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Hajdu D, Huber A, Czajlik A, Tóth L, Kele Z, Kocsubé S, Fizil Á, Marx F, Galgóczy L, Batta G. Solution structure and novel insights into phylogeny and mode of action of the Neosartorya (Aspergillus) fischeri antifungal protein (NFAP). Int J Biol Macromol 2019; 129:511-522. [PMID: 30738898 DOI: 10.1016/j.ijbiomac.2019.02.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/22/2019] [Accepted: 02/03/2019] [Indexed: 01/02/2023]
Abstract
Small, cysteine-rich and cationic antifungal proteins from natural sources are promising candidates for the development of novel treatment strategies to prevent and combat infections caused by drug-resistant fungi. However, limited information about their structure and antifungal mechanism hampers their future applications. In the present study, we determined the solution structure, dynamics and associated solvent areas of the Neosartorya (Aspergillus) fischeri antifungal protein NFAP. Genome mining within the genus revealed the presence of orthologous genes in N. fischeri and Neosartorya spathulata, and genes encoding closely related proteins can be found in Penicillium brasiliensis and Penicillium oxalicum. We show that the tertiary structure of these putative proteins can be resolved using the structure of NFAP as reliable template for in silico prediction. Localization studies with fluorescence-labelled protein pointed at an energy-dependent uptake mechanism of NFAP in the sensitive model fungus Neurospora crassa and subsequent cytoplasmic localization coincided with cell-death induction. The presented results contribute to a better understanding of the structure/function relationship of NFAP and related proteins and pave the way towards future antifungal drug development.
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Affiliation(s)
- Dorottya Hajdu
- Department of Organic Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Anna Huber
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - András Czajlik
- Department of Organic Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Liliána Tóth
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary; Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Zoltán Kele
- Department of Medical Chemistry, Faculty of Medicine, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
| | - Sándor Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Ádám Fizil
- Department of Organic Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Florentine Marx
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - László Galgóczy
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria; Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary; Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - Gyula Batta
- Department of Organic Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; Department of Organic Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary.
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2
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Neira JL, Cámara-Artigas A. Trifluoroethanol-induced conformational transition of the C-terminal sterile alpha motif (SAM) of human p73. Arch Biochem Biophys 2017; 619:1-9. [DOI: 10.1016/j.abb.2017.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 02/16/2017] [Accepted: 02/17/2017] [Indexed: 01/03/2023]
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3
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Neira JL, Hornos F, Bacarizo J, Cámara-Artigás A, Gómez J. The Monomeric Species of the Regulatory Domain of Tyrosine Hydroxylase Has a Low Conformational Stability. Biochemistry 2016; 55:3418-31. [PMID: 27224548 DOI: 10.1021/acs.biochem.6b00135] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tyrosine hydroxylase (TyrH) catalyzes the hydroxylation of tyrosine to form 3,4-dihydroxyphenylalanine, the first step in the synthesis of catecholamine neurotransmitters. The protein contains a 159-residue regulatory domain (RD) at its N-terminus that forms dimers in solution; the N-terminal region of RDTyrH (residues 1-71) is absent in the solution structure of the domain. We have characterized the conformational stability of two species of RDTyrH (one containing the N-terminal region and another lacking the first 64 residues) to clarify how that N-terminal region modulates the conformational stability of RD. Under the conditions used in this study, the RD species lacking the first 64 residues is a monomer at pH 7.0, with a small conformational stability at 25 °C (4.7 ± 0.8 kcal mol(-1)). On the other hand, the entire RDTyrH is dimeric at physiological pH, with an estimated dissociation constant of 1.6 μM, as determined by zonal gel filtration chromatography; dimer dissociation was spectroscopically silent to circular dichroism but not to fluoresecence. Both RD species were disordered below physiological pH, but the acquisition of secondary native-like structure occurs at pHs lower than those measured for the attainment of tertiary native- and compactness-like arrangements.
