perspective. In spite of extensive characterization in the context of biochemical and structural aspects, we know very little about the unfolding behavior of hAR. This study reports equilibrium unfolding studies of hAR. Methods: We carried out thermal denaturation and chemical-induced equilibrium unfolding studies of hAR monitored by circular dichroism and fluorescence spectroscopy. Results: Thermal denaturation studies presented a classical picture of two-state unfolding from native to the denatured state. The data was used to derive thermodynamic parameters and study the thermostability of hAR. Chemical induced equilibrium unfolding studies led us to discover an intermediate state, which gets populated at 3.5-4.0 M and 0.7-2.0 M of urea and GuHCl, respectively. Thermodynamic parameters derived from chemical-induced unfolding are in agreement with those obtained from thermal denaturation of hAR. Conclusion: This study revealed that aldose reductase unfolds from native to the unfolded state via an intermediate. Assessment of the thermodynamic stability of native, intermediate, and unfolded states shows that significant energy barriers separate these states, which ensures the cooperativity of unfolding. As hAR functions in cells that are under osmotic and oxidative stress, these
in vitro findings may have implications for its native conformation under the physiological state.
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Affiliation(s)
- Gurprit Sekhon
- Department cum National Center for Human Genome Studies and Research, Panjab University, Chandigarh, 160014, India
| | - Ranvir Singh
- Department cum National Center for Human Genome Studies and Research, Panjab University, Chandigarh, 160014, India
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30
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Galano-Frutos JJ, Sancho J. Accurate Calculation of Barnase and SNase Folding Energetics Using Short Molecular Dynamics Simulations and an Atomistic Model of the Unfolded Ensemble: Evaluation of Force Fields and Water Models. J Chem Inf Model 2019; 59:4350-4360. [PMID: 31513394 DOI: 10.1021/acs.jcim.9b00430] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
As proteins perform most cellular functions, quantitative understanding of protein energetics is required to gain control of biological phenomena. Accurate models of native proteins can be obtained experimentally, but the lack of equally fine models of unfolded ensembles impedes the calculation of protein folding energetics from first principles. Here, we show that an atomistic unfolded ensemble model, consisting of a few dozen conformations built from a protein sequence, can be used in conjunction with an X-ray structure of its native state to calculate accurately by difference the changes in enthalpy and heat capacity of the polypeptide upon folding. The calculation is done using molecular dynamics simulations, popular force fields, and water models, and for the two model proteins studied (barnase and SNase), the results agree within error or are very close to their experimentally determined properties. The enthalpy sampling of the unfolded ensemble is done through short 2 ns simulations that do not significantly modify the representative distribution of Rg of the starting conformations. The impressive accuracy obtained opens the possibility to investigate quantitatively systems or phenomena not amenable to experiment and paves the way for addressing the calculation of protein conformational stability (i.e., the change in Gibbs energy upon folding), a central goal of structural biology. So far, these calculated enthalpy and heat capacity changes, combined with the experimentally determined melting temperatures of the corresponding protein, allow us to reproduce the stability curves of both barnase and SNase.
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Affiliation(s)
- Juan José Galano-Frutos
- Department of Biochemistry and Molecular and Cellular Biology , University of Zaragoza , Pedro Cerbuna 12 , Zaragoza 50009 , Spain.,Biocomputation and Complex Systems Physics Institute (Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC) , University of Zaragoza , Mariano Esquillor s/n, Edificio I + D , Zaragoza 50018 , Spain
| | - Javier Sancho
- Department of Biochemistry and Molecular and Cellular Biology , University of Zaragoza , Pedro Cerbuna 12 , Zaragoza 50009 , Spain.,Biocomputation and Complex Systems Physics Institute (Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC) , University of Zaragoza , Mariano Esquillor s/n, Edificio I + D , Zaragoza 50018 , Spain.,Aragon Health Research Institute (IIS Aragón) , Avda. San Juan Bosco 13 , Zaragoza 50009 , Spain
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31
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Yaacob N, Ahmad Kamarudin NH, Leow ATC, Salleh AB, Rahman RNZRA, Ali MSM. Effects of Lid 1 Mutagenesis on Lid Displacement, Catalytic Performances and Thermostability of Cold-active Pseudomonas AMS8 Lipase in Toluene. Comput Struct Biotechnol J 2019; 17:215-228. [PMID: 30828413 PMCID: PMC6383135 DOI: 10.1016/j.csbj.2019.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/14/2019] [Accepted: 01/19/2019] [Indexed: 11/23/2022] Open
Abstract
Pseudomonas fluorescens AMS8 lipase lid 1 structure is rigid and holds unclear roles due to the absence of solvent-interactions. Lid 1 region was stabilized by 17 hydrogen bond linkages and displayed lower mean hydrophobicity (0.596) compared to MIS38 lipase. Mutating lid 1 residues, Thr-52 and Gly-55 to aromatic hydrophobic-polar tyrosine would churned more side-chain interactions between lid 1 and water or toluene. This study revealed that T52Y leads G55Y and its recombinant towards achieving higher solvent-accessible surface area and longer half-life at 25 to 37 °C in 0.5% (v/v) toluene. T52Y also exhibited better substrate affinity with long-chain carbon substrate in aqueous media. The affinity for pNP palmitate, laurate and caprylate increased in 0.5% (v/v) toluene in recombinant AMS8, but the affinity in similar substrates was substantially declined in lid 1 mutated lipases. Regarding enzyme efficiency, the recombinant AMS8 lipase displayed highest value of kcat/Km in 0.5% (v/v) toluene, mainly with pNPC. In both hydrolysis reactions with 0% and 0.5% (v/v) toluene, the enzyme efficiency of G55Y was found higher than T52Y for pNPL and pNPP. At 0.5% (v/v) toluene, both mutants showed reductions in activation energy and enthalpy values as temperature increased from 25 to 35 °C, displaying better catalytic functions. Only T52Y exhibited increase in entropy values at 0.5% (v/v) toluene indicating structure stability. As a conclusion, Thr-52 and Gly-55 are important residues for lid 1 stability as their existence helps to retain the geometrical structure of alpha-helix and connecting hinge.
