1
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Pereira AF, Martínez L. Helical Content Correlations and Hydration Structures of the Folding Ensemble of the B Domain of Protein A. J Chem Inf Model 2024; 64:3350-3359. [PMID: 38566451 DOI: 10.1021/acs.jcim.3c01822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The B domain of protein A (BdpA), a small three-helix bundle, folds on a time scale of a few microseconds with heterogeneous native and unfolded states. It is widely used as a model for understanding protein folding mechanisms. In this work, we use structure-based models (SBMs) and atomistic simulations to comprehensively investigate how BdpA folding is associated with the formation of its secondary structure. The energy landscape visualization method (ELViM) was used to characterize the pathways that connect the folded and unfolded states of BdpA as well as the sets of structures displaying specific ellipticity patterns. We show that the native state conformational diversity is due mainly to the conformational variability of helix I. Helices I, II, and III occur in a weakly correlated manner, with Spearman's rank correlation coefficients of 0.1539 (I and II), 0.1259 (I and III), and 0.2561 (II and III). These results, therefore, suggest the highest cooperativity between helices II and III. Our results allow the clustering of partially folded structures of folding of the B domain of protein A on the basis of its secondary structure, paving the way to an understanding of environmental factors in the relative stability of the basins of the folding ensemble, which are illustrated by the structural dependency of the protein hydration structures, as computed with minimum-distance distribution functions.
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Affiliation(s)
- Ander Francisco Pereira
- Institute of Chemistry and Center for Computing in Engineering & Science, Universidade Estadual de Campinas (UNICAMP), 13083-861 Campinas, SP, Brazil
| | - Leandro Martínez
- Institute of Chemistry and Center for Computing in Engineering & Science, Universidade Estadual de Campinas (UNICAMP), 13083-861 Campinas, SP, Brazil
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2
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Zhao H, Wu H, Guseman A, Abeykoon D, Camara CM, Dalal Y, Fushman D, Papoian GA. The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea. PLoS Comput Biol 2024; 20:e1011721. [PMID: 38181064 PMCID: PMC10796010 DOI: 10.1371/journal.pcbi.1011721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/18/2024] [Accepted: 11/28/2023] [Indexed: 01/07/2024] Open
Abstract
Histones compact and store DNA in both Eukarya and Archaea, forming heterodimers in Eukarya and homodimers in Archaea. Despite this, the folding mechanism of histones across species remains unclear. Our study addresses this gap by investigating 11 types of histone and histone-like proteins across humans, Drosophila, and Archaea through multiscale molecular dynamics (MD) simulations, complemented by NMR and circular dichroism experiments. We confirm and elaborate on the widely applied "folding upon binding" mechanism of histone dimeric proteins and report a new alternative conformation, namely, the inverted non-native dimer, which may be a thermodynamically metastable configuration. Protein sequence analysis indicated that the inverted conformation arises from the hidden ancestral head-tail sequence symmetry underlying all histone proteins, which is congruent with the previously proposed histone evolution hypotheses. Finally, to explore the potential formations of homodimers in Eukarya, we utilized MD-based AWSEM and AI-based AlphaFold-Multimer models to predict their structures and conducted extensive all-atom MD simulations to examine their respective structural stabilities. Our results suggest that eukaryotic histones may also form stable homodimers, whereas their disordered tails bring significant structural asymmetry and tip the balance towards the formation of commonly observed heterotypic dimers.
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Affiliation(s)
- Haiqing Zhao
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hao Wu
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America
| | - Alex Guseman
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
| | - Dulith Abeykoon
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
| | - Christina M. Camara
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
| | - Yamini Dalal
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - David Fushman
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
| | - Garegin A. Papoian
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
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3
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Ghosh C, Jana B. Curious Case of MAD2 Protein: Diverse Folding Intermediates Leading to Alternate Native States. J Phys Chem B 2022; 126:1904-1916. [PMID: 35230837 DOI: 10.1021/acs.jpcb.2c00382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Anfinsen's dogma postulates that for one sequence there will be only one unique structure that is necessary for the functioning of the protein. However, over the years there have been a number of departures from this postulate. As far as function is considered, there are growing examples of proteins that "moonlight", perform multiple unrelated functions. With the discovery of intrinsically disordered proteins, morpheeins, chameleonic sequences, and metamorphic proteins that can switch folds, we have acquired a more nuanced understanding of protein folding and dynamics. Appearing to apparently contradict the classical folding paradigm, metamorphic proteins are considered exotic species. In this work, we have explored the free energy landscape and folding pathways of the metamorphic protein MAD2 which is an important component of the spindle checkpoint. It coexists in two alternate states: the inactive open state and the active closed state. Using a dual-basin structure-based model approach we have shown that a variety of intermediates and multiple pathways are available to MAD2 to fold into its alternate forms. This approach involves performing molecular dynamics simulations of coarse-grained models of MAD2 where the structural information regarding both of its native conformations is explicitly included in terms of their native contacts in the force field used. Detailed analyses have indicated that some of the contacts within the protein play a key role in determining which folding pathway will be selected and point to a probable long-range communication between the N and the C termini of the protein that seems to control its folding. Finally, our work also provides a rationale for the experimentally observed preference of the ΔC10 variant of MAD2 to exist in the open state.
