1
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Yang H, Luo Y, Jin B, Chi S, Li X. Convoluted micellar morphological transitions driven by tailorable mesogenic ordering effect from discotic mesogen-containing block copolymer. Nat Commun 2024; 15:2968. [PMID: 38580629 PMCID: PMC10997646 DOI: 10.1038/s41467-024-47312-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 03/27/2024] [Indexed: 04/07/2024] Open
Abstract
Solution-state self-assemblies of block copolymers to form nanostructures are tremendously attractive for their tailorable morphologies and functionalities. While incorporating moieties with strong ordering effects may introduce highly orientational control over the molecular packing and dictate assembly behaviors, subtle and delicate driving forces can yield slower kinetics to reveal manifold metastable morphologies. Herein, we report the unusually convoluted self-assembly behaviors of a liquid crystalline block copolymer bearing triphenylene discotic mesogens. They undergo unusual multiple morphological transitions spontaneously, driven by their intrinsic subtle liquid crystalline ordering effect. Meanwhile, liquid crystalline orderedness can also be built very quickly by doping the mesogens with small-molecule dopants, and the morphological transitions are dramatically accelerated and various exotic micelles are produced. Surprisingly, with high doping levels, the self-assembly mechanism of this block copolymer is completely changed from intramolecular chain shuffling and rearrangement to nucleation-growth mode, based on which self-seeding experiments can be conducted to produce highly uniform fibrils.
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Affiliation(s)
- Huanzhi Yang
- School of Materials Science and Engineering. Beijing Institute of Technology, 100081, Beijing, China
| | - Yunjun Luo
- School of Materials Science and Engineering. Beijing Institute of Technology, 100081, Beijing, China
- Key Laboratory of High Energy Density Materials, MOE. Beijing Institute of Technology, 100081, Beijing, China
| | - Bixin Jin
- School of Materials Science and Engineering. Beijing Institute of Technology, 100081, Beijing, China.
| | - Shumeng Chi
- School of Materials Science and Engineering. Beijing Institute of Technology, 100081, Beijing, China
- Experimental Center of Advanced Materials, Beijing Institute of Technology, 100081, Beijing, China
| | - Xiaoyu Li
- School of Materials Science and Engineering. Beijing Institute of Technology, 100081, Beijing, China.
- Key Laboratory of High Energy Density Materials, MOE. Beijing Institute of Technology, 100081, Beijing, China.
- Experimental Center of Advanced Materials, Beijing Institute of Technology, 100081, Beijing, China.
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2
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Exploring protein symmetry at the RCSB Protein Data Bank. Emerg Top Life Sci 2022; 6:231-243. [PMID: 35801924 PMCID: PMC9472815 DOI: 10.1042/etls20210267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 11/17/2022]
Abstract
The symmetry of biological molecules has fascinated structural biologists ever since the structure of hemoglobin was determined. The Protein Data Bank (PDB) archive is the central global archive of three-dimensional (3D), atomic-level structures of biomolecules, providing open access to the results of structural biology research with no limitations on usage. Roughly 40% of the structures in the archive exhibit some type of symmetry, including formal global symmetry, local symmetry, or pseudosymmetry. The Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (founding member of the Worldwide Protein Data Bank partnership that jointly manages, curates, and disseminates the archive) provides a variety of tools to assist users interested in exploring the symmetry of biological macromolecules. These tools include multiple modalities for searching and browsing the archive, turnkey methods for biomolecular visualization, documentation, and outreach materials for exploring functional biomolecular symmetry.
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3
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Sowdhamini R. Biography of a scientist with strength, substance, sincerity and service: Late N. Srinivasan (1962-2021). Bioinformation 2022; 18:600-603. [PMID: 37168784 PMCID: PMC10165036 DOI: 10.6026/97320630018600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/12/2022] [Accepted: 06/12/2022] [Indexed: 11/23/2022] Open
Abstract
Late N. Srinivasan belongs to the GN Ramachandran lineage of protein structural analysts. His role in the advancement of the structure based understanding of signal transduction, protein kinase analyses and host-pathogen interactions both developing and using Bioinformatics tools for protein-protein interactions, protein dynamics, remote homology detection and polypeptide stereochemistry is well documented in the literature. Thus, his contribution to the understanding of protein function through structural analysis, using computational models and tools, is exceptional.
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Affiliation(s)
- R Sowdhamini
- National Centre for Biological Sciences (NCBS-TIFR), GKVK Campus, Bangalore, Karnataka 560065, India
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4
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Marques-Pereira C, Pires MN, Gouveia RP, Pereira NN, Caniceiro AB, Rosário-Ferreira N, Moreira IS. SARS-CoV-2 Membrane Protein: From Genomic Data to Structural New Insights. Int J Mol Sci 2022; 23:2986. [PMID: 35328409 PMCID: PMC8948900 DOI: 10.3390/ijms23062986] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 01/27/2023] Open
Abstract
Severe Acute Respiratory Syndrome CoronaVirus-2 (SARS-CoV-2) is composed of four structural proteins and several accessory non-structural proteins. SARS-CoV-2's most abundant structural protein, Membrane (M) protein, has a pivotal role both during viral infection cycle and host interferon antagonism. This is a highly conserved viral protein, thus an interesting and suitable target for drug discovery. In this paper, we explain the structural nature of M protein homodimer. To do so, we developed and applied a detailed and robust in silico workflow to predict M protein dimeric structure, membrane orientation, and interface characterization. Single Nucleotide Polymorphisms (SNPs) in M protein were retrieved from over 1.2 M SARS-CoV-2 genomes and proteins from the Global Initiative on Sharing All Influenza Data (GISAID) database, 91 of which were located at the predicted dimer interface. Among those, we identified SNPs in Variants of Concern (VOC) and Variants of Interest (VOI). Binding free energy differences were evaluated for dimer interfacial SNPs to infer mutant protein stabilities. A few high-prevalent mutated residues were found to be especially relevant in VOC and VOI. This realization may be a game-changer to structure-driven formulation of new therapeutics for SARS-CoV-2.
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Affiliation(s)
- Catarina Marques-Pereira
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
- IIIs—Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Manuel N. Pires
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
- Department of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Raquel P. Gouveia
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
| | - Nádia N. Pereira
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
| | - Ana B. Caniceiro
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
| | - Nícia Rosário-Ferreira
- CNC—Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal; (C.M.-P.); (M.N.P.); (R.P.G.); (N.N.P.); (A.B.C.); (N.R.-F.)
- CQC—Coimbra Chemistry Center, Chemistry Department, Faculty of Science and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Irina S. Moreira
- Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-535 Coimbra, Portugal
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5
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Symmetry of Post-Translational Modifications in a Human Enzyme. Symmetry (Basel) 2022. [DOI: 10.3390/sym14020212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Paraoxonase 2 (PON2) is a member of a small family of human lactonases. Recently, post-translational modifications (PTMs) of PON2 were highlighted, one of which involved the modulation of the enzyme activity. Furthermore, two important single nucleotide polymorphisms (SNPs) involved in type 2 diabetes and its consequences, were found to modulate the enzyme activity as well. The position on the PON2 structural model of both residues corresponding to SNPs and PTMs suggested a symmetry of the molecule. By sequence and structure superposition we were able to confirm this finding. The result will be discussed in light of the evolution of symmetry in biological molecules and their function.
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6
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Affiliation(s)
- Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore.,Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore.,School of Biological Sciences, Nanyang Technological University (NTU), Singapore
| | - Chandra Verma
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore.,School of Biological Sciences, Nanyang Technological University (NTU), Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| | - Tom Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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7
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Human FoxP Transcription Factors as Tractable Models of the Evolution and Functional Outcomes of Three-Dimensional Domain Swapping. Int J Mol Sci 2021; 22:ijms221910296. [PMID: 34638644 PMCID: PMC8508939 DOI: 10.3390/ijms221910296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 01/18/2023] Open
Abstract
The association of two or more proteins to adopt a quaternary complex is one of the most widespread mechanisms by which protein function is modulated. In this scenario, three-dimensional domain swapping (3D-DS) constitutes one plausible pathway for the evolution of protein oligomerization that exploits readily available intramolecular contacts to be established in an intermolecular fashion. However, analysis of the oligomerization kinetics and thermodynamics of most extant 3D-DS proteins shows its dependence on protein unfolding, obscuring the elucidation of the emergence of 3D-DS during evolution, its occurrence under physiological conditions, and its biological relevance. Here, we describe the human FoxP subfamily of transcription factors as a feasible model to study the evolution of 3D-DS, due to their significantly faster dissociation and dimerization kinetics and lower dissociation constants in comparison to most 3D-DS models. Through the biophysical and functional characterization of FoxP proteins, relevant structural aspects highlighting the evolutionary adaptations of these proteins to enable efficient 3D-DS have been ascertained. Most biophysical studies on FoxP suggest that the dynamics of the polypeptide chain are crucial to decrease the energy barrier of 3D-DS, enabling its fast oligomerization under physiological conditions. Moreover, comparison of biophysical parameters between human FoxP proteins in the context of their minute sequence differences suggests differential evolutionary strategies to favor homoassociation and presages the possibility of heteroassociations, with direct impacts in their gene regulation function.
