1
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Marchenkov V, Surin A, Ugarov V, Kotova N, Marchenko N, Fedorov A, Finkelstein A, Filimonov V, Semisotnov G. Co-chaperonin GroES subunit exchange as dependent on time, pH, protein concentration, and urea. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141032. [PMID: 39004159 DOI: 10.1016/j.bbapap.2024.141032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/27/2024] [Accepted: 07/09/2024] [Indexed: 07/16/2024]
Abstract
The discovery of a subunit exchange in some oligomeric proteins, implying short-term dissociation of their oligomeric structure, requires new insights into the role of the quaternary structure in oligomeric protein stability and function. Here we demonstrate the effect of pH, protein concentration, and urea on the efficiency of GroES heptamer (GroES7) subunit exchange. A mixture of equimolar amounts of wild-type (WT) GroES7 and its Ala97Cys mutant modified with iodoacetic acid (97-carboxymethyl cysteine or CMC-GroES7) was incubated in various conditions and subjected to isoelectric focusing (IEF) in polyacrylamide gel. For each sample, there are eight Coomassie-stained electrophoretic bands showing different charges that result from a different number of included mutant subunits, each carrying an additional negative charge. The intensities of these bands serve to analyze the protein subunit exchange. The protein stability is evaluated using the transverse urea gradient gel electrophoresis (TUGGE). At pH 8.0, the intensities of the initial bands corresponding to WT-GroES7 and CMC-GroES7 are decreased with a half-time of (23 ± 2) min. The exchange decreases with decreasing pH and seems to be strongly hindered at pH 5.2 due to the protonation of groups with pK ∼ 6.3, which stabilizes the protein quaternary structure. The destabilization of the protein quaternary structure caused by increased pH, decreased protein concentration, or urea accelerates the GroES subunit exchange. This study allows visualizing the subunit exchange in oligomeric proteins and confirms its direct connection with the stability of the protein quaternary structure.
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Affiliation(s)
- Victor Marchenkov
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya Street, 142290 Pushchino, Russia
| | - Alexey Surin
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya Street, 142290 Pushchino, Russia; Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 6 Prospekt Nauki, 142290 Pushchino, Russia; State Research Centre for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - Victor Ugarov
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya Street, 142290 Pushchino, Russia
| | - Nina Kotova
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya Street, 142290 Pushchino, Russia
| | - Natalia Marchenko
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya Street, 142290 Pushchino, Russia
| | - Alexey Fedorov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, Bld. 2 Leninsky Ave., 119071 Moscow, Russia
| | - Alexei Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya Street, 142290 Pushchino, Russia
| | - Vladimir Filimonov
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya Street, 142290 Pushchino, Russia
| | - Gennady Semisotnov
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya Street, 142290 Pushchino, Russia.
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2
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Györffy D, Závodszky P, Szilágyi A. A Kinetic Transition Network Model Reveals the Diversity of Protein Dimer Formation Mechanisms. Biomolecules 2023; 13:1708. [PMID: 38136580 PMCID: PMC10741920 DOI: 10.3390/biom13121708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Protein homodimers have been classified as three-state or two-state dimers depending on whether a folded monomer forms before association, but the details of the folding-binding mechanisms are poorly understood. Kinetic transition networks of conformational states have provided insight into the folding mechanisms of monomeric proteins, but extending such a network to two protein chains is challenging as all the relative positions and orientations of the chains need to be included, greatly increasing the number of degrees of freedom. Here, we present a simplification of the problem by grouping all states of the two chains into two layers: a dissociated and an associated layer. We combined our two-layer approach with the Wako-Saito-Muñoz-Eaton method and used Transition Path Theory to investigate the dimer formation kinetics of eight homodimers. The analysis reveals a remarkable diversity of dimer formation mechanisms. Induced folding, conformational selection, and rigid docking are often simultaneously at work, and their contribution depends on the protein concentration. Pre-folded structural elements are always present at the moment of association, and asymmetric binding mechanisms are common. Our two-layer network approach can be combined with various methods that generate discrete states, yielding new insights into the kinetics and pathways of flexible binding processes.
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Affiliation(s)
- Dániel Györffy
- Systems Biology of Reproduction Research Group, Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary;
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, 1083 Budapest, Hungary
| | - Péter Závodszky
- Structural Biophysics Research Group, Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary;
| | - András Szilágyi
- Systems Biology of Reproduction Research Group, Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, 1117 Budapest, Hungary;
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3
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Retamal-Farfán I, González-Higueras J, Galaz-Davison P, Rivera M, Ramírez-Sarmiento CA. Exploring the structural acrobatics of fold-switching proteins using simplified structure-based models. Biophys Rev 2023; 15:787-799. [PMID: 37681096 PMCID: PMC10480104 DOI: 10.1007/s12551-023-01087-0] [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: 03/27/2023] [Accepted: 06/22/2023] [Indexed: 09/09/2023] Open
Abstract
Metamorphic proteins are a paradigm of the protein folding process, by encoding two or more native states, highly dissimilar in terms of their secondary, tertiary, and even quaternary structure, on a single amino acid sequence. Moreover, these proteins structurally interconvert between these native states in a reversible manner at biologically relevant timescales as a result of different environmental cues. The large-scale rearrangements experienced by these proteins, and their sometimes high mass interacting partners that trigger their metamorphosis, makes the computational and experimental study of their structural interconversion challenging. Here, we present our efforts in studying the refolding landscapes of two quintessential metamorphic proteins, RfaH and KaiB, using simplified dual-basin structure-based models (SBMs), rigorously footed on the energy landscape theory of protein folding and the principle of minimal frustration. By using coarse-grained models in which the native contacts and bonded interactions extracted from the available experimental structures of the two native states of RfaH and KaiB are merged into a single Hamiltonian, dual-basin SBM models can be generated and savvily calibrated to explore their fold-switch in a reversible manner in molecular dynamics simulations. We also describe how some of the insights offered by these simulations have driven the design of experiments and the validation of the conformational ensembles and refolding routes observed using this simple and computationally efficient models.
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Affiliation(s)
- Ignacio Retamal-Farfán
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
- ANID — Millennium Science Initiative Program — Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Jorge González-Higueras
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
- ANID — Millennium Science Initiative Program — Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Pablo Galaz-Davison
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
- ANID — Millennium Science Initiative Program — Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Maira Rivera
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
- Department of Chemistry, Faculty of Science, McGill University, Montreal, Quebec H3A 0B8 Canada
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
- ANID — Millennium Science Initiative Program — Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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4
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Mouro PR, Sanches MN, Leite VBP, Chahine J. Exploring the Folding Mechanism of Dimeric Superoxide Dismutase. J Phys Chem B 2023; 127:1338-1349. [PMID: 36716437 DOI: 10.1021/acs.jpcb.2c08877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The Cu/Zn Human Superoxide Dismutase (SOD1) is a dimeric metalloenzyme whose genetic mutations are directly related to amyotrophic lateral sclerosis (ALS), so understanding its folding mechanism is of fundamental importance. Currently, the SOD1 dimer formation is studied via molecular dynamics simulations using a simplified structure-based model and an all-atom model. Results from the simplified model reveal a mechanism dependent on distances between monomers, which are limited by constraints to mimic concentration dependence. The stability of intermediates (during the int state) is significantly affected by this distance, as well as by the presence of two folded monomers prior to dimer formation. The kinetics of interface formation are also highly dependent on the separation distance. The folding temperature of the dimer is about 4.2% higher than that of the monomer, a value not too different from experimental data. All-atom simulations on the apo dimer give binding free energy between monomers similar to experimental values. An intermediate state is evident for the apo form at a separation distance between monomers slightly larger than the native distance which has little formed interface between monomers. We have shown that this intermediate is stabilized by non-native intra- and intercontacts.
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Affiliation(s)
- Paulo R Mouro
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto15054-000, Brazil
| | - Murilo N Sanches
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto15054-000, Brazil
| | - Vitor B P Leite
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto15054-000, Brazil
| | - Jorge Chahine
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto15054-000, Brazil
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5
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Prakash DL, Gosavi S. The diversity of protein-protein interaction interfaces within T=3 icosahedral viral capsids. Front Mol Biosci 2022; 9:967877. [PMID: 36339706 PMCID: PMC9631432 DOI: 10.3389/fmolb.2022.967877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/08/2022] [Indexed: 11/20/2022] Open
Abstract
Some non-enveloped virus capsids assemble from multiple copies of a single type of coat-protein (CP). The comparative energetics of the diverse CP-CP interfaces present in such capsids likely govern virus assembly-disassembly mechanisms. The T = 3 icosahedral capsids comprise 180 CP copies arranged about two-, three-, five- and six-fold axes of (quasi-)rotation symmetry. Structurally diverse CPs can assemble into T = 3 capsids. Specifically, the Leviviridae CPs are structurally distinct from the Bromoviridae, Tombusviridae and Tymoviridae CPs which fold into the classic “jelly-roll” fold. However, capsids from across the four families are known to disassemble into dimers. To understand whether the overall symmetry of the capsid or the structural details of the CP determine virus assembly-disassembly mechanisms, we analyze the different CP-CP interfaces that occur in the four virus families. Previous work studied protein homodimer interfaces using interface size (relative to the monomer) and hydrophobicity. Here, we analyze all CP-CP interfaces using these two parameters and find that the dimerization interface (present between two CPs congruent through a two-fold axis of rotation) has a larger relative size in the Leviviridae than in the other viruses. The relative sizes of the other Leviviridae interfaces and all the jelly-roll interfaces are similar. However, the dimerization interfaces across families have slightly higher hydrophobicity, potentially making them stronger than other interfaces. Finally, although the CP-monomers of the jelly-roll viruses are structurally similar, differences in their dimerization interfaces leads to varied dimer flexibility. Overall, differences in CP-structures may induce different modes of swelling and assembly-disassembly in the T = 3 viruses.