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Affiliation(s)
- Catherine Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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4
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Reinartz I, Sarter M, Otten J, Höfig H, Pohl M, Schug A, Stadler AM, Fitter J. Structural Analysis of a Genetically Encoded FRET Biosensor by SAXS and MD Simulations. SENSORS 2021; 21:s21124144. [PMID: 34208740 PMCID: PMC8234384 DOI: 10.3390/s21124144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 12/27/2022]
Abstract
Inspired by the modular architecture of natural signaling proteins, ligand binding proteins are equipped with two fluorescent proteins (FPs) in order to obtain Förster resonance energy transfer (FRET)-based biosensors. Here, we investigated a glucose sensor where the donor and acceptor FPs were attached to a glucose binding protein using a variety of different linker sequences. For three resulting sensor constructs the corresponding glucose induced conformational changes were measured by small angle X-ray scattering (SAXS) and compared to recently published single molecule FRET results (Höfig et al., ACS Sensors, 2018). For one construct which exhibits a high change in energy transfer and a large change of the radius of gyration upon ligand binding, we performed coarse-grained molecular dynamics simulations for the ligand-free and the ligand-bound state. Our analysis indicates that a carefully designed attachment of the donor FP is crucial for the proper transfer of the glucose induced conformational change of the glucose binding protein into a well pronounced FRET signal change as measured in this sensor construct. Since the other FP (acceptor) does not experience such a glucose induced alteration, it becomes apparent that only one of the FPs needs to have a well-adjusted attachment to the glucose binding protein.
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Affiliation(s)
- Ines Reinartz
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany;
- HIDSS4Health-Helmholtz Information and Data Science School for Health, 76344 Eggenstein-Leopoldshafen, Germany
| | - Mona Sarter
- I Physikalisches Institut (IA), AG Biophysik, RWTH Aachen University, 52074 Aachen, Germany; (M.S.); (H.H.)
- Forschungszentrum Jülich, IBI-8/JCNS-1, 52428 Jülich, Germany;
| | - Julia Otten
- Forschungszentrum Jülich, IBG-1, 52426 Jülich, Germany; (J.O.); (M.P.)
| | - Henning Höfig
- I Physikalisches Institut (IA), AG Biophysik, RWTH Aachen University, 52074 Aachen, Germany; (M.S.); (H.H.)
- Forschungszentrum Jülich, IBI-6, 52428 Jülich, Germany
| | - Martina Pohl
- Forschungszentrum Jülich, IBG-1, 52426 Jülich, Germany; (J.O.); (M.P.)
| | - Alexander Schug
- John von Neumann Institute for Computing, Jülich Supercomputing Centre, Forschungszentrum Jülich, 52428 Jülich, Germany;
- Faculty of Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Andreas M. Stadler
- Forschungszentrum Jülich, IBI-8/JCNS-1, 52428 Jülich, Germany;
- Institut für Physikalische Chemie, RWTH Aachen University, 52074 Aachen, Germany
| | - Jörg Fitter
- I Physikalisches Institut (IA), AG Biophysik, RWTH Aachen University, 52074 Aachen, Germany; (M.S.); (H.H.)
- Forschungszentrum Jülich, IBI-6, 52428 Jülich, Germany
- Correspondence: ; Tel.: +49-241-80-27209
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5
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Gómez-González J, Pérez Y, Sciortino G, Roldan-Martín L, Martínez-Costas J, Maréchal JD, Alfonso I, Vázquez López M, Vázquez ME. Dynamic Stereoselection of Peptide Helicates and Their Selective Labeling of DNA Replication Foci in Cells*. Angew Chem Int Ed Engl 2021; 60:8859-8866. [PMID: 33290612 DOI: 10.1002/anie.202013039] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/12/2020] [Indexed: 01/03/2023]
Abstract
Although largely overlooked in peptide engineering, coordination chemistry offers a new set of interactions that opens unexplored design opportunities for developing complex molecular structures. In this context, we report new artificial peptide ligands that fold into chiral helicates in the presence of labile metal ions such as FeII and CoII . Heterochiral β-turn-promoting sequences encode the stereoselective folding of the peptide ligands and define the physicochemical properties of their corresponding metal complexes. Circular dichroism and NMR spectroscopy in combination with computational methods allowed us to identify and determine the structure of two isochiral ΛΛ-helicates, folded as topological isomers. Finally, in addition to the in-vitro characterization of their selective binding to DNA three-way junctions, cell-microscopy experiments demonstrated that a rhodamine-labeled FeII helicate was internalized and selectively stains DNA replication factories in functional cells.
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Affiliation(s)
- Jacobo Gómez-González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain
| | - Yolanda Pérez
- NMR Facility, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Giuseppe Sciortino
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola, Spain.,Institute of Chemical Research of Catalonia (ICIQ), Avgda. Països Catalans, 16, 43007, Tarragona, Spain
| | - Lorena Roldan-Martín
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola, Spain
| | - José Martínez-Costas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Bioquímica y Biología Molecular, Universidade de Santiago de Compostela, Spain
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola, Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela, Spain
| | - M Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain
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6
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Gómez‐González J, Pérez Y, Sciortino G, Roldan‐Martín L, Martínez‐Costas J, Maréchal J, Alfonso I, Vázquez López M, Vázquez ME. Dynamic Stereoselection of Peptide Helicates and Their Selective Labeling of DNA Replication Foci in Cells**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jacobo Gómez‐González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Química Orgánica Universidade de Santiago de Compostela Spain
| | - Yolanda Pérez
- NMR Facility Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Giuseppe Sciortino
- Departament de Química Universitat Autònoma de Barcelona 08193 Cerdanyola Spain
- Institute of Chemical Research of Catalonia (ICIQ) Avgda. Països Catalans, 16 43007 Tarragona Spain
| | | | - José Martínez‐Costas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Bioquímica y Biología Molecular Universidade de Santiago de Compostela Spain
| | | | - Ignacio Alfonso
- Department of Biological Chemistry Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Química Inorgánica Universidade de Santiago de Compostela Spain
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Química Orgánica Universidade de Santiago de Compostela Spain
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7
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Reinartz I, Weiel M, Schug A. FRET Dyes Significantly Affect SAXS Intensities of Proteins. Isr J Chem 2020. [DOI: 10.1002/ijch.202000007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ines Reinartz
- Institute for Automation and Applied InformaticsKarlsruhe Institute of Technology Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
- HIDSS4Health – Helmholtz Information and Data Science School for Health Karlsruhe/Heidelberg Germany
| | - Marie Weiel
- Department of PhysicsKarlsruhe Institute of Technology Wolfgang-Gaede-Str. 1 76131 Karlsruhe Germany
- Steinbuch Centre for ComputingKarlsruhe Institute of Technology Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Alexander Schug
- Institute for Advanced Simulation Jülich Supercomputing Center Wilhelm-Johnen-Straße 52428 Jülich Germany
- Faculty of BiologyUniversity of Duisburg-Essen Germany
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8
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Abstract
It is a common belief that metamorphic proteins challenge Anfinsen's thermodynamic hypothesis (or dogma). Here we argue against this view and aim to show that metamorphic proteins not only fulfill Anfinsen's dogma but also exhibit marginal stability comparable to that seen on biomolecules and macromolecular complexes. This work contributes to our general understanding of protein classification and may spur significant progress in our effort to analyze protein evolvability.