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Affiliation(s)
- José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández , 03202 Elche (Alicante), Spain.,Biocomputation and Complex Systems Physics Institute , 50009 Zaragoza, Spain
| | - Felipe Hornos
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández , 03202 Elche (Alicante), Spain
| | - Julio Bacarizo
- Department of Physical Chemistry, Biochemistry and Inorganic Chemistry, University of Almería , Agrifood Campus of International Excellence (ceiA3), Almería, Spain
| | - Ana Cámara-Artigás
- Department of Physical Chemistry, Biochemistry and Inorganic Chemistry, University of Almería , Agrifood Campus of International Excellence (ceiA3), Almería, Spain
| | - Javier Gómez
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández , 03202 Elche (Alicante), Spain
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4
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Abstract
The HIV genome materials are encaged by a proteinaceous shell called the capsid, constructed from ∼1000-1500 copies of the capsid proteins. Because its stability and integrity are critical to the normal life cycle and infectivity of the virus, the HIV capsid is a promising antiviral drug target. In this paper, we review the studies shaping our understanding of the structure and dynamics of the capsid proteins and various forms of their assemblies, as well as the assembly mechanism.
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Affiliation(s)
- Bo Chen
- Department of Physics, University of Central Florida , Orlando, Florida 32816, United States
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5
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Affiliation(s)
- Fangqiang Zhu
- Department
of Physics, Indiana University - Purdue University, Indianapolis, Indiana 46202, United States
| | - Bo Chen
- Department
of Physics, University of Central Florida, Orlando, Florida 32816, United States
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6
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Abstract
UNLABELLED During virion maturation, the Rous sarcoma virus (RSV) capsid protein is cleaved from the Gag protein as the proteolytic intermediate CA-SP. Further trimming at two C-terminal sites removes the spacer peptide (SP), producing the mature capsid proteins CA and CA-S. Abundant genetic and structural evidence shows that the SP plays a critical role in stabilizing hexameric Gag interactions that form immature particles. Freeing of CA-SP from Gag breaks immature interfaces and initiates the formation of mature capsids. The transient persistence of CA-SP in maturing virions and the identification of second-site mutations in SP that restore infectivity to maturation-defective mutant viruses led us to hypothesize that SP may play an important role in promoting the assembly of mature capsids. This study presents a biophysical and biochemical characterization of CA-SP and its assembly behavior. Our results confirm cryo-electron microscopy (cryo-EM) structures reported previously by Keller et al. (J. Virol. 87:13655-13664, 2013, doi:10.1128/JVI.01408-13) showing that monomeric CA-SP is fully capable of assembling into capsid-like structures identical to those formed by CA. Furthermore, SP confers aggressive assembly kinetics, which is suggestive of higher-affinity CA-SP interactions than observed with either of the mature capsid proteins. This aggressive assembly is largely independent of the SP amino acid sequence, but the formation of well-ordered particles is sensitive to the presence of the N-terminal β-hairpin. Additionally, CA-SP can nucleate the assembly of CA and CA-S. These results suggest a model in which CA-SP, once separated from the Gag lattice, can actively promote the interactions that form mature capsids and provide a nucleation point for mature capsid assembly. IMPORTANCE The spacer peptide is a documented target for antiretroviral therapy. This study examines the biochemical and biophysical properties of CA-SP, an intermediate form of the retrovirus capsid protein. The results demonstrate a previously unrecognized activity of SP in promoting capsid assembly during maturation.
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7
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Bayro MJ, Chen B, Yau WM, Tycko R. Site-specific structural variations accompanying tubular assembly of the HIV-1 capsid protein. J Mol Biol 2013; 426:1109-27. [PMID: 24370930 DOI: 10.1016/j.jmb.2013.12.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/16/2013] [Accepted: 12/17/2013] [Indexed: 10/25/2022]
Abstract
The 231-residue capsid (CA) protein of human immunodeficiency virus type 1 (HIV-1) spontaneously self-assembles into tubes with a hexagonal lattice that is believed to mimic the surface lattice of conical capsid cores within intact virions. We report the results of solid-state nuclear magnetic resonance (NMR) measurements on HIV-1 CA tubes that provide new information regarding changes in molecular structure that accompany CA self-assembly, local dynamics within CA tubes, and possible mechanisms for the generation of lattice curvature. This information is contained in site-specific assignments of signals in two- and three-dimensional solid-state NMR spectra, conformation-dependent (15)N and (13)C NMR chemical shifts, detection of highly dynamic residues under solution NMR conditions, measurements of local variations in transverse spin relaxation rates of amide (1)H nuclei, and quantitative measurements of site-specific (15)N-(15)N dipole-dipole couplings. Our data show that most of the CA sequence is conformationally ordered and relatively rigid in tubular assemblies and that structures of the N-terminal domain (NTD) and the C-terminal domain (CTD) observed in solution are largely retained. However, specific segments, including the N-terminal β-hairpin, the cyclophilin A binding loop, the inter-domain linker, segments involved in intermolecular NTD-CTD interactions, and the C-terminal tail, have substantial static or dynamical disorder in tubular assemblies. Other segments, including the 310-helical segment in CTD, undergo clear conformational changes. Structural variations associated with curvature of the CA lattice appear to be localized in the inter-domain linker and intermolecular NTD-CTD interface, while structural variations within NTD hexamers, around local 3-fold symmetry axes, and in CTD-CTD dimerization interfaces are less significant.