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6
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Scalone E, Broggini L, Visentin C, Erba D, Bačić Toplek F, Peqini K, Pellegrino S, Ricagno S, Paissoni C, Camilloni C. Multi-eGO: An in silico lens to look into protein aggregation kinetics at atomic resolution. Proc Natl Acad Sci U S A 2022; 119:e2203181119. [PMID: 35737839 PMCID: PMC9245614 DOI: 10.1073/pnas.2203181119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/17/2022] [Indexed: 12/25/2022] Open
Abstract
Protein aggregation into amyloid fibrils is the archetype of aberrant biomolecular self-assembly processes, with more than 50 associated diseases that are mostly uncurable. Understanding aggregation mechanisms is thus of fundamental importance and goes in parallel with the structural characterization of the transient oligomers formed during the process. Oligomers have been proven elusive to high-resolution structural techniques, while the large sizes and long time scales, typical of aggregation processes, have limited the use of computational methods to date. To surmount these limitations, we here present multi-eGO, an atomistic, hybrid structure-based model which, leveraging the knowledge of monomers conformational dynamics and of fibril structures, efficiently captures the essential structural and kinetics aspects of protein aggregation. Multi-eGO molecular dynamics simulations can describe the aggregation kinetics of thousands of monomers. The concentration dependence of the simulated kinetics, as well as the structural features of the resulting fibrils, are in qualitative agreement with in vitro experiments carried out on an amyloidogenic peptide from Transthyretin, a protein responsible for one of the most common cardiac amyloidoses. Multi-eGO simulations allow the formation of primary nuclei in a sea of transient lower-order oligomers to be observed over time and at atomic resolution, following their growth and the subsequent secondary nucleation events, until the maturation of multiple fibrils is achieved. Multi-eGO, combined with the many experimental techniques deployed to study protein aggregation, can provide the structural basis needed to advance the design of molecules targeting amyloidogenic diseases.
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Affiliation(s)
- Emanuele Scalone
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Luca Broggini
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 San Donato Milanese, Italy
| | - Cristina Visentin
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 San Donato Milanese, Italy
| | - Davide Erba
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Fran Bačić Toplek
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Kaliroi Peqini
- Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica, Università degli Studi di Milano, 20133 Milano, Italy
| | - Sara Pellegrino
- Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica, Università degli Studi di Milano, 20133 Milano, Italy
| | - Stefano Ricagno
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, 20097 San Donato Milanese, Italy
| | - Cristina Paissoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
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7
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Freitas FC, Maldonado M, Oliveira Junior AB, Onuchic JN, Oliveira RJD. Biotin-painted proteins have thermodynamic stability switched by kinetic folding routes. J Chem Phys 2022; 156:195101. [PMID: 35597640 DOI: 10.1063/5.0083875] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Biotin-labeled proteins are widely used as tools to study protein-protein interactions and proximity in living cells. Proteomic methods broadly employ proximity-labeling technologies based on protein biotinylation in order to investigate the transient encounters of biomolecules in subcellular compartments. Biotinylation is a post-translation modification in which the biotin molecule is attached to lysine or tyrosine residues. So far, biotin-based technologies proved to be effective instruments as affinity and proximity tags. However, the influence of biotinylation on aspects such as folding, binding, mobility, thermodynamic stability, and kinetics needs to be investigated. Here, we selected two proteins [biotin carboxyl carrier protein (BCCP) and FKBP3] to test the influence of biotinylation on thermodynamic and kinetic properties. Apo (without biotin) and holo (biotinylated) protein structures were used separately to generate all-atom structure-based model simulations in a wide range of temperatures. Holo BCCP contains one biotinylation site, and FKBP3 was modeled with up to 23 biotinylated lysines. The two proteins had their estimated thermodynamic stability changed by altering their energy landscape. In all cases, after comparison between the apo and holo simulations, differences were observed on the free-energy profiles and folding routes. Energetic barriers were altered with the density of states clearly showing changes in the transition state. This study suggests that analysis of large-scale datasets of biotinylation-based proximity experiments might consider possible alterations in thermostability and folding mechanisms imposed by the attached biotins.
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Affiliation(s)
- Frederico Campos Freitas
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
| | - Michelli Maldonado
- Departamento de Matemática, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
| | - Antonio Bento Oliveira Junior
- Center for Theoretical Biological Physics, Rice University, BioScience Research Collaborative, 6566 Main St., Houston, Texas 77030, USA
| | - José Nelson Onuchic
- Center for Theoretical Biological Physics, Rice University, BioScience Research Collaborative, 6566 Main St., Houston, Texas 77030, USA
| | - Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG 38064-200, Brazil
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8
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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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9
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Perspectives on the landscape and flux theory for describing emergent behaviors of the biological systems. J Biol Phys 2022; 48:1-36. [PMID: 34822073 PMCID: PMC8866630 DOI: 10.1007/s10867-021-09586-5] [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: 05/20/2021] [Accepted: 09/07/2021] [Indexed: 10/19/2022] Open
Abstract
We give a review on the landscape theory of the equilibrium biological systems and landscape-flux theory of the nonequilibrium biological systems as the global driving force. The emergences of the behaviors, the associated thermodynamics in terms of the entropy and free energy and dynamics in terms of the rate and paths have been quantitatively demonstrated. The hierarchical organization structures have been discussed. The biological applications ranging from protein folding, biomolecular recognition, specificity, biomolecular evolution and design for equilibrium systems as well as cell cycle, differentiation and development, cancer, neural networks and brain function, and evolution for nonequilibrium systems, cross-scale studies of genome structural dynamics and experimental quantifications/verifications of the landscape and flux are illustrated. Together, this gives an overall global physical and quantitative picture in terms of the landscape and flux for the behaviors, dynamics and functions of biological systems.
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10
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Chu X, Suo Z, Wang J. Investigating the Conformational Dynamics of a Y-Family DNA Polymerase during Its Folding and Binding to DNA and a Nucleotide. JACS AU 2022; 2:341-356. [PMID: 35252985 PMCID: PMC8889613 DOI: 10.1021/jacsau.1c00368] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Indexed: 06/14/2023]
Abstract
During DNA polymerization, the Y-family DNA polymerases are capable of bypassing various DNA damage, which can stall the replication fork progression. It has been well acknowledged that the structures of the Y-family DNA polymerases have been naturally evolved to undertake this vital task. However, the mechanisms of how these proteins utilize their unique structural and conformational dynamical features to perform the translesion DNA synthesis are less understood. Here, we developed structure-based models to study the precatalytic DNA polymerization process, including DNA and nucleotide binding to DPO4, a paradigmatic Y-family polymerase from Sulfolobus solfataricus. We studied the interplay between the folding and the conformational dynamics of DPO4 and found that DPO4 undergoes first unraveling (unfolding) and then folding for accomplishing the functional "open-to-closed" conformational transition. DNA binding dynamically modulates the conformational equilibrium in DPO4 during the stepwise binding through different types of interactions, leading to different conformational distributions of DPO4 at different DNA binding stages. We observed that nucleotide binding induces modulation of a few contacts surrounding the active site of the DPO4-DNA complex associated with a high free energy barrier. Our simulation results resonate with the experimental evidence that the conformational change at the active site led by nucleotide is the rate-limiting step of nucleotide incorporation. In combination with localized frustration analyses, we underlined the importance of DPO4 conformational dynamics and fluctuations in facilitating DNA and nucleotide binding. Our findings offer mechanistic insights into the processes of DPO4 conformational dynamics associated with the substrate binding and contribute to the understanding of the "structure-dynamics-function" relationship in the Y-family DNA polymerases.
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Affiliation(s)
- Xiakun Chu
- Department
of Chemistry, State University of New York
at Stony Brook, Stony
Brook, New York 11794, United States
| | - Zucai Suo
- Department
of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, United States
| | - Jin Wang
- Department
of Chemistry, State University of New York
at Stony Brook, Stony
Brook, New York 11794, United States
- Department
of Physics and Astronomy, State University
of New York at Stony Brook, Stony Brook, New York 11794, United States
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11
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Molecular Simulations of Intrinsically Disordered Proteins and Their Binding Mechanisms. Methods Mol Biol 2022; 2376:343-362. [PMID: 34845619 DOI: 10.1007/978-1-0716-1716-8_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) lack well-defined secondary or tertiary structures in solution but are found to be involved in a wide range of critical cellular processes that highlight their functional importance. IDPs usually undergo folding upon binding to their targets. Such binding coupled to folding behavior has widened our perspective on the protein structure-dynamics-function paradigm in molecular biology. However, characterizing the folding upon binding mechanism of IDPs experimentally remains quite challenging. Molecular simulations emerge as a potentially powerful tool that offers information complementary to experiments. Here we present a general computational framework for the molecular simulations of IDP folding upon binding processes that combines all-atom molecular dynamics (MD) and coarse-grained simulations. The classical all-atom molecular dynamics approach using GPU acceleration allows the researcher to explore the properties of the IDP conformational ensemble, whereas coarse-grained structure-based models implemented with parameters carefully calibrated to available experimental measurements can be used to simulate the entire folding upon binding process. We also discuss a set of tools for the analysis of MD trajectories and describe the details of the computational protocol to follow so that it can be adapted by the user to study any IDP in isolation and in complex with partners.