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Affiliation(s)
- Jorge A Vila
- IMASL-CONICET, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700 San Luis, Argentina
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9
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Oliveira AB, Yang H, Whitford PC, Leite VBP. Distinguishing Biomolecular Pathways and Metastable States. J Chem Theory Comput 2019; 15:6482-6490. [DOI: 10.1021/acs.jctc.9b00704] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Antonio B. Oliveira
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Huan Yang
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Paul C. Whitford
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Vitor B. P. Leite
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto, São Paulo 15054-000, Brazil
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
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10
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Martin OA, Vorobjev Y, Scheraga HA, Vila JA. Outline of an experimental design aimed to detect a protein A mirror image in solution. PEERJ PHYSICAL CHEMISTRY 2019; 1. [PMID: 34079958 DOI: 10.7717/peerj-pchem.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There is abundant theoretical evidence indicating that a mirror image of Protein A may occur during the protein folding process. However, as to whether such mirror image exists in solution is an unsolved issue. Here we provide outline of an experimental design aimed to detect the mirror image of Protein A in solution. The proposal is based on computational simulations indicating that the use of a mutant of protein A, namely Q10H, could be used to detect the mirror image conformation in solution. Our results indicate that the native conformation of the protein A should have a pKa, for the Q10H mutant, at ≈6.2, while the mirror-image conformation should have a pKa close to ≈7.3. Naturally, if all the population is in the native state for the Q10H mutant, the pKa should be ≈6.2, while, if all are in the mirror-image state, it would be ≈7.3, and, if it is a mixture, the pKa should be largerthan 6.2, presumably in proportion to the mirror population. In addition, evidence is provided indicating the tautomeric distribution of H10 must also change between the native and mirror conformations. Although this may not be completely relevant for the purpose of determining whether the protein A mirror image exists in solution, it could provide valuable information to validate the pKa findings. We hope this proposal will foster experimental work on this problem either by direct application of our proposed experimental design or serving as inspiration and motivation for other experiments.
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Affiliation(s)
- Osvaldo A Martin
- Instituto de Matemática Aplicada San Luis, UNSL-CONICET, San Luis, Argentina
| | - Yury Vorobjev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
| | - Harold A Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States
| | - Jorge A Vila
- Instituto de Matemática Aplicada San Luis, UNSL-CONICET, San Luis, Argentina.,Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States
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11
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Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level. Biomolecules 2019; 9:biom9020077. [PMID: 30813315 PMCID: PMC6406393 DOI: 10.3390/biom9020077] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/10/2019] [Accepted: 02/10/2019] [Indexed: 01/10/2023] Open
Abstract
Folded proteins show a high degree of structural order and undergo (fairly constrained) collective motions related to their functions. On the other hand, intrinsically disordered proteins (IDPs), while lacking a well-defined three-dimensional structure, do exhibit some structural and dynamical ordering, but are less constrained in their motions than folded proteins. The larger structural plasticity of IDPs emphasizes the importance of entropically driven motions. Many IDPs undergo function-related disorder-to-order transitions driven by their interaction with specific binding partners. As experimental techniques become more sensitive and become better integrated with computational simulations, we are beginning to see how the modest structural ordering and large amplitude collective motions of IDPs endow them with an ability to mediate multiple interactions with different partners in the cell. To illustrate these points, here, we use Prostate-associated gene 4 (PAGE4), an IDP implicated in prostate cancer (PCa) as an example. We first review our previous efforts using molecular dynamics simulations based on atomistic AWSEM to study the conformational dynamics of PAGE4 and how its motions change in its different physiologically relevant phosphorylated forms. Our simulations quantitatively reproduced experimental observations and revealed how structural and dynamical ordering are encoded in the sequence of PAGE4 and can be modulated by different extents of phosphorylation by the kinases HIPK1 and CLK2. This ordering is reflected in changing populations of certain secondary structural elements as well as in the regularity of its collective motions. These ordered features are directly correlated with the functional interactions of WT-PAGE4, HIPK1-PAGE4 and CLK2-PAGE4 with the AP-1 signaling axis. These interactions give rise to repeated transitions between (high HIPK1-PAGE4, low CLK2-PAGE4) and (low HIPK1-PAGE4, high CLK2-PAGE4) cell phenotypes, which possess differing sensitivities to the standard PCa therapies, such as androgen deprivation therapy (ADT). We argue that, although the structural plasticity of an IDP is important in promoting promiscuous interactions, the modulation of the structural ordering is important for sculpting its interactions so as to rewire with agility biomolecular interaction networks with significant functional consequences.