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Affiliation(s)
- Marvin J Bayro
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Bo Chen
- Department of Physics, University of Central Florida, Orlando, FL 32816, USA
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
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8
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NMR as a tool to identify and characterize protein folding intermediates. Arch Biochem Biophys 2013; 531:90-9. [DOI: 10.1016/j.abb.2012.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/03/2012] [Accepted: 09/04/2012] [Indexed: 11/20/2022]
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9
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Simulations of HIV capsid protein dimerization reveal the effect of chemistry and topography on the mechanism of hydrophobic protein association. Biophys J 2013; 103:1363-9. [PMID: 22995509 DOI: 10.1016/j.bpj.2012.08.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 07/31/2012] [Accepted: 08/06/2012] [Indexed: 01/17/2023] Open
Abstract
Recent work has shown that the hydrophobic protein surfaces in aqueous solution sit near a drying transition. The tendency for these surfaces to expel water from their vicinity leads to self-assembly of macromolecular complexes. In this article, we show with a realistic model for a biologically pertinent system how this phenomenon appears at the molecular level. We focus on the association of the C-terminal domain (CA-C) of the human immunodeficiency virus capsid protein. By combining all-atom simulations with specialized sampling techniques, we measure the water density distribution during the approach of two CA-C proteins as a function of separation and amino acid sequence in the interfacial region. The simulations demonstrate that CA-C protein-protein interactions sit at the edge of a dewetting transition and that this mesoscopic manifestation of the underlying liquid-vapor phase transition can be readily manipulated by biology or protein engineering to significantly affect association behavior. Although the wild-type protein remains wet until contact, we identify a set of in silico mutations, in which three hydrophilic amino acids are replaced with nonpolar residues, that leads to dewetting before association. The existence of dewetting depends on the size and relative locations of substituted residues separated by nanometer length scales, indicating long-range cooperativity and a sensitivity to surface topography. These observations identify important details that are missing from descriptions of protein association based on buried hydrophobic surface area.
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10
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Bocanegra R, Rodríguez-Huete A, Fuertes MÁ, del Álamo M, Mateu MG. Molecular recognition in the human immunodeficiency virus capsid and antiviral design. Virus Res 2012; 169:388-410. [DOI: 10.1016/j.virusres.2012.06.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 06/11/2012] [Accepted: 06/12/2012] [Indexed: 01/07/2023]
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11
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Byeon IJL, Hou G, Han Y, Suiter CL, Ahn J, Jung J, Byeon CH, Gronenborn AM, Polenova T. Motions on the millisecond time scale and multiple conformations of HIV-1 capsid protein: implications for structural polymorphism of CA assemblies. J Am Chem Soc 2012; 134:6455-66. [PMID: 22428579 PMCID: PMC3325613 DOI: 10.1021/ja300937v] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The capsid protein (CA) of human immunodeficiency virus 1 (HIV-1) assembles into a cone-like structure that encloses the viral RNA genome. Interestingly, significant heterogeneity in shape and organization of capsids can be observed in mature HIV-1 virions. In vitro, CA also exhibits structural polymorphism and can assemble into various morphologies, such as cones, tubes, and spheres. Many intermolecular contacts that are critical for CA assembly are formed by its C-terminal domain (CTD), a dimerization domain, which was found to adopt different orientations in several X-ray and NMR structures of the CTD dimer and full-length CA proteins. Tyr145 (Y145), residue two in our CTD construct used for NMR structure determination, but not present in the crystallographic constructs, was found to be crucial for infectivity and engaged in numerous interactions at the CTD dimer interface. Here we investigate the origin of CA structural plasticity using solid-state NMR and solution NMR spectroscopy. In the solid state, the hinge region connecting the NTD and CTD is flexible on the millisecond time scale, as evidenced by the backbone motions of Y145 in CA conical assemblies and in two CTD constructs (137-231 and 142-231), allowing the protein to access multiple conformations essential for pleimorphic capsid assemblies. In solution, the CTD dimer exists as two major conformers, whose relative populations differ for the different CTD constructs. In the longer CTD (144-231) construct that contains the hinge region between the NTD and CTD, the populations of the two conformers are likely determined by the protonation state of the E175 side chain that is located at the dimer interface and within hydrogen-bonding distance of the W184 side chain on the other monomer. At pH 6.5, the major conformer exhibits the same dimer interface as full-length CA. In the short CTD (150-231) construct, no pH-dependent conformational shift is observed. These findings suggest that the presence of structural plasticity at the CTD dimer interface permits pleiotropic HIV-1 capsid assembly, resulting in varied capsid morphologies.