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8
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Asymmetrizing an icosahedral virus capsid by hierarchical assembly of subunits with designed asymmetry. Nat Commun 2021; 12:589. [PMID: 33500404 PMCID: PMC7838286 DOI: 10.1038/s41467-020-20862-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 12/07/2020] [Indexed: 11/08/2022] Open
Abstract
Symmetrical protein complexes are ubiquitous in biology. Many have been re-engineered for chemical and medical applications. Viral capsids and their assembly are frequent platforms for these investigations. A means to create asymmetric capsids may expand applications. Here, starting with homodimeric Hepatitis B Virus capsid protein, we develop a heterodimer, design a hierarchical assembly pathway, and produce asymmetric capsids. In the heterodimer, the two halves have different growth potentials and assemble into hexamers. These preformed hexamers can nucleate co-assembly with other dimers, leading to Janus-like capsids with a small discrete hexamer patch. We can remove the patch specifically and observe asymmetric holey capsids by cryo-EM reconstruction. The resulting hole in the surface can be refilled with fluorescently labeled dimers to regenerate an intact capsid. In this study, we show how an asymmetric subunit can be used to generate an asymmetric particle, creating the potential for a capsid with different surface chemistries.
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9
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Vrancken JPM, Tame JRH, Voet ARD. Development and applications of artificial symmetrical proteins. Comput Struct Biotechnol J 2020; 18:3959-3968. [PMID: 33335692 PMCID: PMC7734218 DOI: 10.1016/j.csbj.2020.10.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/27/2020] [Accepted: 10/31/2020] [Indexed: 12/28/2022] Open
Abstract
Since the determination of the first molecular models of proteins there has been interest in creating proteins artificially, but such methods have only become widely successful in the last decade. Gradual improvements over a long period of time have now yielded numerous examples of non-natural proteins, many of which are built from repeated elements. In this review we discuss the design of such symmetrical proteins and their various applications in chemistry and medicine.
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Affiliation(s)
- Jeroen P M Vrancken
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium
| | - Jeremy R H Tame
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Arnout R D Voet
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium
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10
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Quantifying the distribution of protein oligomerization degree reflects cellular information capacity. Sci Rep 2020; 10:17689. [PMID: 33077848 PMCID: PMC7573690 DOI: 10.1038/s41598-020-74811-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 09/29/2020] [Indexed: 11/08/2022] Open
Abstract
The generation of information, energy and biomass in living cells involves integrated processes that optimally evolve into complex and robust cellular networks. Protein homo-oligomerization, which is correlated with cooperativity in biology, is one means of scaling the complexity of protein networks. It can play critical roles in determining the sensitivity of genetic regulatory circuits and metabolic pathways. Therefore, understanding the roles of oligomerization may lead to new approaches of probing biological functions. Here, we analyzed the frequency of protein oligomerization degree in the cell proteome of nine different organisms, and then, we asked whether there are design trade-offs between protein oligomerization, information precision and energy costs of protein synthesis. Our results indicate that there is an upper limit for the degree of protein oligomerization, possibly because of the trade-off between cellular resource limitations and the information precision involved in biochemical reaction networks. These findings can explain the principles of cellular architecture design and provide a quantitative tool to scale synthetic biological systems.
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11
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Roy P, Roy S, Sengupta N. Disulfide Reduction Allosterically Destabilizes the β-Ladder Subdomain Assembly within the NS1 Dimer of ZIKV. Biophys J 2020; 119:1525-1537. [PMID: 32946768 DOI: 10.1016/j.bpj.2020.08.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/13/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
The Zika virus (ZIKV) was responsible for a recent debilitating epidemic that till date has no cure. A potential way to reduce ZIKV virulence is to limit the action of the nonstructural proteins involved in its viral replication. One such protein, NS1, encoded as a monomer by the viral genome, plays a major role via symmetric oligomerization. We examine the homodimeric structure of the dominant β-ladder segment of NS1 with extensive all atom molecular dynamics. We find it stably bounded by two spatially separated interaction clusters (C1 and C2) with significant differences in the nature of their interactions. Four pairs of distal, intramonomeric disulfide bonds are found to be coupled to the stability, local structure, and wettability of the interfacial region. Symmetric reduction of the intramonomeric disulfides triggers marked dynamical heterogeneity, interfacial wettability, and asymmetric salt-bridging propensity. Harnessing the model-free Lipari-Szabo based formalism for estimation of conformational entropy (Sconf), we find clear signatures of heterogeneity in the monomeric conformational entropies. The observed asymmetry, very small in the unperturbed state, expands significantly in the reduced states. This allosteric effect is most noticeable in the electrostatically bound C2 cluster that underlies the greatest stability in the unperturbed state. Allosteric induction of conformational and thermodynamic asymmetry is expected to affect the pathways leading to symmetric higher-ordered oligomerization, and thereby affect crucial replication pathways.
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Affiliation(s)
- Priti Roy
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Subhajit Roy
- Centre for Excellence in Basic Sciences (CBS), University of Mumbai, Vidyanagari, Mumbai, India
| | - Neelanjana Sengupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India.
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12
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Shalit Y, Tuvi-Arad I. Side chain flexibility and the symmetry of protein homodimers. PLoS One 2020; 15:e0235863. [PMID: 32706779 PMCID: PMC7380632 DOI: 10.1371/journal.pone.0235863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/24/2020] [Indexed: 01/22/2023] Open
Abstract
A comprehensive analysis of crystallographic data of 565 high-resolution protein homodimers comprised of over 250,000 residues suggests that amino acids form two groups that differ in their tendency to distort or symmetrize the structure of protein homodimers. Residues of the first group tend to distort the protein homodimer and generally have long or polar side chains. These include: Lys, Gln, Glu, Arg, Asn, Met, Ser, Thr and Asp. Residues of the second group contribute to protein symmetry and are generally characterized by short or aromatic side chains. These include: Ile, Pro, His, Val, Cys, Leu, Trp, Tyr, Phe, Ala and Gly. The distributions of the continuous symmetry measures of the proteins and the continuous chirality measures of their building blocks highlight the role of side chain geometry and the interplay between entropy and symmetry in dictating the conformational flexibility of proteins.
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Affiliation(s)
- Yaffa Shalit
- Department of Natural Sciences, The Open University of Israel, Raanana, Israel
| | - Inbal Tuvi-Arad
- Department of Natural Sciences, The Open University of Israel, Raanana, Israel
- * E-mail:
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13
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Bonjack M, Avnir D. The near-symmetry of protein oligomers: NMR-derived structures. Sci Rep 2020; 10:8367. [PMID: 32433550 PMCID: PMC7239866 DOI: 10.1038/s41598-020-65097-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 03/18/2020] [Indexed: 02/07/2023] Open
Abstract
The majority of oligomeric proteins form clusters which have rotational or dihedral symmetry. Despite the many advantages of symmetric packing, protein oligomers are only nearly symmetric, and the origin of this phenomenon is still in need to be fully explored. Here we apply near-symmetry analyses by the Continuous Symmetry Measures methodology of protein homomers to their natural state, namely their structures in solution. NMR-derived structural data serves us for that purpose. We find that symmetry deviations of proteins are by far higher in solution, compared to the crystalline state; that much of the symmetry distortion is due to amino acids along the interface between the subunits; that the distortions are mainly due to hydrophilic amino acids; and that distortive oligomerization processes such as the swap-domain mechanism can be identified by the symmetry analysis. Most of the analyses were carried out on distorted C2-symmetry dimers, but C3 and D2 cases were analyzed as well. Our NMR analysis supports the idea that the crystallographic B-factor represents non-classical crystals, in which different conformers pack in the crystal, perhaps from the conformers which the NMR analysis provides.