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12
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Atomistic simulations indicate the functional loop-to-coiled-coil transition in influenza hemagglutinin is not downhill. Proc Natl Acad Sci U S A 2018; 115:E7905-E7913. [PMID: 30012616 DOI: 10.1073/pnas.1805442115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Influenza hemagglutinin (HA) mediates viral entry into host cells through a large-scale conformational rearrangement at low pH that leads to fusion of the viral and endosomal membranes. Crystallographic and biochemical data suggest that a loop-to-coiled-coil transition of the B-loop region of HA is important for driving this structural rearrangement. However, the microscopic picture for this proposed "spring-loaded" movement is missing. In this study, we focus on understanding the transition of the B loop and perform a set of all-atom molecular dynamics simulations of the full B-loop trimeric structure with the CHARMM36 force field. The free-energy profile constructed from our simulations describes a B loop that stably folds half of the postfusion coiled coil in tens of microseconds, but the full coiled coil is unfavorable. A buried hydrophilic residue, Thr59, is implicated in destabilizing the coiled coil. Interestingly, this conserved threonine is the only residue in the B loop that strictly differentiates between the group 1 and 2 HA molecules. Microsecond-scale constant temperature simulations revealed that kinetic traps in the structural switch of the B loop can be caused by nonnative, intramonomer, or intermonomer β-sheets. The addition of the A helix stabilized the postfusion state of the B loop, but introduced the possibility for further β-sheet structures. Overall, our results do not support a description of the B loop in group 2 HAs as a stiff spring, but, rather, it allows for more structural heterogeneity in the placement of the fusion peptides during the fusion process.
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13
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Kurczynska M, Kotulska M. Automated method to differentiate between native and mirror protein models obtained from contact maps. PLoS One 2018; 13:e0196993. [PMID: 29787567 PMCID: PMC5963800 DOI: 10.1371/journal.pone.0196993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 04/24/2018] [Indexed: 11/23/2022] Open
Abstract
Mirror protein structures are often considered as artifacts in modeling protein structures. However, they may soon become a new branch of biochemistry. Moreover, methods of protein structure reconstruction, based on their residue-residue contact maps, need methodology to differentiate between models of native and mirror orientation, especially regarding the reconstructed backbones. We analyzed 130 500 structural protein models obtained from contact maps of 1 305 SCOP domains belonging to all 7 structural classes. On average, the same numbers of native and mirror models were obtained among 100 models generated for each domain. Since their structural features are often not sufficient for differentiating between the two types of model orientations, we proposed to apply various energy terms (ETs) from PyRosetta to separate native and mirror models. To automate the procedure for differentiating these models, the k-means clustering algorithm was applied. Using total energy did not allow to obtain appropriate clusters–the accuracy of the clustering for class A (all helices) was no more than 0.52. Therefore, we tested a series of different k-means clusterings based on various combinations of ETs. Finally, applying two most differentiating ETs for each class allowed to obtain satisfying results. To unify the method for differentiating between native and mirror models, independent of their structural class, the two best ETs for each class were considered. Finally, the k-means clustering algorithm used three common ETs: probability of amino acid assuming certain values of dihedral angles Φ and Ψ, Ramachandran preferences and Coulomb interactions. The accuracies of clustering with these ETs were in the range between 0.68 and 0.76, with sensitivity and selectivity in the range between 0.68 and 0.87, depending on the structural class. The method can be applied to all fully-automated tools for protein structure reconstruction based on contact maps, especially those analyzing big sets of models.
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Affiliation(s)
- Monika Kurczynska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Malgorzata Kotulska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wroclaw, Poland
- * E-mail:
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14
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Reinartz I, Sinner C, Nettels D, Stucki-Buchli B, Stockmar F, Panek PT, Jacob CR, Nienhaus GU, Schuler B, Schug A. Simulation of FRET dyes allows quantitative comparison against experimental data. J Chem Phys 2018; 148:123321. [DOI: 10.1063/1.5010434] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Ines Reinartz
- Department of Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Claude Sinner
- Department of Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Brigitte Stucki-Buchli
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Florian Stockmar
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Pawel T. Panek
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R. Jacob
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Gerd Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- HEiKA–Heidelberg Karlsruhe Research Partnership, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Nanotechnology and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Department of Physics, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Alexander Schug
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- John von Neumann Institute for Computing, Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425 Jülich, Germany
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15
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Chen M, Lin X, Lu W, Onuchic JN, Wolynes PG. Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β Proteins. J Phys Chem B 2016; 121:3473-3482. [PMID: 27797194 DOI: 10.1021/acs.jpcb.6b09347] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The atomistic associative memory, water mediated, structure and energy model (AAWSEM) is an efficient coarse-grained force field with transferable tertiary interactions that incorporates local in sequence energetic biases using structural information derived from all-atom simulations of long segments of the protein. For α helical proteins, the accuracy of structure prediction using AAWSEM has been established previously. In this article, we examine the capability of AAWSEM to predict the structure of α/β proteins. We also elaborate on an iterative approach that uses the structures from a first round of AAWSEM simulation as fragment memories. This iterative scheme improves the quality of the structure prediction and makes the free energy profile more funneled toward native configurations. We explore the use of clustering analyses as a way of evaluating the confidence in various structure prediction models. Clustering using a local relative order parameter (mutual Q) of the predicted structural ensemble turns out to be optimal. The tightest cluster according to mutual Q generally has the most correctly folded structure. Since there is no bioinformatic input, AAWSEM amounts to an ab initio protein structure prediction method that combines the efficiency of coarse-grained simulations with the local structural accuracy that can be achieved from all-atom simulations.