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12
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Chu WT, Yan Z, Chu X, Zheng X, Liu Z, Xu L, Zhang K, Wang J. Physics of biomolecular recognition and conformational dynamics. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2021; 84:126601. [PMID: 34753115 DOI: 10.1088/1361-6633/ac3800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Biomolecular recognition usually leads to the formation of binding complexes, often accompanied by large-scale conformational changes. This process is fundamental to biological functions at the molecular and cellular levels. Uncovering the physical mechanisms of biomolecular recognition and quantifying the key biomolecular interactions are vital to understand these functions. The recently developed energy landscape theory has been successful in quantifying recognition processes and revealing the underlying mechanisms. Recent studies have shown that in addition to affinity, specificity is also crucial for biomolecular recognition. The proposed physical concept of intrinsic specificity based on the underlying energy landscape theory provides a practical way to quantify the specificity. Optimization of affinity and specificity can be adopted as a principle to guide the evolution and design of molecular recognition. This approach can also be used in practice for drug discovery using multidimensional screening to identify lead compounds. The energy landscape topography of molecular recognition is important for revealing the underlying flexible binding or binding-folding mechanisms. In this review, we first introduce the energy landscape theory for molecular recognition and then address four critical issues related to biomolecular recognition and conformational dynamics: (1) specificity quantification of molecular recognition; (2) evolution and design in molecular recognition; (3) flexible molecular recognition; (4) chromosome structural dynamics. The results described here and the discussions of the insights gained from the energy landscape topography can provide valuable guidance for further computational and experimental investigations of biomolecular recognition and conformational dynamics.
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Affiliation(s)
- Wen-Ting Chu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Zhiqiang Yan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Xiakun Chu
- Department of Chemistry & Physics, State University of New York at Stony Brook, Stony Brook, NY 11794, United States of America
| | - Xiliang Zheng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Zuojia Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Li Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Kun Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Jin Wang
- Department of Chemistry & Physics, State University of New York at Stony Brook, Stony Brook, NY 11794, United States of America
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13
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Lalwani Prakash D, Gosavi S. Understanding the Folding Mediated Assembly of the Bacteriophage MS2 Coat Protein Dimers. J Phys Chem B 2021; 125:8722-8732. [PMID: 34339197 DOI: 10.1021/acs.jpcb.1c03928] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The capsids of RNA viruses such as MS2 are great models for studying protein self-assembly because they are made almost entirely of multiple copies of a single coat protein (CP). Although CP is the minimal repeating unit of the capsid, previous studies have shown that CP exists as a homodimer (CP2) even in an acid-disassembled system, indicating that CP2 is an obligate dimer. Here, we investigate the molecular basis of this obligate dimerization using coarse-grained structure-based models and molecular dynamics simulations. We find that, unlike monomeric proteins of similar size, CP populates a single partially folded ensemble whose "foldedness" is sensitive to denaturing conditions. In contrast, CP2 folds similarly to single-domain proteins populating only the folded and the unfolded ensembles, separated by a prominent folding free energy barrier. Several intramonomer contacts form early, but the CP2 folding barrier is crossed only when the intermonomer contacts are made. A dissection of the structure of CP2 through mutant folding simulations shows that the folding barrier arises both from the topology of CP and the interface contacts of CP2. Together, our results show that CP2 is an obligate dimer because of kinetic stability, that is, dimerization induces a folding barrier and that makes it difficult for proteins in the dimer minimum to partially unfold and access the monomeric state without completely unfolding. We discuss the advantages of this obligate dimerization in the context of dimer design and virus stability.
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Affiliation(s)
- Digvijay Lalwani Prakash
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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14
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Sun B, Kekenes-Huskey PM. Assessing the Role of Calmodulin's Linker Flexibility in Target Binding. Int J Mol Sci 2021; 22:ijms22094990. [PMID: 34066691 PMCID: PMC8125811 DOI: 10.3390/ijms22094990] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/21/2021] [Accepted: 04/28/2021] [Indexed: 12/17/2022] Open
Abstract
Calmodulin (CaM) is a highly-expressed Ca2+ binding protein known to bind hundreds of protein targets. Its binding selectivity to many of these targets is partially attributed to the protein’s flexible alpha helical linker that connects its N- and C-domains. It is not well established how its linker mediates CaM’s binding to regulatory targets yet. Insights into this would be invaluable to understanding its regulation of diverse cellular signaling pathways. Therefore, we utilized Martini coarse-grained (CG) molecular dynamics simulations to probe CaM/target assembly for a model system: CaM binding to the calcineurin (CaN) regulatory domain. The simulations were conducted assuming a ‘wild-type’ calmodulin with normal flexibility of its linker, as well as a labile, highly-flexible linker variant to emulate structural changes that could be induced, for instance, by post-translational modifications. For the wild-type model, 98% of the 600 simulations across three ionic strengths adopted a bound complex within 2 μs of simulation time; of these, 1.7% sampled the fully-bound state observed in the experimentally-determined crystallographic structure. By calculating the mean-first-passage-time for these simulations, we estimated the association rate to be ka= 8.7 × 108 M−1 s−1, which is similar to the diffusion-limited, experimentally-determined rate of 2.2 × 108 M−1 s−1. Furthermore, our simulations recapitulated its well-known inverse relationship between the association rate and the solution ionic strength. In contrast, although over 97% of the labile linker simulations formed tightly-bound complexes, only 0.3% achieved the fully-bound configuration. This effect appears to stem from a difference in the ensembles of extended and collapsed states which are controlled by the linker flexibility. Therefore, our simulations suggest that variations in the CaM linker’s propensity for alpha helical secondary structure can modulate the kinetics of target binding.
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15
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Antoci V, Oniciuc L, Amariucai-Mantu D, Moldoveanu C, Mangalagiu V, Amarandei AM, Lungu CN, Dunca S, Mangalagiu II, Zbancioc G. Benzoquinoline Derivatives: A Straightforward and Efficient Route to Antibacterial and Antifungal Agents. Pharmaceuticals (Basel) 2021; 14:ph14040335. [PMID: 33917439 PMCID: PMC8067460 DOI: 10.3390/ph14040335] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/26/2021] [Accepted: 04/02/2021] [Indexed: 02/07/2023] Open
Abstract
We report here the design, synthesis, experimental and in silico evaluation of the antibacterial and antifungal activity of some new benzo[f]quinoline derivatives. Two classes of benzo[f]quinolinium derivatives—(benzo[f]quinolinium salts (BQS) and pyrrolobenzo[f]quinolinium cycloadducts (PBQC)—were designed and obtained in two steps via a direct and facile procedure: quaternization followed by a cycloaddition reaction. The synthesized compounds were characterized by elemental and spectral analysis (FT-IR, 1H-NMR, 13C-NMR). The antimicrobial assay reveals that the BQS salts have an excellent quasi-nonselective antifungal activity against the fungus Candida albicans (some of them higher that the control drug nystatin) and very good antibacterial activity against the Gram positive bacterium Staphylococcus aureus. The PBQC compounds are inactive. Analysis of the biological data reveals interesting SAR correlations in the benzo[f]quinolinium series of compounds. The in silico studies furnished important data concerning the pharmacodynamics, pharmacokinetics and ADMET parameters of the BQS salts. Studies of the interaction of each BQS salt 3a–o with ATP synthase in the formed complex, reveal that salts 3j, 3i, and 3n have the best fit in a complex with ATP synthase. Study of the interaction of each BQS salt 3a-o with TOPO II in the formed complex reveals that salts 3j and 3n have the best-fit in complex with TOPO II. The in silico ADMET studies reveal that the BQS salts have excellent drug-like properties, including a low toxicity profile. Overall, the experimental and in silico studies indicate that compounds 3e and 3f (from the aliphatic series), respectively, and 3i, 3j and 3n (from the aromatic series), are promising leading drug candidates.
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Affiliation(s)
- Vasilichia Antoci
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol 1st Bvd, 700506 Iasi, Romania; (V.A.); (L.O.); (D.A.-M.); (C.M.); (I.I.M.)
| | - Liliana Oniciuc
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol 1st Bvd, 700506 Iasi, Romania; (V.A.); (L.O.); (D.A.-M.); (C.M.); (I.I.M.)
| | - Dorina Amariucai-Mantu
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol 1st Bvd, 700506 Iasi, Romania; (V.A.); (L.O.); (D.A.-M.); (C.M.); (I.I.M.)
| | - Costel Moldoveanu
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol 1st Bvd, 700506 Iasi, Romania; (V.A.); (L.O.); (D.A.-M.); (C.M.); (I.I.M.)
| | - Violeta Mangalagiu
- Institute of Interdisciplinary Research—CERNESIM Centre, Alexandru Ioan Cuza University of Iasi, 11 Carol I, 700506 Iasi, Romania;
| | | | - Claudiu N. Lungu
- Department of Surgery, Emergency Clinical Hospital, 810325 Braila, Romania
- Correspondence: (C.N.L.); (S.D.); (G.Z.)
| | - Simona Dunca
- Faculty of Biology, Alexandru Ioan Cuza University of Iasi, 11 Carol 1st Bvd, 700506 Iasi, Romania;
- Correspondence: (C.N.L.); (S.D.); (G.Z.)
| | - Ionel I. Mangalagiu
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol 1st Bvd, 700506 Iasi, Romania; (V.A.); (L.O.); (D.A.-M.); (C.M.); (I.I.M.)
- Institute of Interdisciplinary Research—CERNESIM Centre, Alexandru Ioan Cuza University of Iasi, 11 Carol I, 700506 Iasi, Romania;
| | - Gheorghita Zbancioc
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iasi, 11 Carol 1st Bvd, 700506 Iasi, Romania; (V.A.); (L.O.); (D.A.-M.); (C.M.); (I.I.M.)
- Correspondence: (C.N.L.); (S.D.); (G.Z.)