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Affiliation(s)
- Maayan Bonjack
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - David Avnir
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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14
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Cifuente JO, Comino N, D'Angelo C, Marina A, Gil-Carton D, Albesa-Jové D, Guerin ME. The allosteric control mechanism of bacterial glycogen biosynthesis disclosed by cryoEM. Curr Res Struct Biol 2020; 2:89-103. [PMID: 34235472 PMCID: PMC8244506 DOI: 10.1016/j.crstbi.2020.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/12/2020] [Accepted: 04/20/2020] [Indexed: 11/10/2022] Open
Abstract
Glycogen and starch are the major carbon and energy reserve polysaccharides in nature, providing living organisms with a survival advantage. The evolution of the enzymatic machinery responsible for the biosynthesis and degradation of such polysaccharides, led the development of mechanisms to control the assembly and disassembly rate, to store and recover glucose according to cell energy demands. The tetrameric enzyme ADP-glucose pyrophosphorylase (AGPase) catalyzes and regulates the initial step in the biosynthesis of both α-polyglucans. AGPase displays cooperativity and allosteric regulation by sensing metabolites from the cell energy flux. The understanding of the allosteric signal transduction mechanisms in AGPase arises as a long-standing challenge. In this work, we disclose the cryoEM structures of the paradigmatic homotetrameric AGPase from Escherichia coli (EcAGPase), in complex with either positive or negative physiological allosteric regulators, fructose-1,6-bisphosphate (FBP) and AMP respectively, both at 3.0 Å resolution. Strikingly, the structures reveal that FBP binds deeply into the allosteric cleft and overlaps the AMP site. As a consequence, FBP promotes a concerted conformational switch of a regulatory loop, RL2, from a "locked" to a "free" state, modulating ATP binding and activating the enzyme. This notion is strongly supported by our complementary biophysical and bioinformatics evidence, and a careful analysis of vast enzyme kinetics data on single-point mutants of EcAGPase. The cryoEM structures uncover the residue interaction networks (RIN) between the allosteric and the catalytic components of the enzyme, providing unique details on how the signaling information is transmitted across the tetramer, from which cooperativity emerges. Altogether, the conformational states visualized by cryoEM reveal the regulatory mechanism of EcAGPase, laying the foundations to understand the allosteric control of bacterial glycogen biosynthesis at the molecular level of detail.
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Key Words
- AGPase, ADP-glucose pyrophosphorylase
- AMP, adenosine 5′-monophosphate
- ATP, adenosine 5′-triphosphate
- EcAGPase, AGPase from E. coli
- Enzyme allosterism
- FBP, fructose 1,6-bisphosphate
- G1P, α-d-glucose-1-phosphate
- GBE, glycogen branching enzyme
- GDE, glycogen debranching enzyme
- GP, glycogen phosphorylase
- GS, glycogen synthase
- GTA-like, glycosyltransferase-A like domain
- Glycogen biosynthesis
- Glycogen regulation
- LβH, left-handed β-helix domain
- Nucleotide sugar biosynthesis
- PPi, pyrophosphate
- RIN, residue interaction network
- SM, sensory motif
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Affiliation(s)
- Javier O. Cifuente
- Structural Biology Unit, CIC BioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - Natalia Comino
- Structural Biology Unit, CIC BioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - Cecilia D'Angelo
- Structural Biology Unit, CIC BioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - Alberto Marina
- Structural Biology Unit, CIC BioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - David Gil-Carton
- Structural Biology Unit, CIC BioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - David Albesa-Jové
- Structural Biology Unit, CIC BioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - Marcelo E. Guerin
- Structural Biology Unit, CIC BioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
- IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain
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15
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Tuvi-Arad I, Alon G. Improved algorithms for quantifying the near symmetry of proteins: complete side chains analysis. J Cheminform 2019; 11:39. [PMID: 31172379 PMCID: PMC6551912 DOI: 10.1186/s13321-019-0360-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 05/28/2019] [Indexed: 12/12/2022] Open
Abstract
Symmetry of proteins, an important source of their elegant structure and unique functions, is not as perfect as it may seem. In the framework of continuous symmetry, in which symmetry is no longer a binary yes/no property, such imperfections can be quantified and used as a global descriptor of the three-dimensional structure. We present an improved algorithm for calculating the continuous symmetry measure for proteins that takes into account their complete set of atoms including all side chains. Our method takes advantage of the protein sequence and the division into peptides in order to improve the accuracy and efficiency of the calculation over previous methods. The Hungarian algorithm is applied to solve the assignment problem and find the permutation that defines the symmetry operation. Analysis of the symmetry of several sets of protein homomers, with various degrees of rotational symmetry is presented. The new methodology lays the foundations for accurate, efficient and reliable large scale symmetry analysis of protein structure and can be used as a collective variable that describes changes of the protein geometry along various processes, both at the backbone level and for the complete protein structure.
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Affiliation(s)
- Inbal Tuvi-Arad
- Department of Natural Sciences, The Open University of Israel, 4353701, Raanana, Israel.
| | - Gil Alon
- Department of Mathematics and Computer Science, The Open University of Israel, 4353701, Raanana, Israel.
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16
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Simon AJ, Zhou Y, Ramasubramani V, Glaser J, Pothukuchy A, Gollihar J, Gerberich JC, Leggere JC, Morrow BR, Jung C, Glotzer SC, Taylor DW, Ellington AD. Supercharging enables organized assembly of synthetic biomolecules. Nat Chem 2019; 11:204-212. [DOI: 10.1038/s41557-018-0196-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 11/26/2018] [Indexed: 11/09/2022]
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17
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Affiliation(s)
- Julian T. Brennecke
- Department of Theoretical and Computational Biophysics, Computational Biomolecular, Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bert L. de Groot
- Department of Theoretical and Computational Biophysics, Computational Biomolecular, Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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18
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Pagès G, Kinzina E, Grudinin S. Analytical symmetry detection in protein assemblies. I. Cyclic symmetries. J Struct Biol 2018; 203:142-148. [PMID: 29705493 DOI: 10.1016/j.jsb.2018.04.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/18/2018] [Accepted: 04/19/2018] [Indexed: 12/30/2022]
Abstract
Symmetry in protein, and, more generally, in macromolecular assemblies is a key point to understand their structure, stability and function. Many symmetrical assemblies are currently present in the Protein Data Bank (PDB) and some of them are among the largest solved structures, thus an efficient computational method is needed for the exhaustive analysis of these. The cyclic symmetry groups represent the most common assemblies in the PDB. These are also the building blocks for higher-order symmetries. This paper presents a mathematical formulation to find the position and the orientation of the symmetry axis in a cyclic symmetrical protein assembly, and also to assess the quality of this symmetry. Our method can also detect symmetries in partial assemblies. We provide an efficient C++ implementation of the method and demonstrate its efficiency on several examples including partial assemblies and pseudo symmetries. We also compare the method with two other published techniques and show that it is significantly faster on all the tested examples. Our method produces results with a machine precision, its cost function is solely based on 3D Euclidean geometry, and most of the operations are performed analytically. The method is available athttp://team.inria.fr/nano-d/software/ananas. The graphical user interface of the method built for the SAMSON platform is available athttp://samson-connect.net.
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Affiliation(s)
- Guillaume Pagès
- Inria, Univ. Grenoble Alpes, CNRS, Grenoble INP, LJK, Grenoble 38000, France
| | - Elvira Kinzina
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Sergei Grudinin
- Inria, Univ. Grenoble Alpes, CNRS, Grenoble INP, LJK, Grenoble 38000, France.
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19
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Efficient and Accurate Algorithm for Cleaved Fragments Prediction (CFPA) in Protein Sequences Dataset Based on Consensus and Its Variants: A Novel Degradomics Prediction Application. Methods Mol Biol 2018; 1598:329-352. [PMID: 28508371 DOI: 10.1007/978-1-4939-6952-4_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
Degradomics is a novel discipline that involves determination of the proteases/substrate fragmentation profile, called the substrate degradome, and has been recently applied in different disciplines. A major application of degradomics is its utility in the field of biomarkers where the breakdown products (BDPs) of different protease have been investigated. Among the major proteases assessed, calpain and caspase proteases have been associated with the execution phases of the pro-apoptotic and pro-necrotic cell death, generating caspase/calpain-specific cleaved fragments. The distinction between calpain and caspase protein fragments has been applied to distinguish injury mechanisms. Advanced proteomics technology has been used to identify these BDPs experimentally. However, it has been a challenge to identify these BDPs with high precision and efficiency, especially if we are targeting a number of proteins at one time. In this chapter, we present a novel bioinfromatic detection method that identifies BDPs accurately and efficiently with validation against experimental data. This method aims at predicting the consensus sequence occurrences and their variants in a large set of experimentally detected protein sequences based on state-of-the-art sequence matching and alignment algorithms. After detection, the method generates all the potential cleaved fragments by a specific protease. This space and time-efficient algorithm is flexible to handle the different orientations that the consensus sequence and the protein sequence can take before cleaving. It is O(mn) in space complexity and O(Nmn) in time complexity, with N number of protein sequences, m length of the consensus sequence, and n length of each protein sequence. Ultimately, this knowledge will subsequently feed into the development of a novel tool for researchers to detect diverse types of selected BDPs as putative disease markers, contributing to the diagnosis and treatment of related disorders.