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Affiliation(s)
- Norhayati Yaacob
- Enzyme Technology Laboratory, Laboratory of Molecular Biomedicine (MOLEMED), Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Malaysia.,Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 Serdang, Malaysia
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 Serdang, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 Serdang, Malaysia.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Malaysia
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 Serdang, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 Serdang, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 Serdang, Malaysia.,Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Malaysia
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32
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Schulte‐Sasse M, Pardo‐Ávila F, Pulido‐Mayoral NO, Vázquez‐Lobo A, Costas M, García‐Hernández E, Rodríguez‐Romero A, Fernández‐Velasco DA. Structural, thermodynamic and catalytic characterization of an ancestral triosephosphate isomerase reveal early evolutionary coupling between monomer association and function. FEBS J 2019; 286:882-900. [DOI: 10.1111/febs.14741] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 11/01/2018] [Accepted: 12/23/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Mariana Schulte‐Sasse
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas Departamento de Bioquímica Facultad de Medicina Universidad Nacional Autónoma de México Mexico
| | - Fátima Pardo‐Ávila
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas Departamento de Bioquímica Facultad de Medicina Universidad Nacional Autónoma de México Mexico
| | - Nancy O. Pulido‐Mayoral
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas Departamento de Bioquímica Facultad de Medicina Universidad Nacional Autónoma de México Mexico
| | - Alejandra Vázquez‐Lobo
- Centro de Investigación en Biodiversidad y Conservación Universidad Autónoma del Estado de Morelos Cuernavaca Mexico
| | - Miguel Costas
- Laboratorio de Biofisicoquímica Departamento de Fisicoquímica Facultad de Química Universidad Nacional Autónoma de México Mexico
| | | | | | - Daniel Alejandro Fernández‐Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas Departamento de Bioquímica Facultad de Medicina Universidad Nacional Autónoma de México Mexico
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33
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Robalo JR, Vila Verde A. Unexpected trends in the hydrophobicity of fluorinated amino acids reflect competing changes in polarity and conformation. Phys Chem Chem Phys 2019; 21:2029-2038. [DOI: 10.1039/c8cp07025c] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The hydration free energy of fluorinated amino acids is calculated with molecular simulations and explained with an analytical model.
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Affiliation(s)
- João R. Robalo
- Max Planck Institute for Colloids and Interfaces
- Department of Theory & Bio-systems
- Science Park
- Potsdam 14424
- Germany
| | - Ana Vila Verde
- Max Planck Institute for Colloids and Interfaces
- Department of Theory & Bio-systems
- Science Park
- Potsdam 14424
- Germany
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34
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Abstract
Salts differ in their ability to stabilize protein conformations, thereby affecting the thermodynamics and kinetics of protein folding. We developed a coarse-grained protein model that can predict salt-induced changes in protein properties by using the transfer free-energy data of various chemical groups from water to salt solutions. Using this model and molecular dynamics simulations, we probed the effect of seven different salts on the folding thermodynamics of the DNA binding domain of lac repressor protein ( lac-DBD) and N-terminal domain of ribosomal protein (NTL9). We show that a salt can act as a protein stabilizing or destabilizing agent depending on the protein sequence and folded state topology. The computed thermodynamic properties, especially the m values for various salts, which reveal the relative ability of a salt to stabilize the protein folded state, are in quantitative agreement with the experimentally measured values. The computations show that the degree of protein compaction in the denatured ensemble strongly depends on the salt identity, and for the same variation in salt concentration, the compaction in the protein dimensions varies from ∼4% to ∼30% depending on the salt. The transition-state ensemble (TSE) of lac-DBD is homogeneous and polarized, while the TSE of NTL9 is heterogeneous and diffusive. Salts induce subtle structural changes in the TSE that are in agreement with Hammond's postulate. The barrier to protein folding tends to disappear in the presence of moderate concentrations (∼3-4 m) of strongly stabilizing salts.