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Affiliation(s)
- In-Ja L. Byeon
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Guangjin Hou
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Yun Han
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Christopher L. Suiter
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Jinwoo Ahn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Jinwon Jung
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Chang-Hyeock Byeon
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Angela M. Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Tatyana Polenova
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, United States
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
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12
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Spadaccini R, Ercole C, Gentile MA, Sanfelice D, Boelens R, Wechselberger R, Batta G, Bernini A, Niccolai N, Picone D. NMR studies on structure and dynamics of the monomeric derivative of BS-RNase: new insights for 3D domain swapping. PLoS One 2012; 7:e29076. [PMID: 22253705 PMCID: PMC3257227 DOI: 10.1371/journal.pone.0029076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 11/20/2011] [Indexed: 11/18/2022] Open
Abstract
Three-dimensional domain swapping is a common phenomenon in pancreatic-like ribonucleases. In the aggregated state, these proteins acquire new biological functions, including selective cytotoxicity against tumour cells. RNase A is able to dislocate both N- and C-termini, but usually this process requires denaturing conditions. In contrast, bovine seminal ribonuclease (BS-RNase), which is a homo-dimeric protein sharing 80% of sequence identity with RNase A, occurs natively as a mixture of swapped and unswapped isoforms. The presence of two disulfides bridging the subunits, indeed, ensures a dimeric structure also to the unswapped molecule. In vitro, the two BS-RNase isoforms interconvert under physiological conditions. Since the tendency to swap is often related to the instability of the monomeric proteins, in these paper we have analysed in detail the stability in solution of the monomeric derivative of BS-RNase (mBS) by a combination of NMR studies and Molecular Dynamics Simulations. The refinement of NMR structure and relaxation data indicate a close similarity with RNase A, without any evidence of aggregation or partial opening. The high compactness of mBS structure is confirmed also by H/D exchange, urea denaturation, and TEMPOL mapping of the protein surface. The present extensive structural and dynamic investigation of (monomeric) mBS did not show any experimental evidence that could explain the known differences in swapping between BS-RNase and RNase A. Hence, we conclude that the swapping in BS-RNase must be influenced by the distinct features of the dimers, suggesting a prominent role for the interchain disulfide bridges.