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20
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Mahita J, Sowdhamini R. Investigating the effect of key mutations on the conformational dynamics of toll-like receptor dimers through molecular dynamics simulations and protein structure networks. Proteins 2018; 86:475-490. [DOI: 10.1002/prot.25467] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 01/05/2018] [Accepted: 01/23/2018] [Indexed: 01/07/2023]
Affiliation(s)
- Jarjapu Mahita
- National Centre for Biological Sciences, GKVK Campus; Bellary Road, Bangalore 560065 India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, GKVK Campus; Bellary Road, Bangalore 560065 India
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21
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Sanchez-deAlcazar D, Mejias SH, Erazo K, Sot B, Cortajarena AL. Self-assembly of repeat proteins: Concepts and design of new interfaces. J Struct Biol 2018; 201:118-129. [DOI: 10.1016/j.jsb.2017.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/09/2017] [Accepted: 09/02/2017] [Indexed: 11/25/2022]
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22
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Potoyan DA, Bueno C, Zheng W, Komives EA, Wolynes PG. Resolving the NFκB Heterodimer Binding Paradox: Strain and Frustration Guide the Binding of Dimeric Transcription Factors. J Am Chem Soc 2017; 139:18558-18566. [PMID: 29183131 DOI: 10.1021/jacs.7b08741] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many eukaryotic transcription factors function after forming oligomers. The choice of protein partners is a nonrandom event that has distinct functional consequences for gene regulation. In the present work we examine three dimers of transcription factors in the NFκB family: p50p50, p50p65, and p65p65. The NFκB dimers bind to a myriad of genomic sites and switch the targeted genes on or off with precision. The p65p50 heterodimer of NFκB is the strongest DNA binder, and its unbinding is controlled kinetically by molecular stripping from the DNA induced by IκB. In contrast, the homodimeric forms of NFκB, p50p50 and p65p65, bind DNA with significantly less affinity, which places the DNA residence of the homodimers under thermodynamic rather than kinetic control. It seems paradoxical that the heterodimer should bind more strongly than either of the symmetric homodimers since DNA is a nearly symmetric target. Using a variety of energy landscape analysis tools, here we uncover the features in the molecular architecture of NFκB dimers that are responsible for these drastically different binding free energies. We show that frustration in the heterodimer interface gives the heterodimer greater conformational plasticity, allowing the heterodimer to better accommodate the DNA. We also show how the elastic energy and mechanical strain in NFκB dimers can be found by extracting the principal components of the fluctuations in Cartesian coordinates as well as fluctuations in the space of physical contacts, which are sampled via simulations with a predictive energy landscape Hamiltonian. These energetic contributions determine the specific detailed mechanisms of binding and stripping for both homo- and heterodimers.
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Affiliation(s)
- Davit A Potoyan
- Department of Chemistry, Iowa State University , Ames, Iowa 50011, United States.,Department of Chemistry and Center for Theoretical Biological Physics, Rice University , Houston, Texas 77005, United States
| | - Carlos Bueno
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University , Houston, Texas 77005, United States
| | - Weihua Zheng
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University , Houston, Texas 77005, United States
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California San Diego , La Jolla, California 92093, United States
| | - Peter G Wolynes
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University , Houston, Texas 77005, United States
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23
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Bonjack-Shterengartz M, Avnir D. The enigma of the near-symmetry of proteins: Domain swapping. PLoS One 2017; 12:e0180030. [PMID: 28708874 PMCID: PMC5510828 DOI: 10.1371/journal.pone.0180030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 06/08/2017] [Indexed: 01/25/2023] Open
Abstract
The majority of proteins form oligomers which have rotational symmetry. Literature has suggested many functional advantages that the symmetric packing offers. Yet, despite these advantages, the vast majority of protein oligomers are only nearly symmetric. A key question in the field of proteins structure is therefore, if symmetry is so advantageous, why do oligomers settle for aggregates that do not maximize that structural property? The answer to that question is apparently multi-parametric, and involves distortions at the interaction zones of the monomer units of the oligomer in order to minimize the free energy, the dynamics of the protein, the effects of surroundings parameters, and the mechanism of oligomerization. The study of this problem is in its infancy: Only the first parameter has been explored so far. Here we focus on the last parameter-the mechanism of formation. To test this effect we have selected to focus on the domain swapping mechanism of oligomerization, by which oligomers form in a mechanism that swaps identical portions of monomeric units, resulting in an interwoven oligomer. We are using continuous symmetry measures to analyze in detail the oligomer formed by this mechanism, and found, that without exception, in all analyzed cases, perfect symmetry is given away, and we are able to identify that the main burden of distortion lies in the hinge regions that connect the swapped portions. We show that the continuous symmetry analysis method clearly identifies the hinge region of swapped domain proteins-considered to be a non-trivial task. We corroborate our conclusion about the central role of the hinge region in affecting the symmetry of the oligomers, by a special probability analysis developed particularly for that purpose.
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Affiliation(s)
- Maayan Bonjack-Shterengartz
- Institute of Chemistry and the Lise Meitner Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Avnir
- Institute of Chemistry and the Lise Meitner Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
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24
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Bergendahl LT, Marsh JA. Functional determinants of protein assembly into homomeric complexes. Sci Rep 2017; 7:4932. [PMID: 28694495 PMCID: PMC5504011 DOI: 10.1038/s41598-017-05084-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 05/24/2017] [Indexed: 11/24/2022] Open
Abstract
Approximately half of proteins with experimentally determined structures can interact with other copies of themselves and assemble into homomeric complexes, the overwhelming majority of which (>96%) are symmetric. Although homomerisation is often assumed to a functionally beneficial result of evolutionary selection, there has been little systematic analysis of the relationship between homomer structure and function. Here, utilizing the large numbers of structures and functional annotations now available, we have investigated how proteins that assemble into different types of homomers are associated with different biological functions. We observe that homomers from different symmetry groups are significantly enriched in distinct functions, and can often provide simple physical and geometrical explanations for these associations in regards to substrate recognition or physical environment. One of the strongest associations is the tendency for metabolic enzymes to form dihedral complexes, which we suggest is closely related to allosteric regulation. We provide a physical explanation for why allostery is related to dihedral complexes: it allows for efficient propagation of conformational changes across isologous (i.e. symmetric) interfaces. Overall we demonstrate a clear relationship between protein function and homomer symmetry that has important implications for understanding protein evolution, as well as for predicting protein function and quaternary structure.
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Affiliation(s)
- L Therese Bergendahl
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK.
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
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25
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Blundell TL. Protein crystallography and drug discovery: recollections of knowledge exchange between academia and industry. IUCRJ 2017; 4:308-321. [PMID: 28875019 PMCID: PMC5571795 DOI: 10.1107/s2052252517009241] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 06/20/2017] [Indexed: 05/19/2023]
Abstract
The development of structure-guided drug discovery is a story of knowledge exchange where new ideas originate from all parts of the research ecosystem. Dorothy Crowfoot Hodgkin obtained insulin from Boots Pure Drug Company in the 1930s and insulin crystallization was optimized in the company Novo in the 1950s, allowing the structure to be determined at Oxford University. The structure of renin was developed in academia, on this occasion in London, in response to a need to develop antihypertensives in pharma. The idea of a dimeric aspartic protease came from an international academic team and was discovered in HIV; it eventually led to new HIV antivirals being developed in industry. Structure-guided fragment-based discovery was developed in large pharma and biotechs, but has been exploited in academia for the development of new inhibitors targeting protein-protein interactions and also antimicrobials to combat mycobacterial infections such as tuberculosis. These observations provide a strong argument against the so-called 'linear model', where ideas flow only in one direction from academic institutions to industry. Structure-guided drug discovery is a story of applications of protein crystallography and knowledge exhange between academia and industry that has led to new drug approvals for cancer and other common medical conditions by the Food and Drug Administration in the USA, as well as hope for the treatment of rare genetic diseases and infectious diseases that are a particular challenge in the developing world.