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16
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Freitas FC, Ferreira PHB, Favaro DC, Oliveira RJD. Shedding Light on the Inhibitory Mechanisms of SARS-CoV-1/CoV-2 Spike Proteins by ACE2-Designed Peptides. J Chem Inf Model 2021; 61:1226-1243. [PMID: 33619962 PMCID: PMC7931628 DOI: 10.1021/acs.jcim.0c01320] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Indexed: 01/07/2023]
Abstract
Angiotensin-converting enzyme 2 (ACE2) is the host cellular receptor that locks onto the surface spike protein of the 2002 SARS coronavirus (SARS-CoV-1) and of the novel, highly transmissible and deadly 2019 SARS-CoV-2, responsible for the COVID-19 pandemic. One strategy to avoid the virus infection is to design peptides by extracting the human ACE2 peptidase domain α1-helix, which would bind to the coronavirus surface protein, preventing the virus entry into the host cells. The natural α1-helix peptide has a stronger affinity to SARS-CoV-2 than to SARS-CoV-1. Another peptide was designed by joining α1 with the second portion of ACE2 that is far in the peptidase sequence yet grafted in the spike protein interface with ACE2. Previous studies have shown that, among several α1-based peptides, the hybrid peptidic scaffold is the one with the highest/strongest affinity for SARS-CoV-1, which is comparable to the full-length ACE2 affinity. In this work, binding and folding dynamics of the natural and designed ACE2-based peptides were simulated by the well-known coarse-grained structure-based model, with the computed thermodynamic quantities correlating with the experimental binding affinity data. Furthermore, theoretical kinetic analysis of native contact formation revealed the distinction between these processes in the presence of the different binding partners SARS-CoV-1 and SARS-CoV-2 spike domains. Additionally, our results indicate the existence of a two-state folding mechanism for the designed peptide en route to bind to the spike proteins, in contrast to a downhill mechanism for the natural α1-helix peptides. The presented low-cost simulation protocol demonstrated its efficiency in evaluating binding affinities and identifying the mechanisms involved in the neutralization of spike-ACE2 interaction by designed peptides. Finally, the protocol can be used as a computer-based screening of more potent designed peptides by experimentalists searching for new therapeutics against COVID-19.
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Affiliation(s)
- Frederico Campos Freitas
- Laboratório de Biofísica Teórica,
Departamento de Física, Instituto de Ciências Exatas, Naturais
e Educação, Universidade Federal do Triângulo
Mineiro, Uberaba, MG 38064-200, Brazil
| | - Paulo Henrique Borges Ferreira
- Laboratório de Biofísica Teórica,
Departamento de Física, Instituto de Ciências Exatas, Naturais
e Educação, Universidade Federal do Triângulo
Mineiro, Uberaba, MG 38064-200, Brazil
| | - Denize Cristina Favaro
- Departamento de Química Orgânica,
Instituto de Química, Universidade Estadual de
Campinas, São Paulo, SP 13083-970, Brazil
| | - Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica,
Departamento de Física, Instituto de Ciências Exatas, Naturais
e Educação, Universidade Federal do Triângulo
Mineiro, Uberaba, MG 38064-200, Brazil
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17
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The concept of protein folding/unfolding and its impacts on human health. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021. [PMID: 34090616 DOI: 10.1016/bs.apcsb.2021.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Proteins have evolved in specific 3D structures and play different functions in cells and determine various reactions and pathways. The newly synthesized amino acid chains once depart ribosome must crumple into three-dimensional structures so can be biologically active. This process of protein that makes a functional molecule is called protein folding. The protein folding is both a biological and a physicochemical process that depends on the sequence of it. In fact, this process occurs more complicated and in some cases and in exposure to some molecules like glucose (glycation), mistaken folding leads to amyloid structures and fatal disorders called conformational diseases. Such conditions are detected by the quality control system of the cell and these abnormal proteins undergo renovation or degradation. This scenario takes place by the chaperones, chaperonins, and Ubiquitin-proteasome complex. Understanding of protein folding mechanisms from different views including experimental and computational approaches has revealed some intermediate ensembles such as molten globule and has been subjected to biophysical and molecular biology attempts to know more about prevalent conformational diseases.
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18
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Zerze GH, Stillinger FH, Debenedetti PG. Thermodynamics of DNA Hybridization from Atomistic Simulations. J Phys Chem B 2021; 125:771-779. [PMID: 33434025 DOI: 10.1021/acs.jpcb.0c09237] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Studying DNA hybridization equilibrium at atomistic length scales, either via molecular dynamics (MD) or through commonly used advanced sampling approaches, is notoriously difficult. In this work, we describe an order-parameter-based advanced sampling technique to calculate the free energy of hybridization, and estimate the melting temperature of DNA oligomers at atomistic resolution. The free energy landscapes are reported as a function of a native-topology-based order parameter for the Drew-Dickerson dodecamer and for a range of DNA decamer sequences of different GC content. Our estimated melting temperatures match the experimental numbers within ±15 °C. As a test of the numerical reliability of the procedures employed, it was verified that the predicted free energy surfaces and melting temperatures of the d- and l-enantiomers of the Drew-Dickerson dodecamer were indistinguishable within numerical accuracy.
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Affiliation(s)
- Gül H Zerze
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Frank H Stillinger
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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19
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Pal A, Greenblatt HM, Levy Y. Prerecognition Diffusion Mechanism of Human DNA Mismatch Repair Proteins along DNA: Msh2-Msh3 versus Msh2-Msh6. Biochemistry 2020; 59:4822-4832. [PMID: 33319999 PMCID: PMC7872316 DOI: 10.1021/acs.biochem.0c00669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
DNA
mismatch repair (MMR) is an important postreplication process
that eliminates mispaired or unpaired nucleotides to ensure genomic
replication fidelity. In humans, Msh2-Msh6 and Msh2-Msh3 are the two
mismatch repair initiation factors that recognize DNA lesions. While
X-ray crystal structures exist for these proteins in complex with
DNA lesions, little is known about their structures during the initial
search along nonspecific double-stranded DNA, because they are short-lived
and difficult to determine experimentally. In this study, various
computational approaches were used to sidestep these difficulties.
All-atom and coarse-grained simulations based on the crystal structures
of Msh2-Msh3 and Msh2-Msh6 showed no translation along the DNA, suggesting
that the initial search conformation differs from the lesion-bound
crystal structure. We modeled probable search-mode structures of MSH
proteins and showed, using coarse-grained molecular dynamics simulations,
that they can perform rotation-coupled diffusion on DNA, which is
a suitable and efficient search mechanism for their function and one
predicted earlier by fluorescence resonance energy transfer and fluorescence
microscopy studies. This search mechanism is implemented by electrostatic
interactions among the mismatch-binding domain (MBD), the clamp domains,
and the DNA backbone. During simulations, their diffusion rate did
not change significantly with an increasing salt concentration, which
is consistent with observations from experimental studies. When the
gap between their DNA-binding clamps was increased, Msh2-Msh3 diffused
mostly via the clamp domains while Msh2-Msh6 still diffused using
the MBD, reproducing the experimentally measured lower diffusion coefficient
of Msh2-Msh6. Interestingly, Msh2-Msh3 was capable of dissociating
from the DNA, whereas Msh2-Msh6 always diffused on the DNA duplex.
This is consistent with the experimental observation that Msh2-Msh3,
unlike Msh2-Msh6, can overcome obstacles such as nucleosomes. Our
models provide a molecular picture of the different mismatch search
mechanisms undertaken by Msh2-Msh6 and Msh2-Msh3, despite the similarity
of their structures.
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Affiliation(s)
- Arumay Pal
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Harry M Greenblatt
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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20
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Wang Z, Zhou X, Zuo G. EspcTM: Kinetic Transition Network Based on Trajectory Mapping in Effective Energy Rescaling Space. Front Mol Biosci 2020; 7:589718. [PMID: 33195438 PMCID: PMC7653181 DOI: 10.3389/fmolb.2020.589718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/24/2020] [Indexed: 11/27/2022] Open
Abstract
The transition network provides a key to reveal the thermodynamic and kinetic properties of biomolecular systems. In this paper, we introduce a new method, named effective energy rescaling space trajectory mapping (EspcTM), to detect metastable states and construct transition networks based on the simulation trajectories of the complex biomolecular system. It mapped simulation trajectories into an orthogonal function space, whose bases were rescaled by effective energy, and clustered the interrelation between these trajectories to locate metastable states. By using the EspcTM method, we identified the metastable states and elucidated interstate transition kinetics of a Brownian particle and a dodecapeptide. It was found that the scaling parameters of effective energy also provided a clue to the dominating factors in dynamics. We believe that the EspcTM method is a useful tool for the studies of dynamics of the complex system and may provide new insight into the understanding of thermodynamics and kinetics of biomolecular systems.
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Affiliation(s)
- Zhenyu Wang
- T-Life Research Center, State Key Laboratory of Surface Physics, Department of Physics, Fudan University, Shanghai, China
| | - Xin Zhou
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Guanghong Zuo
- T-Life Research Center, State Key Laboratory of Surface Physics, Department of Physics, Fudan University, Shanghai, China
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21
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Chu X, Suo Z, Wang J. Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase. eLife 2020; 9:60434. [PMID: 33079059 PMCID: PMC7641590 DOI: 10.7554/elife.60434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/16/2020] [Indexed: 01/01/2023] Open
Abstract
The way in which multidomain proteins fold has been a puzzling question for decades. Until now, the mechanisms and functions of domain interactions involved in multidomain protein folding have been obscure. Here, we develop structure-based models to investigate the folding and DNA-binding processes of the multidomain Y-family DNA polymerase IV (DPO4). We uncover shifts in the folding mechanism among ordered domain-wise folding, backtracking folding, and cooperative folding, modulated by interdomain interactions. These lead to ‘U-shaped’ DPO4 folding kinetics. We characterize the effects of interdomain flexibility on the promotion of DPO4–DNA (un)binding, which probably contributes to the ability of DPO4 to bypass DNA lesions, which is a known biological role of Y-family polymerases. We suggest that the native topology of DPO4 leads to a trade-off between fast, stable folding and tight functional DNA binding. Our approach provides an effective way to quantitatively correlate the roles of protein interactions in conformational dynamics at the multidomain level.