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Affiliation(s)
- Mingchen Chen
- Center for Theoretical Biological Physics, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States.,Department of Bioengineering, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States
| | - Xingcheng Lin
- Center for Theoretical Biological Physics, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States.,Department of Physics and Astronomy, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States
| | - Wei Lu
- Center for Theoretical Biological Physics, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States.,Department of Physics and Astronomy, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States.,Department of Physics and Astronomy, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States.,Department of Chemistry, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States.,Department of Biosciences, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States.,Department of Physics and Astronomy, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States.,Department of Chemistry, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States.,Department of Biosciences, Rice University , 6100 Main St., Houston, Texas 77005-1892, United States
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16
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Lin X, Noel JK, Wang Q, Ma J, Onuchic JN. Lowered pH Leads to Fusion Peptide Release and a Highly Dynamic Intermediate of Influenza Hemagglutinin. J Phys Chem B 2016; 120:9654-60. [PMID: 27541202 DOI: 10.1021/acs.jpcb.6b06775] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hemagglutinin (HA), the membrane-bound fusion protein of the influenza virus, enables the entry of virus into host cells via a structural rearrangement. There is strong evidence that the primary trigger for this rearrangement is the low pH environment of a late endosome. To understand the structural basis and the dynamic consequences of the pH trigger, we employed explicit-solvent molecular dynamics simulations to investigate the initial stages of the HA transition. Our results indicate that lowered pH destabilizes HA and speeds up the dissociation of the fusion peptides (FPs). A buried salt bridge between the N-terminus and Asp1122 of HA stem domain locks the FPs and may act as one of the pH sensors. In line with recent observations from simplified protein models, we find that, after the dissociation of FPs, a structural order-disorder transition in a loop connecting the central coiled-coil to the C-terminal domains produces a highly mobile HA. This motion suggests the existence of a long-lived asymmetric or "symmetry-broken" intermediate during the HA conformational change. This intermediate conformation is consistent with models of hemifusion, and its early formation during the conformational change has implications for the aggregation seen in HA activity.
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Affiliation(s)
- Xingcheng Lin
- Center for Theoretical Biological Physics, Rice University , Houston, Texas 77030, United States.,Department of Physics and Astronomy, Rice University , Houston, Texas 77005, United States
| | - Jeffrey K Noel
- Max Delbrück Center for Molecular Medicine , Berlin 13125, Germany.,Fritz Haber Institute of the Max Planck Society , Berlin 14195, Germany
| | - Qinghua Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine , Houston 77030, Texas, United States
| | - Jianpeng Ma
- Center for Theoretical Biological Physics, Rice University , Houston, Texas 77030, United States.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine , Houston 77030, Texas, United States.,Department of Bioengineering, Rice University , Houston, Texas 77005, United States
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University , Houston, Texas 77030, United States.,Department of Physics and Astronomy, Rice University , Houston, Texas 77005, United States.,Departments of Chemistry and Biosciences, Rice University , Houston, Texas 77005, United States
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17
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Kurczynska M, Kania E, Konopka BM, Kotulska M. Applying PyRosetta molecular energies to separate properly oriented protein models from mirror models, obtained from contact maps. J Mol Model 2016; 22:111. [PMID: 27107578 PMCID: PMC4842210 DOI: 10.1007/s00894-016-2975-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 04/05/2016] [Indexed: 11/30/2022]
Abstract
Reconstructing protein structure based on contact maps leads to two types of models: properly oriented models and mirror models. This is due to the fact that contact maps do not include information on protein chirality. Therefore, both types of model orientations share the same contact map and are geometrically allowed. In this work, we verified the hypothesis that some of the energy terms calculated by PyRosetta could be useful to distinguish between properly oriented and mirror models. We studied 440 models of all-alpha protein domains reconstructed manually from their contact maps, where 50 % of the models were properly oriented and 50 % had mirror orientation. We showed that dihedral angles and energy terms, based on the probability of specific geometrical arrangement of the residues, differed significantly for properly oriented and mirror models.
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Affiliation(s)
- Monika Kurczynska
- Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Ewa Kania
- Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland.,Biotechnology Center, Dresden University of Technology, Tatzberg 47/49, 01307, Dresden, Germany
| | - Bogumil M Konopka
- Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Malgorzata Kotulska
- Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland.
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18
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SMOG 2: A Versatile Software Package for Generating Structure-Based Models. PLoS Comput Biol 2016; 12:e1004794. [PMID: 26963394 PMCID: PMC4786265 DOI: 10.1371/journal.pcbi.1004794] [Citation(s) in RCA: 191] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 02/07/2016] [Indexed: 12/01/2022] Open
Abstract
Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to be an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Originally developed in the context of protein folding, structure-based models (SBMs) have since been extended to probe a diverse range of biomolecular processes, spanning from protein and RNA folding to functional transitions in molecular machines. The hallmark feature of a structure-based model is that part, or all, of the potential energy function is defined by a known structure. Within this general class of models, there exist many possible variations in resolution and energetic composition. SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD. SMOG 2 is bundled with XML-formatted template files that define commonly used SBMs, and it can process template files that are altered according to the needs of each user. This computational infrastructure also allows for experimental or bioinformatics-derived restraints or novel structural features to be included, e.g. novel ligands, prosthetic groups and post-translational/transcriptional modifications. The code and user guide can be downloaded at http://smog-server.org/smog2.