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Affiliation(s)
- Tom L. Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, England
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26
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Song G. The finite number of global motion patterns available to symmetric protein complexes. Proteins 2017; 85:1741-1758. [DOI: 10.1002/prot.25331] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 05/18/2017] [Accepted: 06/07/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Guang Song
- Graduate Program of Bioinformatics and Computational Biology; Iowa State University; Ames Iowa
- Department of Computer Science; Iowa State University; Ames Iowa
- L. H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University; Ames Iowa
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27
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Symmetry breaking during homodimeric assembly activates an E3 ubiquitin ligase. Sci Rep 2017; 7:1789. [PMID: 28496195 PMCID: PMC5431976 DOI: 10.1038/s41598-017-01880-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 04/04/2017] [Indexed: 12/20/2022] Open
Abstract
C-terminus of Hsc/p70-Interacting Protein (CHIP) is a homodimeric E3 ubiquitin ligase. Each CHIP monomer consists of a tetratricopeptide-repeat (TPR), helix-turn-helix (HH), and U-box domain. In contrast to nearly all homodimeric proteins, CHIP is asymmetric. To uncover the origins of asymmetry, we performed molecular dynamics simulations of dimer assembly. We determined that a CHIP monomer is most stable when the HH domain has an extended helix that supports intra-monomer TPR-U-box interaction, blocking the E2-binding surface of the U-box. We also discovered that monomers first dimerize symmetrically through their HH domains, which then triggers U-box dimerization. This brings the extended helices into close proximity, including a repulsive stretch of positively charged residues. Unable to smoothly unwind, this conflict bends the helices until the helix of one protomer breaks to relieve the repulsion. The abrupt snapping of the helix forces the C-terminal residues of the other protomer to disrupt that protomer’s TPR-U-box tight binding interface, swiftly exposing and activating one of the E2 binding sites. Mutagenesis and biochemical experiments confirm that C-terminal residues are necessary both to maintain CHIP stability and function. This novel mechanism indicates how a ubiquitin ligase maintains an inactive monomeric form that rapidly activates only after asymmetric assembly.
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28
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Madsen J, Sinitskiy AV, Li J, Voth GA. Highly Coarse-Grained Representations of Transmembrane Proteins. J Chem Theory Comput 2017; 13:935-944. [PMID: 28043122 PMCID: PMC5312841 DOI: 10.1021/acs.jctc.6b01076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Indexed: 01/04/2023]
Abstract
Numerous biomolecules and biomolecular complexes, including transmembrane proteins (TMPs), are symmetric or at least have approximate symmetries. Highly coarse-grained models of such biomolecules, aiming at capturing the essential structural and dynamical properties on resolution levels coarser than the residue scale, must preserve the underlying symmetry. However, making these models obey the correct physics is in general not straightforward, especially at the highly coarse-grained resolution where multiple (∼3-30 in the current study) amino acid residues are represented by a single coarse-grained site. In this paper, we propose a simple and fast method of coarse-graining TMPs obeying this condition. The procedure involves partitioning transmembrane domains into contiguous segments of equal length along the primary sequence. For the coarsest (lowest-resolution) mappings, it turns out to be most important to satisfy the symmetry in a coarse-grained model. As the resolution is increased to capture more detail, however, it becomes gradually more important to match modular repeats in the secondary structure (such as helix-loop repeats) instead. A set of eight TMPs of various complexity, functionality, structural topology, and internal symmetry, representing different classes of TMPs (ion channels, transporters, receptors, adhesion, and invasion proteins), has been examined. The present approach can be generalized to other systems possessing exact or approximate symmetry, allowing for reliable and fast creation of multiscale, highly coarse-grained mappings of large biomolecular assemblies.
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Affiliation(s)
| | | | | | - Gregory A. Voth
- Department of Chemistry,
Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
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29
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Fraser NJ, Liu JW, Mabbitt PD, Correy GJ, Coppin CW, Lethier M, Perugini MA, Murphy JM, Oakeshott JG, Weik M, Jackson CJ. Evolution of Protein Quaternary Structure in Response to Selective Pressure for Increased Thermostability. J Mol Biol 2016; 428:2359-2371. [DOI: 10.1016/j.jmb.2016.03.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 03/07/2016] [Accepted: 03/16/2016] [Indexed: 10/22/2022]
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30
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Sudha G, Naveenkumar N, Srinivasan N. Evolutionary and structural analyses of heterodimeric proteins composed of subunits with same fold. Proteins 2015; 83:1766-86. [PMID: 26148218 DOI: 10.1002/prot.24849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Revised: 05/30/2015] [Accepted: 06/21/2015] [Indexed: 11/10/2022]
Abstract
Heterodimeric proteins with homologous subunits of same fold are involved in various biological processes. The objective of this study is to understand the evolution of structural and functional features of such heterodimers. Using a non-redundant dataset of 70 such heterodimers of known 3D structure and an independent dataset of 173 heterodimers from yeast, we note that the mean sequence identity between interacting homologous subunits is only 23-24% suggesting that, generally, highly diverged paralogues assemble to form such a heterodimer. We also note that the functional roles of interacting subunits/domains are generally quite different. This suggests that, though the interacting subunits/domains are homologous, the high evolutionary divergence characterize their high functional divergence which contributes to a gross function for the heterodimer considered as a whole. The inverse relationship between sequence identity and RMSD of interacting homologues in heterodimers is not followed. We also addressed the question of formation of homodimers of the subunits of heterodimers by generating models of fictitious homodimers on the basis of the 3D structures of the heterodimers. Interaction energies associated with these homodimers suggests that, in overwhelming majority of the cases, such homodimers are unlikely to be stable. Majority of the homologues of heterodimers of known structures form heterodimers (51.8%) and a small proportion (14.6%) form homodimers. Comparison of 3D structures of heterodimers with homologous homodimers suggests that interfacial nature of residues is not well conserved. In over 90% of the cases we note that the interacting subunits of heterodimers are co-localized in the cell.
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Affiliation(s)
- Govindarajan Sudha
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Nagarajan Naveenkumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, 560065, India.,Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
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31
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Thompson MC, Cascio D, Leibly DJ, Yeates TO. An allosteric model for control of pore opening by substrate binding in the EutL microcompartment shell protein. Protein Sci 2015; 24:956-75. [PMID: 25752492 DOI: 10.1002/pro.2672] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 02/23/2015] [Accepted: 03/03/2015] [Indexed: 01/01/2023]
Abstract
The ethanolamine utilization (Eut) microcompartment is a protein-based metabolic organelle that is strongly associated with pathogenesis in bacteria that inhabit the human gut. The exterior shell of this elaborate protein complex is composed from a few thousand copies of BMC-domain shell proteins, which form a semi-permeable diffusion barrier that provides the interior enzymes with substrates and cofactors while simultaneously retaining metabolic intermediates. The ability of this protein shell to regulate passage of substrate and cofactor molecules is critical for microcompartment function, but the details of how this diffusion barrier can allow the passage of large cofactors while still retaining small intermediates remain unclear. Previous work has revealed two conformations of the EutL shell protein, providing substantial evidence for a gated pore that might allow the passage of large cofactors. Here we report structural and biophysical evidence to show that ethanolamine, the substrate of the Eut microcompartment, acts as a negative allosteric regulator of EutL pore opening. Specifically, a series of X-ray crystal structures of EutL from Clostridium perfringens, along with equilibrium binding studies, reveal that ethanolamine binds to EutL at a site that exists in the closed-pore conformation and which is incompatible with opening of the large pore for cofactor transport. The allosteric mechanism we propose is consistent with the cofactor requirements of the Eut microcompartment, leading to a new model for EutL function. Furthermore, our results suggest the possibility of redox modulation of the allosteric mechanism, opening potentially new lines of investigation.
