1
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Hommel K, Kauth AMA, Kirupakaran A, Theisen S, Hayduk M, Niemeyer FC, Beuck C, Zadmard R, Bayer P, Jan Ravoo B, Voskuhl J, Schrader T, Knauer SK. Functional Linkers Support Targeting of Multivalent Tweezers to Taspase1. Chemistry 2024; 30:e202401542. [PMID: 38958349 DOI: 10.1002/chem.202401542] [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: 04/20/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/04/2024]
Abstract
Taspase 1 is a unique protease not only pivotal for embryonic development but also implicated in leukemias and solid tumors. As such, this enzyme is a promising while still challenging therapeutic target, and with its protein structure featuring a flexible loop preceding the active site a versatile model system for drug development. Supramolecular ligands provide a promising complementary approach to traditional small-molecule inhibitors. Recently, the multivalent arrangement of molecular tweezers allowed the successful targeting of Taspase 1's surface loop. With this study we now want to take the next logic step und utilize functional linker systems that not only allow the implementation of novel properties but also engage in protein surface binding. Consequently, we chose two different linker types differing from the original divalent assembly: a backbone with aggregation-induced emission (AIE) properties to enable monitoring of binding and a calix[4]arene scaffold initially pre-positioning the supramolecular binding units. With a series of four AIE-equipped ligands with stepwise increased valency we demonstrated that the functionalized AIE linkers approach ligand binding affinities in the nanomolar range and allow efficient proteolytic inhibition of Taspase 1. Moreover, implementation of the calix[4]arene backbone further enhanced the ligands' inhibitory potential, pointing to a specific linker contribution.
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Affiliation(s)
- Katrin Hommel
- Molecular Biology II, Center of Medical Biotechnology (ZMB) and Center for Nanointegration (CENIDE), University of Duisburg-Essen, Universitätsstrasse 5, 45141, Essen, Germany
| | - Alisa-Maite A Kauth
- Organic Chemistry Institute and Center for Soft Nanoscience, University of Münster, Busso-Peus-Straße 10, 48149, Münster, Germany
| | - Abbna Kirupakaran
- Institute of Organic Chemistry I, Biosupramolecular Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Sebastian Theisen
- Institute of Organic Chemistry I, Biosupramolecular Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Matthias Hayduk
- Faculty of Chemistry (Organic Chemistry II), Center of Medical Biotechnology (ZMB) and Center for Nanointegration (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Felix C Niemeyer
- Institute of Organic Chemistry I, Biosupramolecular Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141, Essen, Germany
| | - Reza Zadmard
- Department of Organic Chemistry, Chemistry and Chemical Engineering Research Center of Iran (CCERCI), P. O. Box 14335-186, Tehran, Iran
| | - Peter Bayer
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141, Essen, Germany
| | - Bart Jan Ravoo
- Organic Chemistry Institute and Center for Soft Nanoscience, University of Münster, Busso-Peus-Straße 10, 48149, Münster, Germany
| | - Jens Voskuhl
- Faculty of Chemistry (Organic Chemistry II), Center of Medical Biotechnology (ZMB) and Center for Nanointegration (CENIDE), University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Thomas Schrader
- Institute of Organic Chemistry I, Biosupramolecular Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Shirley K Knauer
- Molecular Biology II, Center of Medical Biotechnology (ZMB) and Center for Nanointegration (CENIDE), University of Duisburg-Essen, Universitätsstrasse 5, 45141, Essen, Germany
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2
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Zhang Y, Liu X, Chen J. Re-Balancing Replica Exchange with Solute Tempering for Sampling Dynamic Protein Conformations. J Chem Theory Comput 2023; 19:1602-1614. [PMID: 36791464 PMCID: PMC10795075 DOI: 10.1021/acs.jctc.2c01139] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Replica exchange with solute tempering (REST) is a highly effective variant of replica exchange for enhanced sampling in explicit solvent simulations of biomolecules. By scaling the Hamiltonian for a selected "solute" region of the system, REST effectively applies tempering only to the degrees of freedom of interest but not the rest of the system ("solvent"), allowing fewer replicas for covering the same temperature range. A key consideration of REST is how the solute-solvent interactions are scaled together with the solute-solute interactions. Here, we critically evaluate the performance of the latest REST2 protocol for sampling large-scale conformation fluctuations of intrinsically disordered proteins (IDPs). The results show that REST2 promotes artificial protein conformational collapse at high effective temperatures, which seems to be a designed feature originally to promote the sampling of reversible folding of small proteins. The collapse is particularly severe with larger IDPs, leading to replica segregation in the effective temperature space and hindering effective sampling of large-scale conformational changes. We propose that the scaling of the solute-solvent interactions can be treated as free parameters in REST, which can be tuned to control the solute conformational properties (e.g., chain expansion) at different effective temperatures and achieve more effective sampling. To this end, we derive a new REST3 protocol, where the strengths of the solute-solvent van der Waals interactions are recalibrated to reproduce the levels of protein chain expansion at high effective temperatures. The efficiency of REST3 is examined using two IDPs with nontrivial local and long-range structural features, including the p53 N-terminal domain and the kinase inducible transactivation domain of transcription factor CREB. The results suggest that REST3 leads to a much more efficient temperature random walk and improved sampling efficiency, which also further reduces the number of replicas required. Nonetheless, our analysis also reveals significant challenges of relying on tempering alone for sampling large-scale conformational fluctuations of disordered proteins. It is likely that more efficient sampling protocols will require incorporating more sophisticated Hamiltonian replica exchange schemes in addition to tempering.