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Affiliation(s)
- Roberta Spadaccini
- Dipartimento di Scienze Biologiche ed Ambientali, Università del Sannio, Benevento, Italy
| | - Carmine Ercole
- Dipartimento di Chimica, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | - Maria A. Gentile
- Dipartimento di Chimica, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | - Domenico Sanfelice
- Dipartimento di Chimica, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | - Rolf Boelens
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Rainer Wechselberger
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Gyula Batta
- Institute of Chemistry, University of Debrecen, Debrecen, Hungary
| | - Andrea Bernini
- Dipartimento di Biotecnologie, Università degli Studi di Siena, Siena, Italy
| | - Neri Niccolai
- Dipartimento di Biotecnologie, Università degli Studi di Siena, Siena, Italy
| | - Delia Picone
- Dipartimento di Chimica, Università degli Studi di Napoli “Federico II”, Napoli, Italy
- * E-mail:
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Doménech R, Bocanegra R, Velázquez-Campoy A, Neira JL. The isolated major homology region of the HIV capsid protein is mainly unfolded in solution and binds to the intact protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1269-78. [DOI: 10.1016/j.bbapap.2011.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 06/22/2011] [Accepted: 06/23/2011] [Indexed: 12/17/2022]
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14
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López CS, Eccles JD, Still A, Sloan RE, Barklis RL, Tsagli SM, Barklis E. Determinants of the HIV-1 core assembly pathway. Virology 2011; 417:137-46. [PMID: 21676426 DOI: 10.1016/j.virol.2011.05.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Revised: 05/20/2011] [Accepted: 05/21/2011] [Indexed: 11/28/2022]
Abstract
Based on structural information, we have analyzed the mechanism of mature HIV-1 core assembly and the contributions of structural elements to the assembly process. Through the use of several in vitro assembly assay systems, we have examined details of how capsid (CA) protein helix 1, ß-hairpin and cyclophilin loop elements impact assembly-dependent protein interactions, and we present evidence for a contribution of CA helix 6 to the mature assembly-competent conformation of CA. Additional experiments with mixtures of proteins in assembly reactions provide novel analyses of the mature core assembly mechanism. Our results support a model in which initial assembly products serve as scaffolds for further assembly by converting incoming subunits to assembly proficient conformations, while mutant subunits increase the probability of assembly termination events.
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Affiliation(s)
- Claudia S López
- Department of Molecular Microbiology and Immunology and Vollum Institute, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA.
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15
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Brun S, Chaloin L, Gay B, Bernard E, Devaux C, Lionne C, Chazal N, Briant L. Electrostatic repulsion between HIV-1 capsid proteins modulates hexamer plasticity and in vitro assembly. Proteins 2010; 78:2144-56. [PMID: 20455269 DOI: 10.1002/prot.22729] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Capsid protein (CA) is the major component of the human immunodeficiency virus type 1 (HIV-1) core. Three major phosphorylation sites have been identified at positions S(109), S(149) and S(178) in the amino-acid sequence of CA. Here, we investigated the possible consequences of phosphorylation at these sites on the CA hexamer organization and plasticity using in silico approaches. The biological relevance of molecular modeling was then evaluated by analyzing the in vitro assembly properties of bacterially expressed CA bearing S(109)D, S(149)D, or S(178)D substitutions that mimic constitutive phosphorylation at these sites. We found that a constitutive negative charge at position 109 or 149 impaired the capacity of mature CA to assemble in vitro. In vivo, HIV-1 mutants bearing the corresponding mutation showed dramatic alterations of core morphology. At the level of CA hexamer, S(149) phosphorylation generates inter-monomer repulsions, while phosphorylation at position 109 resulted in cleavage of important bonds required for preserving the stability of the edifice. Addition of a negative charge at position 178 allowed efficient assembly of CA into core-like structures in vitro and in vivo and significantly increased CA hexamer stability when modeled in silico. All mutant viruses studied lacked infectivity since they were unable to produce proviral DNA. Altogether our data indicate that negative charges, that mimic phosphorylation, modulate assembling capacity of CA and affect structural properties of CA hexamers and of HIV-1 cores. In the context of the assembled core, phosphorylation at these sites may be considered as an event interfering with core organization and HIV-1 replicative cycle.
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Affiliation(s)
- Sonia Brun
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), Université Montpellier 1, Montpellier, France
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16
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Chen B, Tycko R. Structural and dynamical characterization of tubular HIV-1 capsid protein assemblies by solid state nuclear magnetic resonance and electron microscopy. Protein Sci 2010; 19:716-30. [PMID: 20095046 DOI: 10.1002/pro.348] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The wild-type HIV-1 capsid protein (CA) self-assembles in vitro into tubular structures at high ionic strength. We report solid state nuclear magnetic resonance (NMR) and electron microscopy measurements on these tubular CA assemblies, which are believed to contain a triangular lattice of hexameric CA proteins that is similar or identical to the lattice of capsids in intact HIV-1. Mass-per-length values of CA assemblies determined by dark-field transmission electron microscopy indicate a variety of structures, ranging from single-wall tubes to multiwall tubes that approximate solid rods. Two-dimensional (2D) solid state (13)C--(13)C and (15)N--(13)C NMR spectra of uniformly (15)N,(13)C-labeled CA assemblies are highly congested, as expected for a 25.6 kDa protein in which nearly the entire amino acid sequence is immobilized. Solid state NMR spectra of partially labeled CA assemblies, expressed in 1,3-(13)C(2)-glycerol medium, are better resolved, allowing the identification of individual signals with line widths below 1 ppm. Comparison of crosspeak patterns in the experimental 2D spectra with simulated patterns based on solution NMR chemical shifts of the individual N-terminal (NTD) and C-terminal (CTD) domains indicates that NTD and CTD retain their individual structures upon self-assembly of full-length CA into tubes. 2D (1)H-(13)C NMR spectra of CA assemblies recorded under solution NMR conditions show relatively few signals, primarily from segments that link the alpha-helices of NTD and CTD and from the N- and C-terminal ends. Taken together, the data support the idea that CA assemblies contain a highly ordered 2D protein lattice in which the NTD and CTD structures are retained and largely immobilized.