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Affiliation(s)
- Michael C Thompson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, 90095
| | - Duilio Cascio
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California, 90095
| | - David J Leibly
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, 90095
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, 90095.,UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California, 90095
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32
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Bonjack-Shterengartz M, Avnir D. The near-symmetry of proteins. Proteins 2015; 83:722-34. [PMID: 25354765 DOI: 10.1002/prot.24706] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 10/06/2014] [Accepted: 10/18/2014] [Indexed: 11/07/2022]
Abstract
The majority of protein oligomers form clusters which are nearly symmetric. Understanding of that imperfection, its origins, and perhaps also its advantages requires the conversion of the currently used vague qualitative descriptive language of the near-symmetry into an accurate quantitative measure that will allow to answer questions such as: "What is the degree of symmetry deviation of the protein?," "how do these deviations compare within a family of proteins?," and so on. We developed quantitative methods to answer this type of questions, which are capable of analyzing the whole protein, its backbone or selected portions of it, down to comparison of symmetry-related specific amino-acids, and which are capable of visualizing the various levels of symmetry deviations in the form of symmetry maps. We have applied these methods on an extensive list of homomers and heteromers and found that apparently all proteins never reach perfect symmetry. Strikingly, even homomeric protein clusters are never ideally symmetric. We also found that the main burden of symmetry distortion is on the amino-acids near the symmetry axis; that it is mainly the more hydrophilic amino-acids that take place in symmetry-distortive interactions; and more. The remarkable ability of heteromers to preserve near-symmetry, despite the different sequences, was also shown and analyzed. The comprehensive literature on the suggested advantages symmetric oligomerizations raises a yet-unsolved key question: If symmetry is so advantageous, why do proteins stop shy of perfect symmetry? Some tentative answers to be tested in further studies are suggested in a concluding outlook.
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Affiliation(s)
- Maayan Bonjack-Shterengartz
- Institute of Chemistry and the Lise Meitner Minerva Center for Computational Quantum Chemistry, the Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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33
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Ascher DB, Jubb HC, Pires DEV, Ochi T, Higueruelo A, Blundell TL. Protein-Protein Interactions: Structures and Druggability. MULTIFACETED ROLES OF CRYSTALLOGRAPHY IN MODERN DRUG DISCOVERY 2015. [DOI: 10.1007/978-94-017-9719-1_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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34
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Krishna Kumar K, Jacques DA, Guss JM, Gell DA. The structure of α-haemoglobin in complex with a haemoglobin-binding domain from Staphylococcus aureus reveals the elusive α-haemoglobin dimerization interface. Acta Crystallogr F Struct Biol Commun 2014; 70:1032-7. [PMID: 25084376 PMCID: PMC4118798 DOI: 10.1107/s2053230x14012175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Accepted: 05/26/2014] [Indexed: 11/10/2022] Open
Abstract
Adult haemoglobin (Hb) is made up of two α and two β subunits. Mutations that reduce expression of the α- or β-globin genes lead to the conditions α- or β-thalassaemia, respectively. Whilst both conditions are characterized by anaemia of variable severity, other details of their pathophysiology are different, in part owing to the greater stability of the β chains that is conferred through β self-association. In contrast, α subunits interact weakly, and in the absence of stabilizing quaternary interactions the α chain (α) is prone to haem loss and denaturation. The molecular contacts that confer weak self-association of α have not been determined previously. Here, the first structure of an α2 homodimer is reported in complex with one domain of the Hb receptor from Staphylococcus aureus. The α2 dimer interface has a highly unusual, approximately linear, arrangement of four His side chains within hydrogen-bonding distance of each other. Some interactions present in the α1β1 dimer interface of native Hb are preserved in the α2 dimer. However, a marked asymmetry is observed in the α2 interface, suggesting that steric factors limit the number of stabilizing interactions that can form simultaneously across the interface.
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Affiliation(s)
- Kaavya Krishna Kumar
- School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia
| | - David A. Jacques
- School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia
| | - J. Mitchell Guss
- School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia
| | - David A. Gell
- Menzies Research Institute, University of Tasmania, Hobart, TAS 7000, Australia
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35
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Ye C, Wang Z, Lu W, Zhong M, Chai Q, Wei Y. Correlation between AcrB trimer association affinity and efflux activity. Biochemistry 2014; 53:3738-46. [PMID: 24854514 PMCID: PMC4067148 DOI: 10.1021/bi5000838] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
The majority of membrane proteins
function as oligomers. However,
it remains largely unclear how the oligomer stability of protein complexes
correlates with their function. Understanding the relationship between
oligomer stability and activity is essential to protein research and
to virtually all cellular processes that depend on the function of
protein complexes. Proteins make lasting or transient interactions
as they perform their functions. Obligate oligomeric proteins exist
and function exclusively at a specific oligomeric state. Although
oligomerization is clearly critical for such proteins to function,
a direct correlation between oligomer affinity and biological activity
has not yet been reported. Here, we used an obligate trimeric membrane
transporter protein, AcrB, as a model to investigate the correlation
between its relative trimer affinity and efflux activity. AcrB is
a component of the major multidrug efflux system in Escherichia coli. We created six AcrB constructs
with mutations at the transmembrane intersubunit interface, and we
determined their activities using both a drug susceptibility assay
and an ethidium bromide accumulation assay. The relative trimer affinities
of these mutants in detergent micelles were obtained using blue native
polyacrylamide gel electrophoresis. A correlation between the relative
trimer affinity and substrate efflux activity was observed, in which
a threshold trimer stability was required to maintain efflux activity.
The trimer affinity of the wild-type protein was approximately 3 kcal/mol
more stable than the threshold value. Once the threshold was reached,
an additional increase of stability in the range observed had no observable
effect on protein activity.
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Affiliation(s)
- Cui Ye
- Department of Chemistry, University of Kentucky , Lexington, Kentucky 40506, United States
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36
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Marsh JA, Teichmann SA. Protein flexibility facilitates quaternary structure assembly and evolution. PLoS Biol 2014; 12:e1001870. [PMID: 24866000 PMCID: PMC4035275 DOI: 10.1371/journal.pbio.1001870] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 04/17/2014] [Indexed: 11/25/2022] Open
Abstract
The flexibility of individual proteins aids their evolutionary recruitment into complexes with increasing numbers of distinct subunits. The intrinsic flexibility of proteins allows them to undergo large conformational fluctuations in solution or upon interaction with other molecules. Proteins also commonly assemble into complexes with diverse quaternary structure arrangements. Here we investigate how the flexibility of individual protein chains influences the assembly and evolution of protein complexes. We find that flexibility appears to be particularly conducive to the formation of heterologous (i.e., asymmetric) intersubunit interfaces. This leads to a strong association between subunit flexibility and homomeric complexes with cyclic and asymmetric quaternary structure topologies. Similarly, we also observe that the more nonhomologous subunits that assemble together within a complex, the more flexible those subunits tend to be. Importantly, these findings suggest that subunit flexibility should be closely related to the evolutionary history of a complex. We confirm this by showing that evolutionarily more recent subunits are generally more flexible than evolutionarily older subunits. Finally, we investigate the very different explorations of quaternary structure space that have occurred in different evolutionary lineages. In particular, the increased flexibility of eukaryotic proteins appears to enable the assembly of heteromeric complexes with more unique components. Proteins often interact with other proteins and assemble into complexes. Here we show that the flexibility of individual proteins is important for their recruitment to complexes, as it facilitates the formation of asymmetric interfaces between different subunits. The role of flexibility becomes increasingly important as a greater number of distinct proteins are packed together within a single complex: the more distinct subunits, the more flexible those subunits need to be. A consequence of this is that, when a protein complex gains a new subunit during evolution, the newer subunit will tend to be more flexible than the older subunits. This suggests that we may be able to partially reconstruct the evolutionary history of a protein complex by considering the flexibility of its subunits. We also find that the types of protein complexes an organism forms are closely related to the flexibility of its proteins, with eukaryotic species, and particularly animals, using their increased flexibility to assemble complexes involving more distinct components.
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Affiliation(s)
- Joseph A. Marsh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- * E-mail:
| | - Sarah A. Teichmann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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37
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Asymmetric perturbations of signalling oligomers. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 114:153-69. [PMID: 24650570 DOI: 10.1016/j.pbiomolbio.2014.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 02/26/2014] [Accepted: 03/04/2014] [Indexed: 01/06/2023]
Abstract
This review focuses on rapid and reversible noncovalent interactions for symmetric oligomers of signalling proteins. Symmetry mismatch, transient symmetry breaking and asymmetric perturbations via chemical (ligand binding) and physical (electric or mechanic) effects can initiate the signalling events. Advanced biophysical methods can reveal not only structural symmetries of stable membrane-bound signalling proteins but also asymmetric functional transition states. Relevant techniques amenable to distinguish between symmetric and asymmetric architectures are discussed including those with the capability of capturing low-populated transient conformational states. Typical examples of signalling proteins are overviewed for symmetry breaking in dimers (GPCRs, growth factor receptors, transcription factors); trimers (acid-sensing ion channels); tetramers (voltage-gated cation channels, ionotropic glutamate receptor, CNG and CHN channels); pentameric ligand-gated and mechanosensitive channels; higher order oligomers (gap junction channel, chaperonins, proteasome, virus capsid); as well as primary and secondary transporters. In conclusion, asymmetric perturbations seem to play important functional roles in a broad range of communicating networks.