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Affiliation(s)
- Yumeng Zhang
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Xiaorong Liu
- Corresponding Authors: (XL), (JC), Phone: (413) 545-3386 (JC)
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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3
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Shulga DA, Kudryavtsev KV. Theoretical Studies of Leu-Pro-Arg-Asp-Ala Pentapeptide (LPRDA) Binding to Sortase A of Staphylococcus aureus. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238182. [PMID: 36500275 PMCID: PMC9890316 DOI: 10.3390/molecules27238182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/15/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022]
Abstract
Sortase A (SrtA) of Staphylococcus aureus is a well-defined molecular target to combat the virulence of these clinically important bacteria. However up to now no efficient drugs or even clinical candidates are known, hence the search for such drugs is still relevant and necessary. SrtA is a complex target, so many straight-forward techniques for modeling using the structure-based drug design (SBDD) fail to produce the results they used to bring for other, simpler, targets. In this work we conduct theoretical studies of the binding/activity of Leu-Pro-Arg-Asp-Ala (LPRDA) polypeptide, which was recently shown to possess antivirulence activity against S. aureus. Our investigation was aimed at establishing a framework for the estimation of the key interactions and subsequent modification of LPRDA, targeted at non-peptide molecules, with better drug-like properties than the original polypeptide. Firstly, the available PDB structures are critically analyzed and the criteria to evaluate the quality of the ligand-SrtA complex geometry are proposed. Secondly, the docking protocol was investigated to establish its applicability to the LPRDA-SrtA complex prediction. Thirdly, the molecular dynamics studies were carried out to refine the geometries and estimate the stability of the complexes, predicted by docking. The main finding is that the previously reported partially chaotic movement of the β6/β7 and β7/β8 loops of SrtA (being the intrinsically disordered parts related to the SrtA binding site) is exaggerated when SrtA is complexed with LPRDA, which in turn reveals all the signs of the flexible and structurally disordered molecule. As a result, a wealth of plausible LPRDA-SrtA complex conformations are hard to distinguish using simple modeling means, such as docking. The use of more elaborate modeling approaches may help to model the system reliably but at the cost of computational efficiency.
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Affiliation(s)
- Dmitry A. Shulga
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
- Correspondence: (D.A.S.); (K.V.K.)
| | - Konstantin V. Kudryavtsev
- Laboratory of Molecular Pharmacology, Pirogov Russian National Research Medical University, Ostrovityanova Street 1, 117997 Moscow, Russia
- Correspondence: (D.A.S.); (K.V.K.)
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4
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Höing A, Kirupakaran A, Beuck C, Pörschke M, Niemeyer FC, Seiler T, Hartmann L, Bayer P, Schrader T, Knauer SK. Recognition of a Flexible Protein Loop in Taspase 1 by Multivalent Supramolecular Tweezers. Biomacromolecules 2022; 23:4504-4518. [PMID: 36200481 DOI: 10.1021/acs.biomac.2c00652] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many natural proteins contain flexible loops utilizing well-defined complementary surface regions of their interacting partners and usually undergo major structural rearrangements to allow perfect binding. The molecular recognition of such flexible structures is still highly challenging due to the inherent conformational dynamics. Notably, protein-protein interactions are on the other hand characterized by a multivalent display of complementary binding partners to enhance molecular affinity and specificity. Imitating this natural concept, we here report the rational design of advanced multivalent supramolecular tweezers that allow addressing two lysine and arginine clusters on a flexible protein surface loop. The protease Taspase 1, which is involved in cancer development, carries a basic bipartite nuclear localization signal (NLS) and thus interacts with Importin α, a prerequisite for proteolytic activation. Newly established synthesis routes enabled us to covalently fuse several tweezer molecules into multivalent NLS ligands. The resulting bi- up to pentavalent constructs were then systematically compared in comprehensive biochemical assays. In this series, the stepwise increase in valency was robustly reflected by the ligands' gradually enhanced potency to disrupt the interaction of Taspase 1 with Importin α, correlated with both higher binding affinity and inhibition of proteolytic activity.