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Affiliation(s)
- Xiakun Chu
- Department of Chemistry, State University of New York at Stony Brook, New York, United States
| | - Zucai Suo
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, United States
| | - Jin Wang
- Department of Chemistry, State University of New York at Stony Brook, New York, United States
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22
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Mishra G, Bigman LS, Levy Y. ssDNA diffuses along replication protein A via a reptation mechanism. Nucleic Acids Res 2020; 48:1701-1714. [PMID: 31919510 PMCID: PMC7038930 DOI: 10.1093/nar/gkz1202] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/23/2019] [Accepted: 01/08/2020] [Indexed: 01/30/2023] Open
Abstract
Replication protein A (RPA) plays a critical role in all eukaryotic DNA processing involving single-stranded DNA (ssDNA). Contrary to the notion that RPA provides solely inert protection to transiently formed ssDNA, the RPA-ssDNA complex acts as a dynamic DNA processing unit. Here, we studied the diffusion of RPA along 60 nt ssDNA using a coarse-grained model in which the ssDNA-RPA interface was modeled by both aromatic and electrostatic interactions. Our study provides direct evidence of bulge formation during the diffusion of ssDNA along RPA. Bulges can form at a few sites along the interface and store 1-7 nt of ssDNA whose release, upon bulge dissolution, leads to propagation of ssDNA diffusion. These findings thus support the reptation mechanism, which involves bulge formation linked to the aromatic interactions, whose short range nature reduces cooperativity in ssDNA diffusion. Greater cooperativity and a larger diffusion coefficient for ssDNA diffusion along RPA are observed for RPA variants with weaker aromatic interactions and for interfaces homogenously stabilized by electrostatic interactions. ssDNA propagation in the latter instance is characterized by lower probabilities of bulge formation; thus, it may fit the sliding-without-bulge model better than the reptation model. Thus, the reptation mechanism allows ssDNA mobility despite the extensive and high affinity interface of RPA with ssDNA. The short-range aromatic interactions support bulge formation while the long-range electrostatic interactions support the release of the stored excess ssDNA in the bulge and thus the overall diffusion.
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Affiliation(s)
- Garima Mishra
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.,Department of Physics, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Lavi S Bigman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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23
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Chu X, Suo Z, Wang J. Confinement and Crowding Effects on Folding of a Multidomain Y-Family DNA Polymerase. J Chem Theory Comput 2020; 16:1319-1332. [PMID: 31972079 PMCID: PMC7258223 DOI: 10.1021/acs.jctc.9b01146] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Proteins in vivo endure highly various interactions from the luxuriant surrounding macromolecular cosolutes. Confinement and macromolecular crowding are the two major effects that should be considered while comparing the results of protein dynamics from in vitro to in vivo. However, efforts have been largely focused on single domain protein folding up to now, and the quantifications of the in vivo effects in terms of confinements and crowders on modulating the structure and dynamics as well as the physical understanding of the underlying mechanisms on multidomain protein folding are still challenging. Here we developed a topology-based model to investigate folding of a multidomain Y-family DNA polymerase (DPO4) within spherical confined space and in the presence of repulsive and attractive crowders. We uncovered that the entropic component of the thermodynamic driving force led by confinements and repulsive crowders increases the stability of folded states relative to the folding intermediates and unfolded states, while the enthalpic component of the thermodynamic driving force led by attractive crowders gives rise to the opposite effects with less stability. We found that the shapes of DPO4 conformations influenced by the confinements and the crowders are quite different even when only the entropic component of the thermodynamic driving force is considered. We uncovered that under all in vivo conditions, the folding cooperativity of DPO4 decreases compared to that in bulk. We showed that the loss of folding cooperativity can promote the sequential domain-wise folding, which was widely found in cotranslational multidomain protein folding, and effectively prohibit the backtracking led by topological frustrations during multidomain protein folding processes.
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Affiliation(s)
- Xiakun Chu
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794, United States
| | - Zucai Suo
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, United States
| | - Jin Wang
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794, United States
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24
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Liu F, Yang N. Multiscale landscape of molecular mechanism of SIRT1 activation by STACs. Phys Chem Chem Phys 2020; 22:826-837. [PMID: 31840716 DOI: 10.1039/c9cp04931b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Sirtuins are a family of highly conserved NAD-dependent deacetylase that are involved in multiple biological processes in both prokaryotes and eukaryotes. Many sirtuin-activating compounds (STACs) have been reported for SIRT1, which is the best-characterized sirtuin. However, the molecular mechanism of SIRT1 activation by STACs remains controversial. Here, we developed a multiscale simulation model to explore this mechanism. By quantifying the free energy landscape for the closed conformation of a SIRT1-FdL peptide-resveratrol complex, we found a positive correlation between the barrier height of the active free energy basin and the experimentally determined fluctuations in the rate of SIRT1 deacetylation by resveratrol. In addition, by monitoring dynamics, we found that the open conformation of a SIRT1-p53-STAC-1 complex had a faster rate of conformational change than the closed structure. We also determined the structural properties of each thermodynamic or dynamic state and found that two potential activating factors, the stability of FdL peptide (the p53 peptide substrate including an AMC fluorophore group) binding and the stability of the SIRT1 conformation, were weakly correlated under certain conditions. These results address the controversial question of whether the AMC fluorophore group and native hydrophobic residues have similar roles in the SIRT1 activation process. Finally, we captured the global landscape of the transition, including less stable and more stable states, and proposed a global physical landscape for the mechanism of SIRT1 activation by STACs.
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Affiliation(s)
- Fei Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, 300353 Tianjin, China.
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25
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Ghosh C, Jana B. Intersubunit Assisted Folding of DNA Binding Domains in Dimeric Catabolite Activator Protein. J Phys Chem B 2020; 124:1411-1423. [DOI: 10.1021/acs.jpcb.9b10941] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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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26
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Dynamical control by water at a molecular level in protein dimer association and dissociation. Proc Natl Acad Sci U S A 2020; 117:2302-2308. [PMID: 31969453 DOI: 10.1073/pnas.1908379117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Water, often termed as the "lubricant of life," is expected to play an active role in navigating protein dissociation-association reactions. In order to unearth the molecular details, we first compute the free-energy surface (FES) of insulin dimer dissociation employing metadynamics simulation, and then carry out analyses of insulin dimerization and dissociation using atomistic molecular-dynamics simulation in explicit water. We select two sets of initial configurations from 1) the dissociated state and 2) the transition state, and follow time evolution using several long trajectories (∼1-2 μs). During the process we not only monitor configuration of protein monomers, but also the properties of water. Although the equilibrium structural properties of water between the two monomers approach bulklike characteristics at a separation distance of ∼5 nm, the dynamics differ considerably. The complex association process is observed to be accompanied by several structural and dynamical changes of the system, such as large-scale correlated water density fluctuations, coupled conformational fluctuation of protein monomers, a dewettinglike transition with the change of intermonomeric distance RMM from ∼4 to ∼2 nm, orientation of monomers and hydrophobic hydration in the monomers. A quasistable, solvent-shared, protein monomer pair (SSPMP) forms at around 2 nm during association process which is a local free-energy minimum having ∼50-60% of native contacts. Simulations starting with arrangements sampled from the transition state (TS) of the dimer dissociation reveal that the final outcome depends on relative orientation of the backbone in the "hotspot" region.
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27
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Daitchman D, Greenblatt HM, Levy Y. Diffusion of ring-shaped proteins along DNA: case study of sliding clamps. Nucleic Acids Res 2019; 46:5935-5949. [PMID: 29860305 PMCID: PMC6158715 DOI: 10.1093/nar/gky436] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 05/08/2018] [Indexed: 12/13/2022] Open
Abstract
Several DNA-binding proteins, such as topoisomerases, helicases and sliding clamps, have a toroidal (i.e. ring) shape that topologically traps DNA, with this quality being essential to their function. Many DNA-binding proteins that function, for example, as transcription factors or enzymes were shown to be able to diffuse linearly (i.e. slide) along DNA during the search for their target binding sites. The protein's sliding properties and ability to search DNA, which often also involves hopping and dissociation, are expected to be different when it encircles the DNA. In this study, we explored the linear diffusion of four ring-shaped proteins of very similar structure: three sliding clamps (PCNA, β-clamp, and the gp45) and the 9-1-1 protein, with a particular focus on PCNA. Coarse-grained molecular dynamics simulations were performed to decipher the sliding mechanism adopted by these ring-shaped proteins and to determine how the molecular properties of the inner and outer ring govern its search speed. We designed in silico variants to dissect the contributions of ring geometry and electrostatics to the sliding speed of ring-shaped proteins along DNA. We found that the toroidal proteins diffuse when they are tilted relative to the DNA axis and able to rotate during translocation, but that coupling between rotation and translocation is quite weak. Their diffusion speed is affected by the shape of the inner ring and, to a lesser extent, by its electrostatic properties. However, breaking the symmetry of the electrostatic potential can result in deviation of the DNA from the center of the ring and cause slower linear diffusion. The findings are discussed in light of earlier computational and experimental studies on the sliding of clamps.