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Affiliation(s)
- Hiranmay Maity
- Solid State and Structural Chemistry Unit , Indian Institute of Science , Bengaluru , Karnataka , India 560012
| | - Aswathy N Muttathukattil
- Solid State and Structural Chemistry Unit , Indian Institute of Science , Bengaluru , Karnataka , India 560012
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit , Indian Institute of Science , Bengaluru , Karnataka , India 560012
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35
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Lamazares E, Vega S, Ferreira P, Medina M, Galano-Frutos JJ, Martínez-Júlvez M, Velázquez-Campoy A, Sancho J. Direct examination of the relevance for folding, binding and electron transfer of a conserved protein folding intermediate. Phys Chem Chem Phys 2018; 19:19021-19031. [PMID: 28702545 DOI: 10.1039/c7cp02606d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Near the minimum free energy basin of proteins where the native ensemble resides, partly unfolded conformations of slightly higher energy can be significantly populated under native conditions. It has been speculated that they play roles in molecular recognition and catalysis, but they might represent contemporary features of the evolutionary process without functional relevance. Obtaining conclusive evidence on these alternatives is difficult because it requires comparing the performance of a given protein when populating and when not populating one such intermediate, in otherwise identical conditions. Wild type apoflavodoxin populates under native conditions a partly unfolded conformation (10% of molecules) whose unstructured region includes the binding sites for the FMN cofactor and for redox partner proteins. We recently engineered a thermostable variant where the intermediate is no longer detectable. Using the wild type and variant, we assess the relevance of the intermediate comparing folding kinetics, cofactor binding kinetics, cofactor affinity, X-ray structure, intrinsic dynamics, redox potential of the apoflavodoxin-cofactor complex (Fld), its affinity for partner protein FNR, and electron transfer rate within the Fld/FNR physiological complex. Our data strongly suggest the intermediate state, conserved in long-chain apoflavodoxins, is not required for the correct assembly of flavodoxin nor does it contribute to shape its electron transfer properties. This analysis can be applied to evaluate other native basin intermediates.
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Affiliation(s)
- Emilio Lamazares
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Sonia Vega
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain
| | - Patricia Ferreira
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Milagros Medina
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Juan J Galano-Frutos
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Marta Martínez-Júlvez
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain and Fundación ARAID, Gobierno de Aragón, Spain and Aragon Health Research Institute (IIS Aragón), Universidad de Zaragoza, Zaragoza, Spain.
| | - Javier Sancho
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain and Aragon Health Research Institute (IIS Aragón), Universidad de Zaragoza, Zaragoza, Spain.
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36
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Hong J, Xiong S. TMAO-Protein Preferential Interaction Profile Determines TMAO's Conditional In Vivo Compatibility. Biophys J 2017; 111:1866-1875. [PMID: 27806268 DOI: 10.1016/j.bpj.2016.09.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/16/2016] [Accepted: 09/26/2016] [Indexed: 10/20/2022] Open
Abstract
Trimethylamine N-oxide (TMAO) exemplifies how Nature uses the solute effect as a simple chemical strategy to cope with hydrodynamic pressure or urea stress to maintain proteostasis. It is a gut-microbe-generated metabolite that strongly promotes the development of atherosclerosis. It remains unclear how TMAO exerts its effects. In this study, we experimentally characterized the profile of the preferential interaction potential of TMAO with proteins, a thermodynamic key to understanding the effects of TMAO on protein processes and the distinction of TMAO among osmolytes. TMAO is thus found to be highly preferentially excluded from most types of protein surface, which explains why TMAO is a strong globular protein stabilizer and identifies the dominant stabilizing factor as the unfavorable interaction of TMAO with the hydrophobic surface exposed upon unfolding. We dissected the mechanism of the counteracting effects of TMAO and urea: the contrary feature of the interaction profiles of the two solutes maximizes the possibility for them to offset each other's perturbing effect on protein processes. The interaction profile also predicts that TMAO promotes aggregation of amyloidogenic intrinsically disordered peptide, as demonstrated here in Aβ42, and that TMAO has a strong potential to impact protein processes in the absence of stressors. Our data suggest that although TMAO is an evolutionally selected chemical chaperone for some organisms or organs, its compatibility in vivo is conditional and determined by its interaction profile with biopolymers and the nature of the essential biopolymer processes. Our thermodynamic framework plus the TMAO-protein interaction profile provides a basis for exploring the broad biological significance of TMAO, including its pathological impact in the absence of stressors. We argue for the general importance of controlling in vivo background solutes and the pathological significance of a control failure.