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38
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Khazanov N, Marcovitz A, Levy Y. Asymmetric DNA-search dynamics by symmetric dimeric proteins. Biochemistry 2013; 52:5335-44. [PMID: 23866074 DOI: 10.1021/bi400357m] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We focus on dimeric DNA-binding proteins from two well-studied families: orthodox type II restriction endonucleases (REs) and transcription factors (TFs). Interactions of the protein's recognition sites with the DNA and, particularly, the contribution of each of the monomers to one-dimensional (1D) sliding along nonspecific DNA were studied using computational tools. Coarse-grained molecular dynamics simulations of DNA scanning by various TFs and REs provide insights into how the symmetry of a homodimer can be broken while they nonspecifically interact with DNA. The characteristics of protein sliding along DNA, such as the average sliding length, partitioning between 1D and 3D search, and the one-dimensional diffusion coefficient D1, strongly depend on the salt concentration, which in turn affects the probability of the two monomers adopting a cooperative symmetric sliding mechanism. Indeed, we demonstrate that maximal DNA search efficiency is achieved when the protein adopts an asymmetric search mode in which one monomer slides while its partner hops. We find that proteins classified as TFs have a higher affinity for the DNA, longer sliding lengths, and an increased probability of symmetric sliding in comparison with REs. Moreover, TFs can perform their biological function over a much wider range of salt concentrations than REs. Our results demonstrate that the different biological functions of DNA-binding proteins are related to the different nonspecific DNA search mechanisms they adopt.
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Affiliation(s)
- Netaly Khazanov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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39
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Mowrey D, Cheng MH, Liu LT, Willenbring D, Lu X, Wymore T, Xu Y, Tang P. Asymmetric ligand binding facilitates conformational transitions in pentameric ligand-gated ion channels. J Am Chem Soc 2013; 135:2172-80. [PMID: 23339564 DOI: 10.1021/ja307275v] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The anesthetic propofol inhibits the currents of the homopentameric ligand-gated ion channel GLIC, yet the crystal structure of GLIC with five propofol molecules bound symmetrically shows an open-channel conformation. To address this dilemma and determine if the symmetry of propofol binding sites affects the channel conformational transition, we performed a total of 1.5 μs of molecular dynamics simulations for different GLIC systems with propofol occupancies of 0, 1, 2, 3, and 5. GLIC without propofol binding or with five propofol molecules bound symmetrically, showed similar channel conformation and hydration status over multiple replicates of 100-ns simulations. In contrast, asymmetric binding to one, two or three equivalent sites in different subunits accelerated the channel dehydration, increased the conformational heterogeneity of the pore-lining TM2 helices, and shifted the lateral and radial tilting angles of TM2 toward a closed-channel conformation. The results differentiate two groups of systems based on the propofol binding symmetry. The difference between symmetric and asymmetric groups is correlated with the variance in the propofol-binding cavity adjacent to the hydrophobic gate and the force imposed by the bound propofol. Asymmetrically bound propofol produced greater variance in the cavity size that could further elevate the conformation heterogeneity. The force trajectory generated by propofol in each subunit over the course of a simulation exhibits an ellipsoidal shape, which has the larger component tangential to the pore. Asymmetric propofol binding creates an unbalanced force that expedites the channel conformation transitions. The findings from this study not only suggest that asymmetric binding underlies the propofol functional inhibition of GLIC, but also advocate for the role of symmetry breaking in facilitating channel conformational transitions.
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Affiliation(s)
- David Mowrey
- Department of Anesthesiology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
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40
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Abstract
Structural symmetry in homooligomeric proteins has intrigued many researchers over the past several decades. However, the implication of protein symmetry is still not well understood. In this study, we performed molecular dynamics (MD) simulations of two forms of trp RNA binding attenuation protein (TRAP), the wild-type 11-mer and an engineered 12-mer, having two different levels of circular symmetry. The results of the simulations showed that the inter-subunit fluctuations in the 11-mer TRAP were significantly smaller than the fluctuations in the 12-mer TRAP while the internal fluctuations were larger in the 11-mer than in the 12-mer. These differences in thermal fluctuations were interpreted by normal mode analysis and group theory. For the 12-mer TRAP, the wave nodes of the normal modes existed at the flexible interface between the subunits, while the 11-mer TRAP had its nodes within the subunits. The principal components derived from the MD simulations showed similar mode structures. These results demonstrated that the structural symmetry was an important determinant of protein dynamics in circularly symmetric homooligomeric proteins.
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Affiliation(s)
- Yasuhiro Matsunaga
- Special Postdoctoral Researchers Program, RIKEN Advanced Institute for Computational Science, Kobe, Japan.
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41
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Chhikara N, Saraswat M, Tomar AK, Dey S, Singh S, Yadav S. Human epididymis protein-4 (HE-4): a novel cross-class protease inhibitor. PLoS One 2012; 7:e47672. [PMID: 23139753 PMCID: PMC3489902 DOI: 10.1371/journal.pone.0047672] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 09/18/2012] [Indexed: 02/07/2023] Open
Abstract
Epididymal proteins represent the factors necessary for maturation of sperm and play a crucial role in sperm maturation. HE-4, an epididymal protein, is a member of whey acidic protein four-disulfide core (WFDC) family with no known function. A WFDC protein has a conserved WFDC domain of 50 amino acids with eight conserved cystine residue. HE-4 is a 124 amino acid long polypeptide with two WFDC domains. Here, we show that HE-4 is secreted in the human seminal fluid as a disulfide-bonded homo-trimer and is a cross-class protease inhibitor inhibits some of the serine, aspartyl and cysteine proteases tested using hemoglobin as a substrate. Using SPR we have also observed that HE-4 shows a significant binding with all these proteases. Disulfide linkages are essential for this activity. Moreover, HE-4 is N-glycosylated and highly stable on a wide range of pH and temperature. Taken together this suggests that HE-4 is a cross-class protease inhibitor which might confer protection against microbial virulence factors of proteolytic nature.
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Affiliation(s)
- Nirmal Chhikara
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Mayank Saraswat
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Anil Kumar Tomar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Sharmistha Dey
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Sarman Singh
- Department of Lab Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Savita Yadav
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
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42
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Micheletti C. Comparing proteins by their internal dynamics: exploring structure-function relationships beyond static structural alignments. Phys Life Rev 2012. [PMID: 23199577 DOI: 10.1016/j.plrev.2012.10.009] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The growing interest for comparing protein internal dynamics owes much to the realisation that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional structural elements, those aspects of protein flexibility and dynamics that are functionally oriented should be subject to evolutionary conservation. Accordingly, dynamics-based protein comparisons or alignments could be used to detect protein relationships that are more elusive to sequence and structural alignments. Here we provide an account of the progress that has been made in recent years towards developing and applying general methods for comparing proteins in terms of their internal dynamics and advance the understanding of the structure-function relationship.
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Affiliation(s)
- Cristian Micheletti
- Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, Trieste, Italy.
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43
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Swapna LS, Srikeerthana K, Srinivasan N. Extent of structural asymmetry in homodimeric proteins: prevalence and relevance. PLoS One 2012; 7:e36688. [PMID: 22629324 PMCID: PMC3358323 DOI: 10.1371/journal.pone.0036688] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 04/11/2012] [Indexed: 11/21/2022] Open
Abstract
Most homodimeric proteins have symmetric structure. Although symmetry is known to confer structural and functional advantage, asymmetric organization is also observed. Using a non-redundant dataset of 223 high-resolution crystal structures of biologically relevant homodimers, we address questions on the prevalence and significance of asymmetry. We used two measures to quantify global and interface asymmetry, and assess the correlation of several molecular and structural parameters with asymmetry. We have identified rare cases (11/223) of biologically relevant homodimers with pronounced global asymmetry. Asymmetry serves as a means to bring about 2∶1 binding between the homodimer and another molecule; it also enables cellular signalling arising from asymmetric macromolecular ligands such as DNA. Analysis of these cases reveals two possible mechanisms by which possible infinite array formation is prevented. In case of homodimers associating via non-topologically equivalent surfaces in their tertiary structures, ligand-dependent mechanisms are used. For stable dimers binding via large surfaces, ligand-dependent structural change regulates polymerisation/depolymerisation; for unstable dimers binding via smaller surfaces that are not evolutionarily well conserved, dimerisation occurs only in the presence of the ligand. In case of homodimers associating via interaction surfaces with parts of the surfaces topologically equivalent in the tertiary structures, steric hindrance serves as the preventive mechanism of infinite array. We also find that homodimers exhibiting grossly symmetric organization rarely exhibit either perfect local symmetry or high local asymmetry. Binding of small ligands at the interface does not cause any significant variation in interface asymmetry. However, identification of biologically relevant interface asymmetry in grossly symmetric homodimers is confounded by the presence of similar small magnitude changes caused due to artefacts of crystallisation. Our study provides new insights regarding accommodation of asymmetry in homodimers.