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Affiliation(s)
- Dina Daitchman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Harry M Greenblatt
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
- To whom correspondence should be addressed. Tel: +972 8 9344587;
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28
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Studying ribosome dynamics with simplified models. Methods 2019; 162-163:128-140. [DOI: 10.1016/j.ymeth.2019.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 12/24/2022] Open
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29
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Pal A, Levy Y. Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins. PLoS Comput Biol 2019; 15:e1006768. [PMID: 30933978 PMCID: PMC6467422 DOI: 10.1371/journal.pcbi.1006768] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 04/16/2019] [Accepted: 01/01/2019] [Indexed: 02/06/2023] Open
Abstract
Recognition of single-stranded DNA (ssDNA) or single-stranded RNA (ssRNA) is important for many fundamental cellular functions. A variety of single-stranded DNA-binding proteins (ssDBPs) and single-stranded RNA-binding proteins (ssRBPs) have evolved that bind ssDNA and ssRNA, respectively, with varying degree of affinities and specificities to form complexes. Structural studies of these complexes provide key insights into their recognition mechanism. However, computational modeling of the specific recognition process and to predict the structure of the complex is challenging, primarily due to the heterogeneity of their binding energy landscape and the greater flexibility of ssDNA or ssRNA compared with double-stranded nucleic acids. Consequently, considerably fewer computational studies have explored interactions between proteins and single-stranded nucleic acids compared with protein interactions with double-stranded nucleic acids. Here, we report a newly developed energy-based coarse-grained model to predict the structure of ssDNA–ssDBP and ssRNA–ssRBP complexes and to assess their sequence-specific interactions and stabilities. We tuned two factors that can modulate specific recognition: base–aromatic stacking strength and the flexibility of the single-stranded nucleic acid. The model was successfully applied to predict the binding conformations of 12 distinct ssDBP and ssRBP structures with their cognate ssDNA and ssRNA partners having various sequences. Estimated binding energies agreed well with the corresponding experimental binding affinities. Bound conformations from the simulation showed a funnel-shaped binding energy distribution where the native-like conformations corresponded to the energy minima. The various ssDNA–protein and ssRNA–protein complexes differed in the balance of electrostatic and aromatic energies. The lower affinity of the ssRNA–ssRBP complexes compared with the ssDNA–ssDBP complexes stems from lower flexibility of ssRNA compared to ssDNA, which results in higher rate constants for the dissociation of the complex (koff) for complexes involving the former. Quantifying bimolecular self-assembly is pivotal to understanding cellular function. In recent years, a large progress has been made in understanding the structure and biophysics of protein-protein interactions. Particularly, various computational tools are available for predicting these structures and to estimate their stability and the driving forces of their formation. The understating of the interactions between proteins and nucleic acids, however, is still limited, presumably due to the involvement of non-specific interactions as well as the high conformational plasticity that may demand an induced-fit mechanism. In particular, the interactions between proteins and single-stranded nucleic acids (i.e., single-stranded DNA and RNA) is very challenging due to their high flexibility. Furthermore, the interface between proteins and single-stranded nucleic acids is often chemically more heterogeneous than the interface between proteins and double-stranded DNA. In this study, we developed a coarse-grained computational model to predict the structure of complexes between proteins and single-stranded nucleic acids. The model was applied to estimate binding affinities and the estimated binding energies agreed well with the corresponding experimental binding affinities. The kinetics of association as well as the specificity of the complexes between proteins and ssDNA are different than those with ssRNA, mostly due to differences in their conformational flexibility.
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Affiliation(s)
- Arumay Pal
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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30
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Pal A, Neo K, Rajamani L, Ferrer FJ, Lane DP, Verma CS, Mortellaro A. Inhibition of NLRP3 inflammasome activation by cell-permeable stapled peptides. Sci Rep 2019; 9:4913. [PMID: 30894604 PMCID: PMC6426897 DOI: 10.1038/s41598-019-41211-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 02/22/2019] [Indexed: 12/12/2022] Open
Abstract
Interleukin-1β (IL-1β) is a major cytokine that initiates and enhances inflammatory responses. Excessive IL-1β production is a characteristic of most chronic inflammatory diseases, including atherosclerosis, type 2 diabetes, and obesity, which affect a large proportion of the global population. The production of bioactive IL-1β is mediated by a caspase-1-activating complex known as an 'inflammasome'. The NLRP3 inflammasome has been associated with several human inflammatory and autoimmune diseases and represents a potential therapeutic target for disrupting IL-1β production. We used molecular modeling guided by molecular dynamics simulations to design α-helical stapled peptides targeting the pyrin domain of the adaptor protein ASC to interrupt the development of its filament, which is crucial for NLRP3 inflammasome formation. The peptides were effectively internalized by human monocytic cells and efficiently suppressed the release of the inflammasome-regulated cytokines IL-1β and IL-18, following exogenous activation of the NLRP3 inflammasome. The peptides reduced ASC speck formation and caspase-1 processing thereby suppressing pro-IL-1β processing and release of active IL-1β. This is the first demonstration of the successful use of stapled peptides designed to target the adaptor protein ASC, and can be extended to other inflammatory pathways to disrupt excessive IL-1β production.
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Affiliation(s)
- Arumay Pal
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Kurt Neo
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8a Biomedical Grove, Singapore, 138648, Singapore
| | - Lakshminarayanan Rajamani
- Singapore Eye Research Institute (SERI), The Academia, 20 College Road, Discovery Tower Level 6, Singapore, 169856, Singapore
| | - Fernando Jose Ferrer
- p53Lab, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore, 138648, Singapore
| | - David P Lane
- p53Lab, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore, 138648, Singapore
| | - Chandra S Verma
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore. .,Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.
| | - Alessandra Mortellaro
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8a Biomedical Grove, Singapore, 138648, Singapore. .,San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milano, Italy.
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31
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Chu X, Wang J. Position-, disorder-, and salt-dependent diffusion in binding-coupled-folding of intrinsically disordered proteins. Phys Chem Chem Phys 2019; 21:5634-5645. [PMID: 30793144 PMCID: PMC6589441 DOI: 10.1039/c8cp06803h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Successful extensions of protein-folding energy landscape theory to intrinsically disordered proteins' (IDPs') binding-coupled-folding transition can enormously simplify this biomolecular process into diffusion along a limited number of reaction coordinates, and the dynamics subsequently is described by Kramers' rate theory. As the critical pre-factor, the diffusion coefficient D has direct implications on the binding kinetics. Here, we employ a structure-based model (SBM) to calculate D in the binding-folding of an IDP prototype. We identify a strong position-dependent D during binding by applying a reaction coordinate that directly measures the fluctuations in a Cartesian configuration space. Using the malleability of the SBM, we modulate the degree of conformational disorder in an isolated IDP and determine complex effects of intrinsic disorder on D varying for different binding stages. Here, D tends to increase with disorder during initial binding but shows a non-monotonic relationship with disorder in terms of a decrease-followed-by-increase in D during the late binding stage. The salt concentration, which correlates with electrostatic interactions via Debye-Hückel theory in our SBM, also modulates D in a stepwise way. The speeding up of diffusion by electrostatic interactions is observed during the formation of the encounter complex at the beginning of binding, while the last diffusive binding dynamics is hindered by non-native salt bridges. Because D describes the diffusive speed locally, which implicitly reflects the roughness of the energy landscape, we are eventually able to portray the binding energy landscape, including that from IDPs' binding, then to binding with partial folding, and finally to rigid docking, as well as that under different environmental salt concentrations. Our theoretical results provide key mechanistic insights into IDPs' binding-folding, which is internally conformation- and externally salt-controlled with respect to diffusion.
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Affiliation(s)
- Xiakun Chu
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Jin Wang
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
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32
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Yu Z, Liu Y, Zhu J, Han J, Tian X, Han W, Zhao L. Insights from molecular dynamics simulations and steered molecular dynamics simulations to exploit new trends of the interaction between HIF-1α and p300. J Biomol Struct Dyn 2019; 38:1-12. [DOI: 10.1080/07391102.2019.1580616] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Zhengfei Yu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Ye Liu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Jingxuan Zhu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Jiarui Han
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Xiaopian Tian
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Li Zhao
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, China
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33
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Banerjee P, Mondal S, Bagchi B. Effect of ethanol on insulin dimer dissociation. J Chem Phys 2019; 150:084902. [PMID: 30823756 DOI: 10.1063/1.5079501] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Insulin-dimer dissociation is an essential biochemical process required for the activity of the hormone. We investigate this dissociation process at the molecular level in water and at the same time, in 5% and 10% water-ethanol mixtures. We compute the free energy surface of the protein dissociation processes by employing biased molecular dynamics simulation. In the presence of ethanol (EtOH), we observe a marked lowering in the free energy barrier of activation of dimer dissociation from that in the neat water, by as much as ∼50%, even in the 5% water-ethanol solution. In addition, ethanol is found to induce significant changes in the dissociation pathway. We extract the most probable conformations of the intermediate states along the minimum energy pathway in the case of all the three concentrations (EtOH mole fractions 0, 5, and 10). We explore the change in microscopic structures that occur in the presence of ethanol. Interestingly, we discover a stable intermediate state in the water-ethanol binary mixture where the centers of the monomers are separated by about 3 nm and the contact order parameter is close to zero. This intermediate is stabilized by the wetting of the interface between the two monomers by the preferential distribution of ethanol and water molecules. This wetting serves to reduce the free energy barrier significantly and thus results in an increase in the rate of dimer dissociation. We also analyze the solvation of the two monomers during the dissociation and both the proteins' departure from the native state configuration to obtain valuable insights into the dimer dissociation processes.