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Affiliation(s)
- Jiang Hong
- School of Life Sciences, Shanghai University, Shanghai, China; Experimental Center for Life Sciences, School of Life Sciences, Shanghai University, Shanghai, China.
| | - Shangqin Xiong
- School of Life Sciences, Shanghai University, Shanghai, China
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37
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Natalello A, Santambrogio C, Grandori R. Are Charge-State Distributions a Reliable Tool Describing Molecular Ensembles of Intrinsically Disordered Proteins by Native MS? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:21-28. [PMID: 27730522 DOI: 10.1007/s13361-016-1490-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/13/2016] [Accepted: 08/22/2016] [Indexed: 06/06/2023]
Abstract
Native mass spectrometry (MS) has become a central tool of structural proteomics, but its applicability to the peculiar class of intrinsically disordered proteins (IDPs) is still object of debate. IDPs lack an ordered tridimensional structure and are characterized by high conformational plasticity. Since they represent valuable targets for cancer and neurodegeneration research, there is an urgent need of methodological advances for description of the conformational ensembles populated by these proteins in solution. However, structural rearrangements during electrospray-ionization (ESI) or after the transfer to the gas phase could affect data obtained by native ESI-MS. In particular, charge-state distributions (CSDs) are affected by protein conformation inside ESI droplets, while ion mobility (IM) reflects protein conformation in the gas phase. This review focuses on the available evidence relating IDP solution ensembles with CSDs, trying to summarize cases of apparent consistency or discrepancy. The protein-specificity of ionization patterns and their responses to ligands and buffer conditions suggests that CSDs are imprinted to protein structural features also in the case of IDPs. Nevertheless, it seems that these proteins are more easily affected by electrospray conditions, leading in some cases to rearrangements of the conformational ensembles. Graphical Abstract ᅟ.
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Affiliation(s)
- Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.
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38
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Barnett GV, Razinkov VI, Kerwin BA, Blake S, Qi W, Curtis RA, Roberts CJ. Osmolyte Effects on Monoclonal Antibody Stability and Concentration-Dependent Protein Interactions with Water and Common Osmolytes. J Phys Chem B 2016; 120:3318-30. [DOI: 10.1021/acs.jpcb.6b00621] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gregory V. Barnett
- Department
of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | | | - Bruce A. Kerwin
- Drug
Product Development, Amgen Inc., Seattle, Washington 98119, United States
| | - Steven Blake
- Malvern Biosciences
Inc., Columbia, Maryland 21046, United States
| | - Wei Qi
- Malvern Biosciences
Inc., Columbia, Maryland 21046, United States
| | - Robin A. Curtis
- School
of Chemical Engineering and Analytical Science, The University of Manchester, Manchester, U.K
| | - Christopher J. Roberts
- Department
of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
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39
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Li J, Santambrogio C, Brocca S, Rossetti G, Carloni P, Grandori R. Conformational effects in protein electrospray-ionization mass spectrometry. MASS SPECTROMETRY REVIEWS 2016; 35:111-22. [PMID: 25952139 DOI: 10.1002/mas.21465] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/14/2015] [Indexed: 05/11/2023]
Abstract
Electrospray-ionization mass spectrometry (ESI-MS) is a key tool of structural biology, complementing the information delivered by conventional biochemical and biophysical methods. Yet, the mechanism behind the conformational effects in protein ESI-MS is an object of debate. Two parameters-solvent-accessible surface area (As) and apparent gas-phase basicity (GBapp)-are thought to play a role in controlling the extent of protein ionization during ESI-MS experiments. This review focuses on recent experimental and theoretical investigations concerning the influence of these parameters on ESI-MS results and the structural information that can be derived. The available evidence supports a unified model for the ionization mechanism of folded and unfolded proteins. These data indicate that charge-state distribution (CSD) analysis can provide valuable structural information on normally folded, as well as disordered structures.
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Affiliation(s)
- Jinyu Li
- Computational Biophysics, German Research School for Simulation Sciences, and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, 52057 Aachen, Germany
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Giulia Rossetti
- Computational Biophysics, German Research School for Simulation Sciences, and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany
- Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Paolo Carloni
- Computational Biophysics, German Research School for Simulation Sciences, and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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40
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Estrada J, Echenique P, Sancho J. Predicting stabilizing mutations in proteins using Poisson-Boltzmann based models: study of unfolded state ensemble models and development of a successful binary classifier based on residue interaction energies. Phys Chem Chem Phys 2015; 17:31044-54. [PMID: 26530878 DOI: 10.1039/c5cp04348d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In many cases the stability of a protein has to be increased to permit its biotechnological use. Rational methods of protein stabilization based on optimizing electrostatic interactions have provided some fine successful predictions. However, the precise calculation of stabilization energies remains challenging, one reason being that the electrostatic effects on the unfolded state are often neglected. We have explored here the feasibility of incorporating Poisson-Boltzmann model electrostatic calculations performed on representations of the unfolded state as large ensembles of geometrically optimized conformations calculated using the ProtSA server. Using a data set of 80 electrostatic mutations experimentally tested in two-state proteins, the predictive performance of several such models has been compared to that of a simple one that considers an unfolded structure of non-interacting residues. The unfolded ensemble models, while showing correlation between the predicted stabilization values and the experimental ones, are worse than the simple model, suggesting that the ensembles do not capture well the energetics of the unfolded state. A more attainable goal is classifying potential mutations as either stabilizing or non-stabilizing, rather than accurately calculating their stabilization energies. To implement a fast classification method that can assist in selecting stabilizing mutations, we have used a much simpler electrostatic model based only on the native structure and have determined its precision using different stabilizing energy thresholds. The binary classifier developed finds 7 true stabilizing mutants out of every 10 proposed candidates and can be used as a robust tool to propose stabilizing mutations.