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19
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Noel JK, Morcos F, Onuchic JN. Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics. F1000Res 2016; 5. [PMID: 26918164 PMCID: PMC4755392 DOI: 10.12688/f1000research.7186.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/21/2016] [Indexed: 11/25/2022] Open
Abstract
Experimentally derived structural constraints have been crucial to the implementation of computational models of biomolecular dynamics. For example, not only does crystallography provide essential starting points for molecular simulations but also high-resolution structures permit for parameterization of simplified models. Since the energy landscapes for proteins and other biomolecules have been shown to be minimally frustrated and therefore funneled, these structure-based models have played a major role in understanding the mechanisms governing folding and many functions of these systems. Structural information, however, may be limited in many interesting cases. Recently, the statistical analysis of residue co-evolution in families of protein sequences has provided a complementary method of discovering residue-residue contact interactions involved in functional configurations. These functional configurations are often transient and difficult to capture experimentally. Thus, co-evolutionary information can be merged with that available for experimentally characterized low free-energy structures, in order to more fully capture the true underlying biomolecular energy landscape.
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Affiliation(s)
- Jeffrey K Noel
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA; Kristallographie, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Faruck Morcos
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX, USA
| | - Jose N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
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20
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Using the folding landscapes of proteins to understand protein function. Curr Opin Struct Biol 2016; 36:67-74. [PMID: 26812092 DOI: 10.1016/j.sbi.2016.01.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/31/2015] [Accepted: 01/06/2016] [Indexed: 11/20/2022]
Abstract
Proteins fold on a biologically-relevant timescale because of a funnel-shaped energy landscape. This landscape is sculpted through evolution by selecting amino-acid sequences that stabilize native interactions while suppressing stable non-native interactions that occur during folding. However, there is strong evolutionary selection for functional residues and these cannot be chosen to optimize folding. Their presence impacts the folding energy landscape in a variety of ways. Here, we survey the effects of functional residues on folding by providing several examples. We then review how such effects can be detected computationally and be used as assays for protein function. Overall, an understanding of how functional residues modulate folding should provide insights into the design of natural proteins and their homeostasis.
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21
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Lammert H, Noel JK, Haglund E, Schug A, Onuchic JN. Constructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures. J Chem Phys 2015; 143:243141. [DOI: 10.1063/1.4936881] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Heiko Lammert
- Center for Theoretical Biological Physics and Department of Physics, Rice University, Houston, Texas 77005, USA
| | - Jeffrey K. Noel
- Center for Theoretical Biological Physics and Department of Physics, Rice University, Houston, Texas 77005, USA
| | - Ellinor Haglund
- Center for Theoretical Biological Physics and Department of Physics, Rice University, Houston, Texas 77005, USA
| | - Alexander Schug
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - José N. Onuchic
- Center for Theoretical Biological Physics and Department of Physics, Rice University, Houston, Texas 77005, USA
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22
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Fisher KM, Haglund E, Noel JK, Hailey KL, Onuchic JN, Jennings PA. Geometrical Frustration in Interleukin-33 Decouples the Dynamics of the Functional Element from the Folding Transition State Ensemble. PLoS One 2015; 10:e0144067. [PMID: 26630011 PMCID: PMC4667907 DOI: 10.1371/journal.pone.0144067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/12/2015] [Indexed: 12/27/2022] Open
Abstract
Interleukin-33 (IL-33) is currently the focus of multiple investigations into targeting pernicious inflammatory disorders. This mediator of inflammation plays a prevalent role in chronic disorders such as asthma, rheumatoid arthritis, and progressive heart disease. In order to better understand the possible link between the folding free energy landscape and functional regions in IL-33, a combined experimental and theoretical approach was applied. IL-33 is a pseudo- symmetrical protein composed of three distinct structural elements that complicate the folding mechanism due to competition for nucleation on the dominant folding route. Trefoil 1 constitutes the majority of the binding interface with the receptor whereas Trefoils 2 and 3 provide the stable scaffold to anchor Trefoil 1. We identified that IL-33 folds with a three-state mechanism, leading to a rollover in the refolding arm of its chevron plots in strongly native conditions. In addition, there is a second slower refolding phase that exhibits the same rollover suggesting similar limitations in folding along parallel routes. Characterization of the intermediate state and the rate limiting steps required for folding suggests that the rollover is attributable to a moving transition state, shifting from a post- to pre-intermediate transition state as you move from strongly native conditions to the midpoint of the transition. On a structural level, we found that initially, all independent Trefoil units fold equally well until a QCA of 0.35 when Trefoil 1 will backtrack in order to allow Trefoils 2 and 3 to fold in the intermediate state, creating a stable scaffold for Trefoil 1 to fold onto during the final folding transition. The formation of this intermediate state and subsequent moving transition state is a result of balancing the difficulty in folding the functionally important Trefoil 1 onto the remainder of the protein. Taken together our results indicate that the functional element of the protein is geometrically frustrated, requiring the more stable elements to fold first, acting as a scaffold for docking of the functional element to allow productive folding to the native state.