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44
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Ghosh P, Mushtaq AU, Durani S. Computational design by evolving folds and assemblies over the alphabet in l- and d-α-amino acids. RSC Adv 2012. [DOI: 10.1039/c2ra01012g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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45
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Chan KY, Gumbart J, McGreevy R, Watermeyer JM, Sewell BT, Schulten K. Symmetry-restrained flexible fitting for symmetric EM maps. Structure 2011; 19:1211-8. [PMID: 21893283 DOI: 10.1016/j.str.2011.07.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 07/21/2011] [Accepted: 07/28/2011] [Indexed: 01/25/2023]
Abstract
Many large biological macromolecules have inherent structural symmetry, being composed of a few distinct subunits, repeated in a symmetric array. These complexes are often not amenable to traditional high-resolution structural determination methods, but can be imaged in functionally relevant states using cryo-electron microscopy (cryo-EM). A number of methods for fitting atomic-scale structures into cryo-EM maps have been developed, including the molecular dynamics flexible fitting (MDFF) method. However, quality and resolution of the cryo-EM map are the major determinants of a method's success. In order to incorporate knowledge of structural symmetry into the fitting procedure, we developed the symmetry-restrained MDFF method. The new method adds to the cryo-EM map-derived potential further restraints on the allowed conformations of a complex during fitting, thereby improving the quality of the resultant structure. The benefit of using symmetry-based restraints during fitting, particularly for medium to low-resolution data, is demonstrated for three different systems.
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Affiliation(s)
- Kwok-Yan Chan
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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46
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Roy A, Post CB. Microscopic Symmetry Imposed by Rotational Symmetry Boundary Conditions in Molecular Dynamics Simulation. J Chem Theory Comput 2011; 7:3346-3353. [PMID: 22096451 DOI: 10.1021/ct2000843] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A large number of viral capsids, as well as other macromolecular assemblies, have icosahedral structure or structures with other rotational symmetries. This symmetry can be exploited during molecular dynamics (MD) to model in effect the full viral capsid using only a subset of primary atoms plus copies of image atoms generated from rotational symmetry boundary conditions (RSBC). A pure rotational symmetry operation results in both primary and image atoms at short range, and within nonbonded interaction distance of each other, so that nonbonded interactions can not be specified by the minimum image convention and explicit treatment of image atoms is required. As such an unavoidable consequence of RSBC is that the enumeration of nonbonded interactions in regions surrounding certain rotational axes must include both a primary atom and its copied image atom, thereby imposing microscopic symmetry for some forces. We examined the possibility of artifacts arising from this imposed microscopic symmetry of RSBC using two simulation systems: a water shell and human rhinovirus 14 (HRV14) capsid with explicit water. The primary unit was a pentamer of the icosahedron, which has the advantage of direct comparison of icosahedrally equivalent spatial regions, for example regions near a 2-fold symmetry axis with imposed symmetry and a 2-fold axis without imposed symmetry. Analysis of structural and dynamic properties of water molecules and protein atoms found similar behavior near symmetry axes with imposed symmetry and where the minimum image convention fails compared with that in other regions in the simulation system, even though an excluded volume effect was detected for water molecules near the axes with imposed symmetry. These results validate the use of RSBC for icosahedral viral capsids or other rotationally symmetric systems.
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Affiliation(s)
- Amitava Roy
- Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, USA
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47
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Dryzun C, Zait A, Avnir D. Quantitative symmetry and chirality-A fast computational algorithm for large structures: Proteins, macromolecules, nanotubes, and unit cells. J Comput Chem 2011; 32:2526-38. [DOI: 10.1002/jcc.21828] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 03/29/2011] [Accepted: 04/04/2011] [Indexed: 11/10/2022]
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48
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Barman A, Schürer S, Prabhakar R. Computational modeling of substrate specificity and catalysis of the β-secretase (BACE1) enzyme. Biochemistry 2011; 50:4337-49. [PMID: 21500768 DOI: 10.1021/bi200081h] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In this combined MD simulation and DFT study, interactions of the wild-type (WT) amyloid precursor protein (APP) and its Swedish variant (SW), Lys670 → Asn and Met671 → Leu, with the beta-secretase (BACE1) enzyme and their cleavage mechanisms have been investigated. BACE1 catalyzes the rate-limiting step in the generation of 40-42 amino acid long Alzheimer amyloid beta (Aβ) peptides. All key structural parameters such as position of the flap, volume of the active site, electrostatic binding energy, structures, and positions of the inserts A, D, and F and 10s loop obtained from the MD simulations show that, in comparison to the WT-substrate, BACE1 exhibits greater affinity for the SW-substrate and orients it in a more reactive conformation. The enzyme-substrate models derived from the MD simulations were further utilized to investigate the general acid/base mechanism used by BACE1 to hydrolytically cleave these substrates. This mechanism proceeds through the following two steps: (1) formation of the gem-diol intermediate and (2) cleavage of the peptide bond. For the WT-substrate, the overall barrier of 22.4 kcal/mol for formation of the gem-diol intermediate is 3.3 kcal/mol higher than for the SW-substrate (19.1 kcal/mol). This process is found to be the rate-limiting in the entire mechanism. The computed barrier is in agreement with the measured barrier of ca. 18.00 kcal/mol for the WT-substrate and supports the experimental observation that the cleavage of the SW-substrate is 60 times more efficient than the WT-substrate.
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Affiliation(s)
- Arghya Barman
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
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49
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Gopalan V, Litvin DB. Rotation-reversal symmetries in crystals and handed structures. NATURE MATERIALS 2011; 10:376-381. [PMID: 21460821 DOI: 10.1038/nmat2987] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 02/11/2011] [Indexed: 05/30/2023]
Abstract
Symmetry is a powerful framework to perceive and predict the physical world. The structure of materials is described by a combination of rotations, rotation-inversions and translational symmetries. By recognizing the reversal of static structural rotations between clockwise and counterclockwise directions as a distinct symmetry operation, here we show that there are many more structural symmetries than are currently recognized in right- or left-handed helices, spirals, and in antidistorted structures composed equally of rotations of both handedness. For example, we show that many antidistorted perovskites possess twice the number of symmetry elements as conventionally identified. These new 'roto' symmetries predict new forms for 'roto' properties that relate to static rotations, such as rotoelectricity, piezorotation, and rotomagnetism. They enable a symmetry-based search for new phenomena, such as multiferroicity involving a coupling of spins, electric polarization and static rotations. This work is relevant to structure-property relationships in all materials and structures with static rotations.
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Affiliation(s)
- Venkatraman Gopalan
- Department of Materials Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16803, USA.
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50
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Jeon J, Nam HJ, Choi YS, Yang JS, Hwang J, Kim S. Molecular evolution of protein conformational changes revealed by a network of evolutionarily coupled residues. Mol Biol Evol 2011; 28:2675-85. [PMID: 21470969 DOI: 10.1093/molbev/msr094] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
An improved understanding of protein conformational changes has broad implications for elucidating the mechanisms of various biological processes and for the design of protein engineering experiments. Understanding rearrangements of residue interactions is a key component in the challenge of describing structural transitions. Evolutionary properties of protein sequences and structures are extensively studied; however, evolution of protein motions, especially with respect to interaction rearrangements, has yet to be explored. Here, we investigated the relationship between sequence evolution and protein conformational changes and discovered that structural transitions are encoded in amino acid sequences as coevolving residue pairs. Furthermore, we found that highly coevolving residues are clustered in the flexible regions of proteins and facilitate structural transitions by forming and disrupting their interactions cooperatively. Our results provide insight into the evolution of protein conformational changes and help to identify residues important for structural transitions.
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Affiliation(s)
- Jouhyun Jeon
- Division of Molecular and Life Science, Pohang University of Science and Technology, Pohang, Korea
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