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Affiliation(s)
- Jorge Estrada
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain. and Biocomputation and Complex Systems Physics Institute (BIFI), Joint Unit BIFI-IQFR (CSIC), Mariano Esquillor s/n, Edificio I+D, 50018, Zaragoza, Spain
| | - Pablo Echenique
- Biocomputation and Complex Systems Physics Institute (BIFI), Joint Unit BIFI-IQFR (CSIC), Mariano Esquillor s/n, Edificio I+D, 50018, Zaragoza, Spain and Instituto de Química Física "Rocasolano", CSIC, Serrano 119, 28006, Madrid, Spain
| | - Javier Sancho
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain. and Biocomputation and Complex Systems Physics Institute (BIFI), Joint Unit BIFI-IQFR (CSIC), Mariano Esquillor s/n, Edificio I+D, 50018, Zaragoza, Spain
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41
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Trollope KM, Görgens JF, Volschenk H. Semirational Directed Evolution of Loop Regions in Aspergillus japonicus β-Fructofuranosidase for Improved Fructooligosaccharide Production. Appl Environ Microbiol 2015; 81:7319-29. [PMID: 26253664 PMCID: PMC4579456 DOI: 10.1128/aem.02134-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/04/2015] [Indexed: 11/20/2022] Open
Abstract
The Aspergillus japonicus β-fructofuranosidase catalyzes the industrially important biotransformation of sucrose to fructooligosaccharides. Operating at high substrate loading and temperatures between 50 and 60°C, the enzyme activity is negatively influenced by glucose product inhibition and thermal instability. To address these limitations, the solvent-exposed loop regions of the β-fructofuranosidase were engineered using a combined crystal structure- and evolutionary-guided approach. This semirational approach yielded a functionally enriched first-round library of 36 single-amino-acid-substitution variants with 58% retaining activity, and of these, 71% displayed improved activities compared to the parent. The substitutions yielding the five most improved variants subsequently were exhaustively combined and evaluated. A four-substitution combination variant was identified as the most improved and reduced the time to completion of an efficient industrial-like reaction by 22%. Characterization of the top five combination variants by isothermal denaturation assays indicated that these variants displayed improved thermostability, with the most thermostable variant displaying a 5.7°C increased melting temperature. The variants displayed uniquely altered, concentration-dependent substrate and product binding as determined by differential scanning fluorimetry. The altered catalytic activity was evidenced by increased specific activities of all five variants, with the most improved variant doubling that of the parent. Variant homology modeling and computational analyses were used to rationalize the effects of amino acid changes lacking direct interaction with substrates. Data indicated that targeting substitutions to loop regions resulted in improved enzyme thermostability, specific activity, and relief from product inhibition.
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Affiliation(s)
- K M Trollope
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - J F Görgens
- Department of Process Engineering, Stellenbosch University, Stellenbosch, South Africa
| | - H Volschenk
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
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42
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Castillo MC, Lozano-Juste J, González-Guzmán M, Rodriguez L, Rodriguez PL, León J. Inactivation of PYR/PYL/RCAR ABA receptors by tyrosine nitration may enable rapid inhibition of ABA signaling by nitric oxide in plants. Sci Signal 2015; 8:ra89. [PMID: 26329583 DOI: 10.1126/scisignal.aaa7981] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Abscisic acid (ABA) is a phytohormone that inhibits growth and enhances adaptation to stress in plants. ABA perception and signaling rely on its binding to receptors of the pyrabactin resistance1/PYR1-like/regulatory components of ABA receptors (PYR/PYL/RCAR) family, the subsequent inhibition of clade A type 2C protein phosphatases (PP2Cs), and the phosphorylation of ion channels and transcription factors by protein kinases of the SnRK2 family. Nitric oxide (NO) may inhibit ABA signaling because NO-deficient plants are hypersensitive to ABA. Regulation by NO often involves posttranslational modification of proteins. Mass spectrometry analysis of ABA receptors expressed in plants and recombinant receptors modified in vitro revealed that the receptors were nitrated at tyrosine residues and S-nitrosylated at cysteine residues. In an in vitro ABA-induced, PP2C inhibition assay, tyrosine nitration reduced receptor activity, whereas S-nitrosylated receptors were fully capable of ABA-induced inhibition of the phosphatase. PYR/PYL/RCAR proteins with nitrated tyrosine, which is an irreversible covalent modification, were polyubiquitylated and underwent proteasome-mediated degradation. We propose that tyrosine nitration, which requires NO and superoxide anions, is a rapid mechanism by which NO limits ABA signaling under conditions in which NO and reactive oxygen species are both produced.