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Affiliation(s)
- Puja Banerjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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34
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Nerattini F, Tubiana L, Cardelli C, Bianco V, Dellago C, Coluzza I. Design of Protein–Protein Binding Sites Suggests a Rationale for Naturally Occurring Contact Areas. J Chem Theory Comput 2018; 15:1383-1392. [DOI: 10.1021/acs.jctc.8b00667] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francesca Nerattini
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Luca Tubiana
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Chiara Cardelli
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Valentino Bianco
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Christoph Dellago
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Ivan Coluzza
- CIC biomaGUNE, Paseo Miramon 182, 20014 San Sebastian, Spain
- IKERBASQUE,
Basque Foundation for Science, 48013 Bilbao, Spain
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35
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Xiong J, Gao M, Zhou J, Liu S, Su Z, Liu Z, Huang Y. The influence of intrinsic folding mechanism of an unfolded protein on the coupled folding-binding process during target recognition. Proteins 2018; 87:265-275. [PMID: 30520528 DOI: 10.1002/prot.25646] [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] [Received: 05/12/2018] [Revised: 09/28/2018] [Accepted: 11/29/2018] [Indexed: 11/11/2022]
Abstract
Intrinsically disordered proteins (IDPs) are extensively involved in dynamic signaling processes which require a high association rate and a high dissociation rate for rapid binding/unbinding events and at the same time a sufficient high affinity for specific recognition. Although the coupled folding-binding processes of IDPs have been extensively studied, it is still impossible to predict whether an unfolded protein is suitable for molecular signaling via coupled folding-binding. In this work, we studied the interplay between intrinsic folding mechanisms and coupled folding-binding process for unfolded proteins through molecular dynamics simulations. We first studied the folding process of three representative IDPs with different folded structures, that is, c-Myb, AF9, and E3 rRNase. We found the folding free energy landscapes of IDPs are downhill or show low barriers. To further study the influence of intrinsic folding mechanism on the binding process, we modulated the folding mechanism of barnase via circular permutation and simulated the coupled folding-binding process between unfolded barnase permutant and folded barstar. Although folding of barnase was coupled to target binding, the binding kinetics was significantly affected by the intrinsic folding free energy barrier, where reducing the folding free energy barrier enhances binding rate up to two orders of magnitude. This accelerating effect is different from previous results which reflect the effect of structure flexibility on binding kinetics. Our results suggest that coupling the folding of an unfolded protein with no/low folding free energy barrier with its target binding may provide a way to achieve high specificity and rapid binding/unbinding kinetics simultaneously.
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Affiliation(s)
- Junwen Xiong
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
| | - Meng Gao
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
| | - Jingjing Zhou
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
| | - Sen Liu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
| | - Zhengding Su
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
| | - Zhirong Liu
- College of Chemistry and Molecular Engineering, and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing, China
| | - Yongqi Huang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
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36
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Neelamraju S, Gosavi S, Wales DJ. Energy Landscape of the Designed Protein Top7. J Phys Chem B 2018; 122:12282-12291. [DOI: 10.1021/acs.jpcb.8b08499] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Sridhar Neelamraju
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka 560065, India
- University Chemical Laboratories, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka 560065, India
| | - David J. Wales
- University Chemical Laboratories, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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37
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Yrazu FM, Pinamonti G, Clementi C. The Effect of Electrostatic Interactions on the Folding Kinetics of a 3-α-Helical Bundle Protein Family. J Phys Chem B 2018; 122:11800-11806. [PMID: 30277393 DOI: 10.1021/acs.jpcb.8b08676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The trio of protein segment repeats called spectrins diverges by more than 2 orders of magnitude in their folding and unfolding rates, despite having very similar stabilities and almost coincidental topologies. Experimental studies revealed that the mutation of five particular residues dramatically alters the kinetic rates in the slow folders, making them similar to the rates of the fast folder. This is considered to be an exceptional behavior which seems in principle to challenge the current understanding of the protein folding process. In this work, we analyze this scenario, using a simplified computational model, combined with state-of-the-art kinetic analysis techniques. Our model faithfully separates the kinetics of the fast and slow folders and captures the effect of the five mutations. We show that the inclusion of electrostatics in the model is necessary to explain the experimental findings.
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Affiliation(s)
- Fernando Miguel Yrazu
- Department of Chemical and Biomolecular Engineering , Rice University , Houston , Texas 77005 , United States
| | - Giovanni Pinamonti
- Department of Informatics and Mathematics , Freie Universität Berlin , 14195 Berlin , Germany
| | - Cecilia Clementi
- Department of Chemical and Biomolecular Engineering , Rice University , Houston , Texas 77005 , United States.,Department of Informatics and Mathematics , Freie Universität Berlin , 14195 Berlin , Germany.,Center for Theoretical Biological Physics and Department of Chemistry , Rice University , Houston , Texas 77005 , United States
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38
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Simulations Reveal Multiple Intermediates in the Unzipping Mechanism of Neuronal SNARE Complex. Biophys J 2018; 115:1470-1480. [PMID: 30268539 DOI: 10.1016/j.bpj.2018.08.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/26/2018] [Accepted: 08/16/2018] [Indexed: 11/22/2022] Open
Abstract
The assembling of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor protein complex is a fundamental step in neuronal exocytosis, and it has been extensively studied in the last two decades. Yet, many details of this process remain inaccessible with the current experimental space and time resolution. Here, we study the zipping mechanism of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor complex computationally by using a coarse-grained model. We explore the different pathways available and analyze their dependence on the computational model employed. We reveal and characterize multiple intermediate states, in agreement with previous experimental findings. We use our model to analyze the influence of single-residue mutations on the thermodynamics of the folding process.
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39
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Banerjee P, Mondal S, Bagchi B. Insulin dimer dissociation in aqueous solution: A computational study of free energy landscape and evolving microscopic structure along the reaction pathway. J Chem Phys 2018; 149:114902. [DOI: 10.1063/1.5042290] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Puja Banerjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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40
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Wang Y, Tian P, Boomsma W, Lindorff-Larsen K. Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias. J Phys Chem B 2018; 122:11174-11185. [DOI: 10.1021/acs.jpcb.8b06335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yong Wang
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Pengfei Tian
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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41
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Koch I, Schäfer T. Protein super-secondary structure and quaternary structure topology: theoretical description and application. Curr Opin Struct Biol 2018; 50:134-143. [DOI: 10.1016/j.sbi.2018.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/26/2018] [Accepted: 02/17/2018] [Indexed: 12/13/2022]
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42
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Mascarenhas NM, Terse VL, Gosavi S. Intrinsic Disorder in a Well-Folded Globular Protein. J Phys Chem B 2018; 122:1876-1884. [PMID: 29304275 DOI: 10.1021/acs.jpcb.7b12546] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The folded structure of the heterodimeric sweet protein monellin mimics single-chain proteins with topology β1-α1-β2-β3-β4-β5 (chain A: β3-β4-β5; chain B: β1-α1-β2). Furthermore, like naturally occurring single-chain proteins of a similar size, monellin folds cooperatively with no detectable intermediates. However, the two monellin chains, A and B, are marginally structured in isolation and fold only upon binding to each other. Thus, monellin presents a unique opportunity to understand the design of intrinsically disordered proteins that fold upon binding. Here, we study the folding of a single-chain variant of monellin (scMn) using simulations of an all heavy-atom structure-based model. These simulations can explain mechanistic details derived from scMn experiments performed using several different structural probes. scMn folds cooperatively in our structure-based simulations, as is also seen in experiments. We find that structure formation near the transition-state ensemble of scMn is not uniformly distributed but is localized to a hairpin-like structure which contains one strand from each chain (β2, β3). Thus, the sequence and the underlying energetics of heterodimeric monellin promote the early formation of the interchain interface (β2-β3). By studying computational scMn mutants whose "interchain" interactions are deleted, we infer that this energy distribution allows the two protein chains to remain largely disordered when this interface is not folded. From these results, we suggest that cutting the protein backbone of a globular protein between residues which lie within its folding nucleus may be one way to construct two disordered fragments which fold upon binding.
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Affiliation(s)
| | - Vishram L Terse
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research , Bangalore 560065, India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research , Bangalore 560065, India
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43
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Chu X, Muñoz V. Roles of conformational disorder and downhill folding in modulating protein-DNA recognition. Phys Chem Chem Phys 2018; 19:28527-28539. [PMID: 29044255 DOI: 10.1039/c7cp04380e] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Transcription factors are thought to efficiently search for their target DNA site via a combination of conventional 3D diffusion and 1D diffusion along the DNA molecule mediated by non-specific electrostatic interactions. This process requires the DNA-binding protein to quickly exchange between a search competent and a target recognition mode, but little is known as to how these two binding modes are encoded in the conformational properties of the protein. Here, we investigate this issue on the engrailed homeodomain (EngHD), a DNA-binding domain that folds ultrafast and exhibits a complex conformational behavior consistent with the downhill folding scenario. We explore the interplay between folding and DNA recognition using a coarse-grained computational model that allows us to manipulate the folding properties of the protein and monitor its non-specific and specific binding to DNA. We find that conformational disorder increases the search efficiency of EngHD by promoting a fast gliding search mode in addition to sliding. When gliding, EngHD remains loosely bound to DNA moving linearly along its length. A partially disordered EngHD also binds more dynamically to the target site, reducing the half-life of the specific complex via a spring-loaded mechanism. These findings apply to all conditions leading to partial disorder. However, we also find that at physiologically relevant temperatures EngHD is well folded and can only obtain the conformational flexibility required to accelerate 1D diffusion when it folds/unfolds within the downhill scenario (crossing a marginal free energy barrier). In addition, the conformational flexibility of native downhill EngHD enables its fast reconfiguration to lock into the specific binding site upon arrival, thereby affording finer control of the on- and off-rates of the specific complex. Our results provide key mechanistic insights into how DNA-binding domains optimize specific DNA recognition through the control of their conformational dynamics and folding mechanism.
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Affiliation(s)
- Xiakun Chu
- IMDEA Nanosciences, Faraday 9, Campus de Cantoblanco, Madrid, 28049, Spain
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44
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Zhao L, Lu HP, Wang J. Exploration of Multistate Conformational Dynamics upon Ligand Binding of a Monomeric Enzyme Involved in Pyrophosphoryl Transfer. J Phys Chem B 2018; 122:1885-1897. [PMID: 29385349 DOI: 10.1021/acs.jpcb.7b12562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase) is a monomeric protein with 158 residues, which undergoes large-scale conformational changes between apo, open, and holo states responding to ligand binding for its function. It has been explored widely as an excellent target for potential antibacterial drug development. However, little is known about how conformational dynamics between the native states influences the substrate recognition and the functionality of enzymatic catalysis. Here, we report a coarse-grained triple-basin structure-based model upon ligand binding to describe such multiple-state system by the molecular dynamics simulation. With our model, we have made theoretical predictions that are in good agreement with the experimental measurements. Our results revealed the intrinsic conformational fluctuations between apo and open states without ligand binding. We found that HPPK can switch to the activated holo state upon the ordered binding of the two ligands (ATP and HP). We uncovered the underlying mechanism by which major induced fit and minor population shift pathways coexist upon ligand binding by quantitative flux analysis. Additionally, we pointed out the structural origin for the conformational changes and identified the key residues as well as contact interactions. We further explored the temperature effect on the conformational distributions and pathway weights. It gave strong support that higher temperatures promote population shift, while the induced fit pathway is always the predominant activation route of the HPPK system. These findings will provide significant insights of the mechanisms of the multistate conformational dynamics of HPPK upon ligand binding.