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Affiliation(s)
- Alexander Höing
- Molecular Biology II, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Abbna Kirupakaran
- Institute of Organic Chemistry I, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Marius Pörschke
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Felix C Niemeyer
- Institute of Organic Chemistry I, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Theresa Seiler
- Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Laura Hartmann
- Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Peter Bayer
- Structural and Medicinal Biochemistry, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
| | - Thomas Schrader
- Institute of Organic Chemistry I, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Shirley K Knauer
- Molecular Biology II, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141 Essen, Germany
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5
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Gong X, Zhang Y, Chen J. Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions. Biomolecules 2021; 11:1416. [PMID: 34680048 PMCID: PMC8533332 DOI: 10.3390/biom11101416] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are highly prevalent and play important roles in biology and human diseases. It is now also recognized that many IDPs remain dynamic even in specific complexes and functional assemblies. Computer simulations are essential for deriving a molecular description of the disordered protein ensembles and dynamic interactions for a mechanistic understanding of IDPs in biology, diseases, and therapeutics. Here, we provide an in-depth review of recent advances in the multi-scale simulation of disordered protein states, with a particular emphasis on the development and application of advanced sampling techniques for studying IDPs. These techniques are critical for adequate sampling of the manifold functionally relevant conformational spaces of IDPs. Together with dramatically improved protein force fields, these advanced simulation approaches have achieved substantial success and demonstrated significant promise towards the quantitative and predictive modeling of IDPs and their dynamic interactions. We will also discuss important challenges remaining in the atomistic simulation of larger systems and how various coarse-grained approaches may help to bridge the remaining gaps in the accessible time- and length-scales of IDP simulations.
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Affiliation(s)
- Xiping Gong
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; (X.G.); (Y.Z.)
| | - Yumeng Zhang
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; (X.G.); (Y.Z.)
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; (X.G.); (Y.Z.)
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
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6
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Civera M, Moroni E, Sorrentino L, Vasile F, Sattin S. Chemical and Biophysical Approaches to Allosteric Modulation. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Monica Civera
- Department of Chemistry Università degli Studi di Milano via C. Golgi, 19 20133 Milan Italy
| | - Elisabetta Moroni
- Istituto di Scienze e Tecnologie Chimiche Giulio Natta, SCITEC Via Mario Bianco 9 20131 Milan Italy
| | - Luca Sorrentino
- Department of Chemistry Università degli Studi di Milano via C. Golgi, 19 20133 Milan Italy
| | - Francesca Vasile
- Department of Chemistry Università degli Studi di Milano via C. Golgi, 19 20133 Milan Italy
| | - Sara Sattin
- Department of Chemistry Università degli Studi di Milano via C. Golgi, 19 20133 Milan Italy
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7
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Xie H, Guo C. Albumin Alters the Conformational Ensemble of Amyloid-β by Promiscuous Interactions: Implications for Amyloid Inhibition. Front Mol Biosci 2021; 7:629520. [PMID: 33708792 PMCID: PMC7940760 DOI: 10.3389/fmolb.2020.629520] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 12/30/2020] [Indexed: 12/15/2022] Open
Abstract
Human serum albumin (HSA) is a key endogenous inhibitor of amyloid-β (Αβ) aggregation. In vitro HSA inhibits Aβ fibrillization and targets multiple species along the aggregation pathway including monomers, oligomers, and protofibrils. Amyloid inhibition by HSA has both pathological implications and therapeutic potential, but the underlying molecular mechanism remains elusive. As a first step towards addressing this complex question, we studied the interactions of an Aβ42 monomer with HSA by molecular dynamics simulations. To adequately sample the conformational space, we adapted the replica exchange with solute tempering (REST2) method to selectively heat the Aβ42 peptide in the absence and presence of HSA. Aβ42 binds to multiple sites on HSA with a preference to domain III and adopts various conformations that all differ from the free state. The β-sheet abundances of H14-E22 and A30-M33 regions are significantly reduced by HSA, so are the β-sheet lengths. HSA shifts the conformational ensemble towards more disordered states and alters the β-sheet association patterns. In particular, the frequent association of Q15-V24 and N27-V36 regions into β-hairpin which is critical for aggregation is impeded. HSA primarily interacts with the latter β-region and the N-terminal charged residues. They form promiscuous interactions characterized by salt bridges at the edge of the peptide-protein interface and hydrophobic cores at the center. Consequently, intrapeptide interactions crucial for β-sheet formation are disrupted. Our work builds the bridge between the modification of Aβ conformational ensemble and amyloid inhibition by HSA. It also illustrates the potential of the REST2 method in studying interactions between intrinsically disordered peptides and globular proteins.