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Affiliation(s)
- Mari-Cruz Castillo
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia), CPI Edificio 8E, Avda. Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Jorge Lozano-Juste
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia), CPI Edificio 8E, Avda. Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Miguel González-Guzmán
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia), CPI Edificio 8E, Avda. Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Lesia Rodriguez
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia), CPI Edificio 8E, Avda. Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Pedro L Rodriguez
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia), CPI Edificio 8E, Avda. Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - José León
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia), CPI Edificio 8E, Avda. Ingeniero Fausto Elio s/n, 46022 Valencia, Spain.
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43
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Nakamura T, Asai S, Nakata K, Kunimoto K, Oguri M, Ishikawa K. Thermostability and reactivity in organic solvent of O-phospho-l-serine sulfhydrylase from hyperthermophilic archaeon Aeropyrum pernix K1. Biosci Biotechnol Biochem 2015; 79:1280-6. [DOI: 10.1080/09168451.2015.1020753] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Abstract
O-phospho-l-serine sulfhydrylase (OPSS) from archaeon Aeropyrum pernix K1 is able to synthesize l-cysteine even at 80 °C. In this article, we compared thermal stability and reactivity in organic solvent of OPSS with those of O-acetyl-l-serine sulfhydrylase B (OASS-B) from Escherichia coli. As a result, the thermostability of OPSS was much higher than that of OASS-B. Moreover, the activity of OPSS increased in the reaction mixture containing the organic solvent, such as N, N′-dimethyl formamide and 1,4-dioxane, whereas that of OASS-B gradually decreased as the content of organic solvent increased. From the crystal structural analysis, the intramolecular electrostatic interactions of N-terminal domain in OPSS seemed to be correlated with the tolerance of OPSS to high temperature and organic solvent. These results indicate that OPSS is more superior to OASS-B for the industrial production of l-cysteine and unnatural amino acids that are useful pharmaceuticals in the presence of organic solvent.
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Affiliation(s)
- Takashi Nakamura
- Faculty of Bioscience, Laboratory of Molecular Biochemistry, Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Shinji Asai
- Faculty of Bioscience, Laboratory of Molecular Biochemistry, Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Kaori Nakata
- Faculty of Bioscience, Laboratory of Molecular Biochemistry, Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Kohei Kunimoto
- Faculty of Bioscience, Laboratory of Molecular Biochemistry, Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Masateru Oguri
- Faculty of Bioscience, Laboratory of Molecular Biochemistry, Nagahama Institute of Bio-Science and Technology, Nagahama, Japan
| | - Kazuhiko Ishikawa
- National Institute of Advanced Industrial Science and Technology (AIST), Osaka, Japan
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44
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Huang J, Jones BJ, Kazlauskas RJ. Stabilization of an α/β-Hydrolase by Introducing Proline Residues: Salicylic Acid Binding Protein 2 from Tobacco. Biochemistry 2015; 54:4330-41. [PMID: 26110207 PMCID: PMC4557962 DOI: 10.1021/acs.biochem.5b00333] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
α/β-Hydrolases are important enzymes for biocatalysis, but their stability often limits their application. We investigated a plant esterase, salicylic acid binding protein 2 (SABP2), as a model α/β-hydrolase. SABP2 shows typical stability to urea (unfolding free energy 6.9 ± 1.5 kcal/mol) and to heat inactivation (T1/2 15min 49.2 ± 0.5 °C). Denaturation in urea occurs in two steps, but heat inactivation occurs in a single step. The first unfolding step in urea eliminates catalytic activity. Surprisingly, we found that the first unfolding likely corresponds to the unfolding of the larger catalytic domain. Replacing selected amino acid residues with proline stabilized SABP2. Proline restricts the flexibility of the unfolded protein, thereby shifting the equilibrium toward the folded conformation. Seven locations for proline substitution were chosen either by amino acid sequence alignment with a more stable homologue or by targeting flexible regions in SABP2. Introducing proline in the catalytic domain stabilized SABP2 to the first unfolding in urea for three of five cases: L46P (+0.2 M urea), S70P (+0.1), and E215P (+0.9). Introducing proline in the cap domain did not stabilize SABP2 (two of two cases), supporting the assignment that the first unfolding corresponds to the catalytic domain. Proline substitutions in both domains stabilized SABP2 to heat inactivation: L46P (ΔT1/2 15min = +6.4 °C), S70P (+5.4), S115P (+1.8), S141P (+4.9), and E215P (+4.2). Combining substitutions did not further increase the stability to urea denaturation, but dramatically increased resistance to heat inactivation: L46P−S70P ΔT1/2 15min = +25.7 °C. This straightforward proline substitution approach may also stabilize other α/β-hydrolases.