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Affiliation(s)
- Bo Chen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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Doménech R, Abian O, Bocanegra R, Correa J, Sousa-Herves A, Riguera R, Mateu MG, Fernandez-Megia E, Velázquez-Campoy A, Neira JL. Dendrimers as Potential Inhibitors of the Dimerization of the Capsid Protein of HIV-1. Biomacromolecules 2010; 11:2069-78. [DOI: 10.1021/bm100432x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Rosa Doménech
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain, I+CS (Aragon Health Sciences Institute), CIBERehd, Zaragoza, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain, Departamento de Quimica Orgánica, Facultad de Química, and Unidad de RMN de Biomoléculas Asociada al CSIC, Universidad de Santiago de
| | - Olga Abian
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain, I+CS (Aragon Health Sciences Institute), CIBERehd, Zaragoza, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain, Departamento de Quimica Orgánica, Facultad de Química, and Unidad de RMN de Biomoléculas Asociada al CSIC, Universidad de Santiago de
| | - Rebeca Bocanegra
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain, I+CS (Aragon Health Sciences Institute), CIBERehd, Zaragoza, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain, Departamento de Quimica Orgánica, Facultad de Química, and Unidad de RMN de Biomoléculas Asociada al CSIC, Universidad de Santiago de
| | - Juan Correa
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain, I+CS (Aragon Health Sciences Institute), CIBERehd, Zaragoza, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain, Departamento de Quimica Orgánica, Facultad de Química, and Unidad de RMN de Biomoléculas Asociada al CSIC, Universidad de Santiago de
| | - Ana Sousa-Herves
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain, I+CS (Aragon Health Sciences Institute), CIBERehd, Zaragoza, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain, Departamento de Quimica Orgánica, Facultad de Química, and Unidad de RMN de Biomoléculas Asociada al CSIC, Universidad de Santiago de
| | - Ricardo Riguera
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain, I+CS (Aragon Health Sciences Institute), CIBERehd, Zaragoza, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain, Departamento de Quimica Orgánica, Facultad de Química, and Unidad de RMN de Biomoléculas Asociada al CSIC, Universidad de Santiago de
| | - Mauricio G. Mateu
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain, I+CS (Aragon Health Sciences Institute), CIBERehd, Zaragoza, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain, Departamento de Quimica Orgánica, Facultad de Química, and Unidad de RMN de Biomoléculas Asociada al CSIC, Universidad de Santiago de
| | - Eduardo Fernandez-Megia
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain, I+CS (Aragon Health Sciences Institute), CIBERehd, Zaragoza, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain, Departamento de Quimica Orgánica, Facultad de Química, and Unidad de RMN de Biomoléculas Asociada al CSIC, Universidad de Santiago de
| | - Adrián Velázquez-Campoy
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain, I+CS (Aragon Health Sciences Institute), CIBERehd, Zaragoza, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain, Departamento de Quimica Orgánica, Facultad de Química, and Unidad de RMN de Biomoléculas Asociada al CSIC, Universidad de Santiago de
| | - José L. Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Spain, I+CS (Aragon Health Sciences Institute), CIBERehd, Zaragoza, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain, Departamento de Quimica Orgánica, Facultad de Química, and Unidad de RMN de Biomoléculas Asociada al CSIC, Universidad de Santiago de