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Affiliation(s)
- Lingci Zhao
- College of Physics, Jilin University , Changchun, Jilin 130012, People's Republic of China.,State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, People's Republic of China
| | - H Peter Lu
- Center for Photochemical Sciences, Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Jin Wang
- College of Physics, Jilin University , Changchun, Jilin 130012, People's Republic of China.,State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, People's Republic of China.,Department of Chemistry and Physics, State University of New York , Stony Brook, New York 11794-3400, United States
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45
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Ren W, Li W, Wang J, Zhang J, Wang W. Consequences of Energetic Frustration on the Ligand-Coupled Folding/Dimerization Dynamics of Allosteric Protein S100A12. J Phys Chem B 2017; 121:9799-9806. [DOI: 10.1021/acs.jpcb.7b06919] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Weitong Ren
- National
Laboratory of Solid State Microstructure, Department of Physics, and
Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wenfei Li
- National
Laboratory of Solid State Microstructure, Department of Physics, and
Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Jun Wang
- National
Laboratory of Solid State Microstructure, Department of Physics, and
Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Jian Zhang
- National
Laboratory of Solid State Microstructure, Department of Physics, and
Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wei Wang
- National
Laboratory of Solid State Microstructure, Department of Physics, and
Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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46
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Kubo S, Li W, Takada S. Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations. PLoS Comput Biol 2017; 13:e1005748. [PMID: 28892477 PMCID: PMC5608440 DOI: 10.1371/journal.pcbi.1005748] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 09/21/2017] [Accepted: 08/29/2017] [Indexed: 01/27/2023] Open
Abstract
Cytoplasmic dynein is a giant ATP-driven molecular motor that proceeds to the minus end of the microtubule (MT). Dynein hydrolyzes ATP in a ring-like structure, containing 6 AAA+ (ATPases associated with diverse cellular activities) modules, which is ~15 nm away from the MT binding domain (MTBD). This architecture implies that long-distance allosteric couplings exist between the AAA+ ring and the MTBD in order for dynein to move on the MT, although little is known about the mechanisms involved. Here, we have performed comprehensive molecular simulations of the dynein motor domain based on pre- and post- power-stroke structural information and in doing so we address the allosteric conformational changes that occur during the power-stroke and recovery-stroke processes. In the power-stroke process, the N-terminal linker movement was the prerequisite to the nucleotide-dependent AAA1 transition, from which a transition cascade propagated, on average, in a circular manner on the AAA+ ring until it reached the AAA6/C-terminal module. The recovery-stroke process was initiated by the transition of the AAA6/C-terminal, from which the transition cascade split into the two directions of the AAA+ ring, occurring both clockwise and anti-clockwise. In both processes, the MTBD conformational change was regulated by the AAA4 module and the AAA5/Strut module. The linear molecular motor dynein is an intriguing allosteric model protein. ATP hydrolysis, catalyzed by modules in the AAA+ ring, regulates the binding to the rail molecule, microtubule, which is ~15 nm away from the AAA+ ring. The molecular mechanisms underpinning this long-distance communication are unclear. Based on recently solved pre- and post- power-stroke crystal structure information, we performed, for the first time to our knowledge, molecular simulations of complete conformational changes between the two structures. The simulation revealed that module-by-module allosteric conformational changes occur. Interestingly, the transition cascade from the pre- to the post-power-stroke states propagated in a circular manner around the AAA+ ring, while that of the recovery transitions propagated in a bi-directional manner around the ring.
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Affiliation(s)
- Shintaroh Kubo
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Wenfei Li
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing, China
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
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Zhang P, Tripathi S, Trinh H, Cheung MS. Opposing Intermolecular Tuning of Ca 2+ Affinity for Calmodulin by Neurogranin and CaMKII Peptides. Biophys J 2017; 112:1105-1119. [PMID: 28355539 PMCID: PMC5374985 DOI: 10.1016/j.bpj.2017.01.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/27/2016] [Accepted: 01/23/2017] [Indexed: 12/03/2022] Open
Abstract
We investigated the impact of bound calmodulin (CaM)-target compound structure on the affinity of calcium (Ca2+) by integrating coarse-grained models and all-atomistic simulations with nonequilibrium physics. We focused on binding between CaM and two specific targets, Ca2+/CaM-dependent protein kinase II (CaMKII) and neurogranin (Ng), as they both regulate CaM-dependent Ca2+ signaling pathways in neurons. It was shown experimentally that Ca2+/CaM (holoCaM) binds to the CaMKII peptide with overwhelmingly higher affinity than Ca2+-free CaM (apoCaM); the binding of CaMKII peptide to CaM in return increases the Ca2+ affinity for CaM. However, this reciprocal relation was not observed in the Ng peptide (Ng13–49), which binds to apoCaM or holoCaM with binding affinities of the same order of magnitude. Unlike the holoCaM-CaMKII peptide, whose structure can be determined by crystallography, the structural description of the apoCaM-Ng13–49 is unknown due to low binding affinity, therefore we computationally generated an ensemble of apoCaM-Ng13–49 structures by matching the changes in the chemical shifts of CaM upon Ng13–49 binding from nuclear magnetic resonance experiments. Next, we computed the changes in Ca2+ affinity for CaM with and without binding targets in atomistic models using Jarzynski’s equality. We discovered the molecular underpinnings of lowered affinity of Ca2+ for CaM in the presence of Ng13–49 by showing that the N-terminal acidic region of Ng peptide pries open the β-sheet structure between the Ca2+ binding loops particularly at C-domain of CaM, enabling Ca2+ release. In contrast, CaMKII peptide increases Ca2+ affinity for the C-domain of CaM by stabilizing the two Ca2+ binding loops. We speculate that the distinctive structural difference in the bound complexes of apoCaM-Ng13–49 and holoCaM-CaMKII delineates the importance of CaM’s progressive mechanism of target binding on its Ca2+ binding affinities.
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Affiliation(s)
- Pengzhi Zhang
- Department of Physics, University of Houston, Houston, Texas
| | | | - Hoa Trinh
- Department of Physics, University of Houston, Houston, Texas
| | - Margaret S Cheung
- Department of Physics, University of Houston, Houston, Texas; Center for Theoretical Biological Physics, Rice University, Houston, Texas.
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48
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Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling. Nat Chem 2017; 9:1005-1011. [PMID: 28937668 DOI: 10.1038/nchem.2785] [Citation(s) in RCA: 237] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 04/21/2017] [Indexed: 12/23/2022]
Abstract
Protein-protein association is fundamental to many life processes. However, a microscopic model describing the structures and kinetics during association and dissociation is lacking on account of the long lifetimes of associated states, which have prevented efficient sampling by direct molecular dynamics (MD) simulations. Here we demonstrate protein-protein association and dissociation in atomistic resolution for the ribonuclease barnase and its inhibitor barstar by combining adaptive high-throughput MD simulations and hidden Markov modelling. The model reveals experimentally consistent intermediate structures, energetics and kinetics on timescales from microseconds to hours. A variety of flexibly attached intermediates and misbound states funnel down to a transition state and a native basin consisting of the loosely bound near-native state and the tightly bound crystallographic state. These results offer a deeper level of insight into macromolecular recognition and our approach opens the door for understanding and manipulating a wide range of macromolecular association processes.
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49
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Healy EF. A prion-like mechanism for the propagated misfolding of SOD1 from in silico modeling of solvated near-native conformers. PLoS One 2017; 12:e0177284. [PMID: 28472188 PMCID: PMC5417709 DOI: 10.1371/journal.pone.0177284] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 04/25/2017] [Indexed: 12/11/2022] Open
Abstract
A prion-like mechanism has been developed to explain the observed promotion of amyloid aggregation caused by conversion of structurally intact SOD1 to a misfolded form. Superoxide dismutase [Cu-Zn], or SOD1, is a homo-dimeric protein that functions as an antioxidant by scavenging for superoxide. The misfolding and aggregation of SOD1 is linked to inherited, or familial, amyotrophic lateral sclerosis (FALS), a progressive and fatal neurodegenerative disease. Aberrant SOD1 folding has also been strongly implicated in disease causation for sporadic ALS, or SALS, which accounts for ~90% of ALS cases. Studies have found that mutant, misfolded SOD1 can convert wtSOD1 in a prion-like fashion, and that misfolded wtSOD1 can be propagated by release and uptake of protein aggregates. Here it is demonstrated that enervating the SOD1 electrostatic loop can lead to an experimentally observed gain of interaction (GOI) responsible for the formation of SOD1 amyloid-like filaments. This enervation is caused in turn by the formation of transient, non-obligate oligomers between pathogenic SOD1 mutants and wt SOD1.
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Affiliation(s)
- Eamonn F. Healy
- Department of Chemistry, St. Edward’s University, Austin, Texas, United States of America
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50
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Garg DK, Kundu B. Hyperthermophilic l -asparaginase bypasses monomeric intermediates during folding to retain cooperativity and avoid amyloid assembly. Arch Biochem Biophys 2017; 622:36-46. [DOI: 10.1016/j.abb.2017.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 04/26/2017] [Accepted: 04/27/2017] [Indexed: 10/19/2022]
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