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Affiliation(s)
- Jun Huang
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul MN 55108 USA
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, PR China
| | - Bryan J. Jones
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul MN 55108 USA
| | - Romas J. Kazlauskas
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul MN 55108 USA
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45
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Hong J, Gierasch LM, Liu Z. Its preferential interactions with biopolymers account for diverse observed effects of trehalose. Biophys J 2015; 109:144-53. [PMID: 26153711 PMCID: PMC4572414 DOI: 10.1016/j.bpj.2015.05.037] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/22/2015] [Accepted: 05/28/2015] [Indexed: 10/23/2022] Open
Abstract
Biopolymer homeostasis underlies the health of organisms, and protective osmolytes have emerged as one strategy used by Nature to preserve biopolymer homeostasis. However, a great deal remains unknown about the mechanism of action of osmolytes. Trehalose, as a prominent example, stabilizes proteins against denaturation by extreme temperature and denaturants, preserves membrane integrity upon freezing or in dry conditions, inhibits polyQ-mediated protein aggregation, and suppresses the aggregation of denatured proteins. The underlying thermodynamic mechanisms of such diverse effects of trehalose remain unclear or controversial. In this study, we applied the surface-additive method developed in the Record laboratory to attack this issue. We characterized the key features of trehalose-biopolymer preferential interactions and found that trehalose has strong unfavorable interactions with aliphatic carbon and significant favorable interactions with amide/anionic oxygen. This dissection has allowed us to elucidate the diverse effects of trehalose and to identify the crucial functional group(s) responsible for its effects. With (semi)quantitative thermodynamic analysis, we discovered that 1) the unfavorable interaction of trehalose with hydrophobic surfaces is the dominant factor in its effect on protein stability, 2) the favorable interaction of trehalose with polar amides enables it to inhibit polyQ-mediated protein aggregation and the aggregation of denatured protein in general, and 3) the favorable interaction of trehalose with phosphate oxygens, together with its unfavorable interaction with aliphatic carbons, enables trehalose to preserve membrane integrity in aqueous solution. These results provide a basis for a full understanding of the role of trehalose in biopolymer homeostasis and the reason behind its evolutionary selection as an osmolyte, as well as for a better application of trehalose as a chemical chaperone.
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Affiliation(s)
- Jiang Hong
- School of Life Science, Shanghai University, Shanghai, China.
| | - Lila M Gierasch
- Department of Biochemistry and Molecular Biology and Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts
| | - Zhicheng Liu
- School of Life Science, Shanghai University, Shanghai, China
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46
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Sapir L, Harries D. Macromolecular Stabilization by Excluded Cosolutes: Mean Field Theory of Crowded Solutions. J Chem Theory Comput 2015; 11:3478-90. [DOI: 10.1021/acs.jctc.5b00258] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Liel Sapir
- Institute of Chemistry and
The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Daniel Harries
- Institute of Chemistry and
The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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47
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Lamazares E, Clemente I, Bueno M, Velázquez-Campoy A, Sancho J. Rational stabilization of complex proteins: a divide and combine approach. Sci Rep 2015; 5:9129. [PMID: 25774740 PMCID: PMC4360737 DOI: 10.1038/srep09129] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 02/19/2015] [Indexed: 11/09/2022] Open
Abstract
Increasing the thermostability of proteins is often crucial for their successful use as analytic, synthetic or therapeutic tools. Most rational thermostabilization strategies were developed on small two-state proteins and, unsurprisingly, they tend to fail when applied to the much more abundant, larger, non-fully cooperative proteins. We show that the key to stabilize the latter is to know the regions of lower stability. To prove it, we have engineered apoflavodoxin, a non-fully cooperative protein on which previous thermostabilizing attempts had failed. We use a step-wise combination of structure-based, rationally-designed, stabilizing mutations confined to the less stable structural region, and obtain variants that, according to their van't Hoff to calorimetric enthalpy ratios, exhibit fully-cooperative thermal unfolding with a melting temperature of 75°C, 32 degrees above the lower melting temperature of the non-cooperative wild type protein. The ideas introduced here may also be useful for the thermostabilization of complex proteins through formulation or using specific stabilizing ligands (e.g. pharmacological chaperones).