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Batista PR, Robert CH, Maréchal JD, Hamida-Rebaï MB, Pascutti PG, Bisch PM, Perahia D. Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis—application to the HIV-1 protease. Phys Chem Chem Phys 2010; 12:2850-9. [DOI: 10.1039/b919148h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mateu MG. The capsid protein of human immunodeficiency virus: intersubunit interactions during virus assembly. FEBS J 2009; 276:6098-109. [DOI: 10.1111/j.1742-4658.2009.07313.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Neira JL. The capsid protein of human immunodeficiency virus: designing inhibitors of capsid assembly. FEBS J 2009; 276:6110-7. [DOI: 10.1111/j.1742-4658.2009.07314.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Neira JL, Román-Trufero M, Contreras LM, Prieto J, Singh G, Barrera FN, Renart ML, Vidal M. The transcriptional repressor RYBP is a natively unfolded protein which folds upon binding to DNA. Biochemistry 2009; 48:1348-60. [PMID: 19170609 DOI: 10.1021/bi801933c] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RYBP (Ring1A and YY1 binding protein) is a zinc finger protein with an essential role during embryonic development, which binds transcriptional factors, Polycomb products, and mediators of apoptosis, suggesting roles in, apparently, unrelated functions. To investigate mechanisms underlying its association with functionally diverse partners, we set out to study its structural properties using a number of biophysical (fluorescence, circular dichroism, Fourier transform infrared, and NMR spectroscopies) and hydrodynamic (analytical ultracentrifugation, DOSY-NMR, and gel filtration chromatography) techniques. We find RYBP to be a noncompact protein with little residual secondary structure, lacking a well-defined tertiary structure. These observations are also supported by theoretical calculations using neural networks and pairwise energy content, suggesting that RYBP is a natively unfolded protein. In addition, structural studies on its binding to the C-terminal region of the Polycomb protein Ring1B or to DNA show conformational changes in the complexed RYBP, consistent with the acquisition of a folded structure. The data provide a structural explanation for RYBP engagement in functionally unrelated pathways by means of its assembly into various macromolecular complexes as an unstructured protein with the ability to acquire a well-structured fold due to its association with different partners.
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Affiliation(s)
- José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernandez, 03202 Elche (Alicante), Spain.
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Yu X, Wang Q, Yang JC, Buch I, Tsai CJ, Ma B, Cheng SZD, Nussinov R, Zheng J. Mutational analysis and allosteric effects in the HIV-1 capsid protein carboxyl-terminal dimerization domain. Biomacromolecules 2009; 10:390-9. [PMID: 19199580 PMCID: PMC2651736 DOI: 10.1021/bm801151r] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The carboxyl-terminal domain (CTD, residues 146-231) of the HIV-1 capsid (CA) protein plays an important role in the CA-CA dimerization and viral assembly of the human immunodeficiency virus type 1. Disrupting the native conformation of the CA is essential for blocking viral capsid formation and viral replication. Thus, it is important to identify the exact nature of the structural changes and driving forces of the CTD dimerization that take place in mutant forms. Here, we compare the structural stability, conformational dynamics, and association force of the CTD dimers for both wild-type and mutated sequences using all-atom explicit-solvent molecular dynamics (MD). The simulations show that Q155N and E159D at the major homology region (MHR) and W184A and M185A at the helix 2 region are energetically less favorable than the wild-type, imposing profound negative effects on intermolecular CA-CA dimerization. Detailed structural analysis shows that three mutants (Q155N, E159D, and W184A) display much more flexible local structures and weaker CA-CA association than the wildtype, primarily due to the loss of interactions (hydrogen bonds, side chain hydrophobic contacts, and pi-stacking) with their neighboring residues. Most interestingly, the MHR that is far from the interacting dimeric interface is more sensitive to the mutations than the helix 2 region that is located at the CA-CA dimeric interface, indicating that structural changes in the distinct motif of the CA could similarly allosterically prevent the CA capsid formation. In addition, the structural and free energy comparison of the five residues shorter CA (151-231) dimer with the CA (146-231) dimer further indicates that hydrophobic interactions, side chain packing, and hydrogen bonds are the major, dominant driving forces in stabilizing the CA interface.
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Affiliation(s)
- Xiang Yu
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, USA
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