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Affiliation(s)
- Kaitlin M. Fisher
- Department of Chemistry and Biochemistry, University of California at San Diego (UCSD), La Jolla, CA, United States of America
| | - Ellinor Haglund
- Center for Theoretical Biological Physics (CTBP) and Department of Physics, University of California at San Diego (UCSD), La Jolla, CA, United States of America
- Center for Theoretical Biological Physics (CTBP) and Department of Physics and Astronomy, Chemistry and Biochemistry and Cell Biology, Rice University, Houston, TX, United States of America
| | - Jeffrey K. Noel
- Center for Theoretical Biological Physics (CTBP) and Department of Physics and Astronomy, Chemistry and Biochemistry and Cell Biology, Rice University, Houston, TX, United States of America
| | - Kendra L. Hailey
- Department of Chemistry and Biochemistry, University of California at San Diego (UCSD), La Jolla, CA, United States of America
| | - José N. Onuchic
- Center for Theoretical Biological Physics (CTBP) and Department of Physics and Astronomy, Chemistry and Biochemistry and Cell Biology, Rice University, Houston, TX, United States of America
| | - Patricia A. Jennings
- Department of Chemistry and Biochemistry, University of California at San Diego (UCSD), La Jolla, CA, United States of America
- * E-mail:
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23
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Ramírez-Sarmiento CA, Noel JK, Valenzuela SL, Artsimovitch I. Interdomain Contacts Control Native State Switching of RfaH on a Dual-Funneled Landscape. PLoS Comput Biol 2015; 11:e1004379. [PMID: 26230837 PMCID: PMC4521827 DOI: 10.1371/journal.pcbi.1004379] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 06/03/2015] [Indexed: 11/22/2022] Open
Abstract
RfaH is a virulence factor from Escherichia coli whose C-terminal domain (CTD) undergoes a dramatic α-to-β conformational transformation. The CTD in its α-helical fold is stabilized by interactions with the N-terminal domain (NTD), masking an RNA polymerase binding site until a specific recruitment site is encountered. Domain dissociation is triggered upon binding to DNA, allowing the NTD to interact with RNA polymerase to facilitate transcription while the CTD refolds into the β-barrel conformation that interacts with the ribosome to activate translation. However, structural details of this transformation process in the context of the full protein remain to be elucidated. Here, we explore the mechanism of the α-to-β conformational transition of RfaH in the full-length protein using a dual-basin structure-based model. Our simulations capture several features described experimentally, such as the requirement of disruption of interdomain contacts to trigger the α-to-β transformation, confirms the roles of previously indicated residues E48 and R138, and suggests a new important role for F130, in the stability of the interdomain interaction. These native basins are connected through an intermediate state that builds up upon binding to the NTD and shares features from both folds, in agreement with previous in silico studies of the isolated CTD. We also examine the effect of RNA polymerase binding on the stabilization of the β fold. Our study shows that native-biased models are appropriate for interrogating the detailed mechanisms of structural rearrangements during the dramatic transformation process of RfaH. To carry out their biological functions, proteins must fold into defined three-dimensional structures. In most proteins, a single fold determined by the amino acid sequence, and sometimes influenced by environmental conditions, is believed to be suited for each protein’s dedicated task. However, some proteins challenge this broadly accepted paradigm, adopting different structures that can enable diverse roles or trigger pathological responses, such as prion diseases. Escherichia coli RfaH constitutes a dramatic example of this atypical behavior. RfaH C-terminal domain folds into either a helical bundle that binds to the N-terminal domain and inhibits unregulated recruitment to the transcription complex or, in the presence of a specific DNA target, into a stand-alone β-barrel structure that binds to the ribosome and couples transcription and translation of RfaH-dependent genes. To understand the mechanism of this structural rearrangement, we performed molecular dynamics using a model where the stabilizing interactions from both folds are integrated. Our results argue that this transformation requires destabilization of the domain interface, is favored by interactions between the N-terminal domain of RfaH and RNA polymerase, and proceeds via a bound intermediate state that connects both folds.
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Affiliation(s)
- César A. Ramírez-Sarmiento
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Ñuñoa, Santiago, Chile
- * E-mail: (CARS); (IA)
| | - Jeffrey K. Noel
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
| | - Sandro L. Valenzuela
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Ñuñoa, Santiago, Chile
| | - Irina Artsimovitch
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (CARS); (IA)
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24
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Affiliation(s)
- Qiang Shao
- Drug Discovery and Design
Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
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25
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Shao Q. Important roles of hydrophobic interactions in folding and charge interactions in misfolding of α-helix bundle protein. RSC Adv 2015. [DOI: 10.1039/c4ra14265a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
An enhanced-sampling molecular dynamics simulation is presented to quantitatively demonstrate the important roles of hydrophobic and charge interactions in the folding and misfolding of α-helix bundle protein, respectively.
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Affiliation(s)
- Qiang Shao
- Drug Discovery and Design Center
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
- China
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26
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Order and disorder control the functional rearrangement of influenza hemagglutinin. Proc Natl Acad Sci U S A 2014; 111:12049-54. [PMID: 25082896 DOI: 10.1073/pnas.1412849111] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Influenza hemagglutinin (HA), a homotrimeric glycoprotein crucial for membrane fusion, undergoes a large-scale structural rearrangement during viral invasion. X-ray crystallography has shown that the pre- and postfusion configurations of HA2, the membrane-fusion subunit of HA, have disparate secondary, tertiary, and quaternary structures, where some regions are displaced by more than 100 Å. To explore structural dynamics during the conformational transition, we studied simulations of a minimally frustrated model based on energy landscape theory. The model combines structural information from both the pre- and postfusion crystallographic configurations of HA2. Rather than a downhill drive toward formation of the central coiled-coil, we discovered an order-disorder transition early in the conformational change as the mechanism for the release of the fusion peptides from their burial sites in the prefusion crystal structure. This disorder quickly leads to a metastable intermediate with a broken threefold symmetry. Finally, kinetic competition between the formation of the extended coiled-coil and C-terminal melting results in two routes from this intermediate to the postfusion structure. Our study reiterates the roles that cracking and disorder can play in functional molecular motions, in contrast to the downhill mechanical interpretations of the "spring-loaded" model proposed for the HA2 conformational transition.