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Affiliation(s)
- Emilio Lamazares
- 1] Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR (CSIC), Universidad de Zaragoza, Zaragoza, Spain [2] Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Isabel Clemente
- 1] Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR (CSIC), Universidad de Zaragoza, Zaragoza, Spain [2] Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Marta Bueno
- 1] Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR (CSIC), Universidad de Zaragoza, Zaragoza, Spain [2] Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- 1] Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR (CSIC), Universidad de Zaragoza, Zaragoza, Spain [2] Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain [3] Fundación ARAID, Gobierno de Aragón, Spain
| | - Javier Sancho
- 1] Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR (CSIC), Universidad de Zaragoza, Zaragoza, Spain [2] Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
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48
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Sapir L, Harries D. Is the depletion force entropic? Molecular crowding beyond steric interactions. Curr Opin Colloid Interface Sci 2015. [DOI: 10.1016/j.cocis.2014.12.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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49
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Topham CM, Smith JC. Tri-peptide reference structures for the calculation of relative solvent accessible surface area in protein amino acid residues. Comput Biol Chem 2014; 54:33-43. [PMID: 25544680 DOI: 10.1016/j.compbiolchem.2014.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 11/23/2014] [Accepted: 11/30/2014] [Indexed: 10/24/2022]
Abstract
Relative amino acid residue solvent accessibility values allow the quantitative comparison of atomic solvent-accessible surface areas in different residue types and physical environments in proteins and in protein structural alignments. Geometry-optimised tri-peptide structures in extended solvent-exposed reference conformations have been obtained for 43 amino acid residue types at a high level of quantum chemical theory. Significant increases in side-chain solvent accessibility, offset by reductions in main-chain atom solvent exposure, were observed for standard residue types in partially geometry-optimised structures when compared to non-minimised models built from identical sets of proper dihedral angles abstracted from the literature. Optimisation of proper dihedral angles led most notably to marked increases of up to 54% in proline main-chain atom solvent accessibility compared to literature values. Similar effects were observed for fully-optimised tri-peptides in implicit solvent. The relief of internal strain energy was associated with systematic variation in N, C(α) and C(β) atom solvent accessibility across all standard residue types. The results underline the importance of optimisation of 'hard' degrees of freedom (bond lengths and valence bond angles) and improper dihedral angle values from force field or other context-independent reference values, and impact on the use of standardised fixed internal co-ordinate geometry in sampling approaches to the determination of absolute values of protein amino acid residue solvent accessibility. Quantum chemical methods provide a useful and accurate alternative to molecular mechanics methods to perform energy minimisation of peptides containing non-standard (chemically modified) amino acid residues frequently present in experimental protein structure data sets, for which force field parameters may not be available. Reference tri-peptide atomic co-ordinate sets including hydrogen atoms are made freely available.
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Affiliation(s)
- Christopher M Topham
- Molecular Forces Consulting, 40 Rue Boyssonne, Toulouse 31400, France; Computational Molecular Biophysics, IWR der Universität Heidelberg, Im Neuenheimer Feld 368, Heidelberg D-69120, Germany; University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, P.O. Box 2008, Oak Ridge, TN 37831-6309, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996, USA.
| | - Jeremy C Smith
- Computational Molecular Biophysics, IWR der Universität Heidelberg, Im Neuenheimer Feld 368, Heidelberg D-69120, Germany; University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, P.O. Box 2008, Oak Ridge, TN 37831-6309, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996, USA
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50
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Role of cavities and hydration in the pressure unfolding of T4 lysozyme. Proc Natl Acad Sci U S A 2014; 111:13846-51. [PMID: 25201963 DOI: 10.1073/pnas.1410655111] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is well known that high hydrostatic pressures can induce the unfolding of proteins. The physical underpinnings of this phenomenon have been investigated extensively but remain controversial. Changes in solvation energetics have been commonly proposed as a driving force for pressure-induced unfolding. Recently, the elimination of void volumes in the native folded state has been argued to be the principal determinant. Here we use the cavity-containing L99A mutant of T4 lysozyme to examine the pressure-induced destabilization of this multidomain protein by using solution NMR spectroscopy. The cavity-containing C-terminal domain completely unfolds at moderate pressures, whereas the N-terminal domain remains largely structured to pressures as high as 2.5 kbar. The sensitivity to pressure is suppressed by the binding of benzene to the hydrophobic cavity. These results contrast to the pseudo-WT protein, which has a residual cavity volume very similar to that of the L99A-benzene complex but shows extensive subglobal reorganizations with pressure. Encapsulation of the L99A mutant in the aqueous nanoscale core of a reverse micelle is used to examine the hydration of the hydrophobic cavity. The confined space effect of encapsulation suppresses the pressure-induced unfolding transition and allows observation of the filling of the cavity with water at elevated pressures. This indicates that hydration of the hydrophobic cavity is more energetically unfavorable than global unfolding. Overall, these observations point to a range of cooperativity and energetics within the T4 lysozyme molecule and illuminate the fact that small changes in physical parameters can significantly alter the pressure sensitivity of proteins.
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