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27
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Predictive energy landscapes for folding α-helical transmembrane proteins. Proc Natl Acad Sci U S A 2014; 111:11031-6. [PMID: 25030446 DOI: 10.1073/pnas.1410529111] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
We explore the hypothesis that the folding landscapes of membrane proteins are funneled once the proteins' topology within the membrane is established. We extend a protein folding model, the associative memory, water-mediated, structure, and energy model (AWSEM) by adding an implicit membrane potential and reoptimizing the force field to account for the differing nature of the interactions that stabilize proteins within lipid membranes, yielding a model that we call AWSEM-membrane. Once the protein topology is set in the membrane, hydrophobic attractions play a lesser role in finding the native structure, whereas polar-polar attractions are more important than for globular proteins. We examine both the quality of predictions made with AWSEM-membrane when accurate knowledge of the topology and secondary structure is available and the quality of predictions made without such knowledge, instead using bioinformatically inferred topology and secondary structure based on sequence alone. When no major errors are made by the bioinformatic methods used to assign the topology of the transmembrane helices, these two types of structure predictions yield roughly equivalent quality structures. Although the predictive energy landscape is transferable and not structure based, within the correct topological sector we find the landscape is indeed very funneled: Thermodynamic landscape analysis indicates that both the total potential energy and the contact energy decrease as native contacts are formed. Nevertheless the near symmetry of different helical packings with respect to native contact formation can result in multiple packings with nearly equal thermodynamic occupancy, especially at temperatures just below collapse.
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28
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Sinner C, Lutz B, John S, Reinartz I, Verma A, Schug A. Simulating Biomolecular Folding and Function by Native-Structure-Based/Go-Type Models. Isr J Chem 2014. [DOI: 10.1002/ijch.201400012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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29
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Accounting for a mirror-image conformation as a subtle effect in protein folding. Proc Natl Acad Sci U S A 2014; 111:8458-63. [PMID: 24912167 DOI: 10.1073/pnas.1407837111] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
By using local (free-energy profiles along the amino acid sequence and (13)C(α) chemical shifts) and global (principal component) analyses to examine the molecular dynamics of protein-folding trajectories, generated with the coarse-grained united-residue force field, for the B domain of staphylococcal protein A, we are able to (i) provide the main reason for formation of the mirror-image conformation of this protein, namely, a slow formation of the second loop and part of the third helix (Asp29-Asn35), caused by the presence of multiple local conformational states in this portion of the protein; (ii) show that formation of the mirror-image topology is a subtle effect resulting from local interactions; (iii) provide a mechanism for how protein A overcomes the barrier between the metastable mirror-image state and the native state; and (iv) offer a plausible reason to explain why protein A does not remain in the metastable mirror-image state even though the mirror-image and native conformations are at least energetically compatible.
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30
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Shao Q. Probing Sequence Dependence of Folding Pathway of α-Helix Bundle Proteins through Free Energy Landscape Analysis. J Phys Chem B 2014; 118:5891-900. [DOI: 10.1021/jp5043393] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Qiang Shao
- Drug Discovery and Design
Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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31
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Jana B, Morcos F, Onuchic JN. From structure to function: the convergence of structure based models and co-evolutionary information. Phys Chem Chem Phys 2014; 16:6496-507. [PMID: 24603809 DOI: 10.1039/c3cp55275f] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding protein folding and function is one of the most important problems in biological research. Energy landscape theory and the folding funnel concept have provided a framework to investigate the mechanisms associated to these processes. Since protein energy landscapes are in most cases minimally frustrated, structure based models (SMBs) have successfully determined the geometrical features associated with folding and functional transitions. However, structural information is limited, particularly with respect to different functional configurations. This is a major limitation for SBMs. Alternatively, statistical methods to study amino acid co-evolution provide information on residue-residue interactions useful for the study of structure and function. Here, we show how the combination of these two methods gives rise to a novel way to investigate the mechanisms associated with folding and function. We use this methodology to explore the mechanistic aspects of protein translocation in the integral membrane protease FtsH. Dual basin-SBM simulations using the open and closed state of this hexameric motor reveals a functionally important paddling motion in the catalytic cycle. We also find that Direct Coupling Analysis (DCA) predicts physical contacts between AAA and peptidase domains of the motor, which are crucial for the open to close transition. Our combined method, which uses structural information from the open state experimental structure and co-evolutionary couplings, suggests that this methodology can be used to explore the functional landscape of complex biological macromolecules previously inaccessible to methods dependent on experimental structural information. This efficient way to sample the conformational space of large systems creates a theoretical/computational framework capable of better characterizing the functional landscape in large biomolecular assemblies.
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Affiliation(s)
- Biman Jana
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA.
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Hills RD. Balancing bond, nonbond, and gō-like terms in coarse grain simulations of conformational dynamics. Methods Mol Biol 2014; 1084:123-140. [PMID: 24061919 DOI: 10.1007/978-1-62703-658-0_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Characterization of the protein conformational landscape remains a challenging problem, whether it concerns elucidating folding mechanisms, predicting native structures or modeling functional transitions. Coarse-grained molecular dynamics simulation methods enable exhaustive sampling of the energetic landscape at resolutions of biological interest. The general utility of structure-based models is reviewed along with their differing levels of approximation. Simple Gō models incorporate attractive native interactions and repulsive nonnative contacts, resulting in an ideal smooth landscape. Non-Gō coarse-grained models reduce the parameter set as needed but do not include bias to any desired native structure. While non-Gō models have achieved limited success in protein coarse-graining, they can be combined with native structured-based potentials to create a balanced and powerful force field. Recent applications of such Gō-like models have yielded insight into complex folding mechanisms and conformational transitions in large macromolecules. The accuracy and usefulness of reduced representations are also revealed to be a function of the mathematical treatment of the intrinsic bonded topology.
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Affiliation(s)
- Ronald D Hills
- Department of Pharmaceutical Sciences, University of New England, Portland, ME, USA
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