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Affiliation(s)
| | - Cong Guo
- Department of Physics and International Centre for Quantum and Molecular Structures, College of Sciences, Shanghai University, Shanghai, China
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8
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Abstract
Zinc is an essential nutrient for the virulence of bacterial pathogens such as Streptococcus pneumoniae. Many Gram-positive bacteria use a two-domain lipoprotein for zinc acquisition, but how this class of metal-recruiting proteins acquire zinc and interact with the uptake machinery has remained poorly defined. Zinc is an essential element in all domains of life. Nonetheless, how prokaryotes achieve selective acquisition of zinc from the extracellular environment remains poorly understood. Here, we elucidate a novel mechanism for zinc-binding in AdcA, a solute-binding protein of Streptococcus pneumoniae. Crystal structure analyses reveal the two-domain organization of the protein and show that only the N-terminal domain (AdcAN) is necessary for zinc import. Zinc binding induces only minor changes in the global protein conformation of AdcA and stabilizes a highly mobile loop within the AdcAN domain. This loop region, which is conserved in zinc-specific solute-binding proteins, facilitates closure of the AdcAN binding site and is crucial for zinc acquisition. Collectively, these findings elucidate the structural and functional basis of selective zinc uptake in prokaryotes.
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9
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Tee WV, Guarnera E, Berezovsky IN. Disorder driven allosteric control of protein activity. Curr Res Struct Biol 2020; 2:191-203. [PMID: 34235479 PMCID: PMC8244471 DOI: 10.1016/j.crstbi.2020.09.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/27/2020] [Accepted: 09/02/2020] [Indexed: 12/23/2022] Open
Abstract
Studies of protein allostery increasingly reveal an involvement of the back and forth order-disorder transitions in this mechanism of protein activity regulation. Here, we investigate the allosteric mechanisms mediated by structural disorder using the structure-based statistical mechanical model of allostery (SBSMMA) that we have previously developed. We show that SBSMMA accounts for the energetics and causality of allosteric communication underlying dimerization of the BirA biotin repressor, activation of the sortase A enzyme, and inhibition of the Rac1 GTPase. Using the SBSMMA, we also show that introducing structural order or disorder in various regions of esterases can originate tunable allosteric modulation of the catalytic triad. On the basis of obtained results, we propose that operating with the order-disorder continuum allows one to establish an allosteric control scale for achieving desired modulation of the protein activity. Back and forth order-disorder transitions can induce allosteric signaling. Allosteric signaling originated by order/disorder follow universal rules. Allosteric control scale facilitates engineering of the protein activity regulation.
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Affiliation(s)
- Wei-Ven Tee
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A∗STAR), 30 Biopolis Street, #07-01, Matrix 138671, Singapore.,Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive 117597, Singapore
| | - Enrico Guarnera
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A∗STAR), 30 Biopolis Street, #07-01, Matrix 138671, Singapore
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A∗STAR), 30 Biopolis Street, #07-01, Matrix 138671, Singapore.,Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive 117597, Singapore
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10
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Wójcik M, Szala K, van Merkerk R, Quax WJ, Boersma YL. Engineering the specificity of Streptococcus pyogenes sortase A by loop grafting. Proteins 2020; 88:1394-1400. [PMID: 32501594 PMCID: PMC7586933 DOI: 10.1002/prot.25958] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/30/2020] [Accepted: 05/27/2020] [Indexed: 11/24/2022]
Abstract
Sortases are a group of enzymes displayed on the cell‐wall of Gram‐positive bacteria. They are responsible for the attachment of virulence factors onto the peptidoglycan in a transpeptidation reaction through recognition of a pentapeptide substrate. Most housekeeping sortases recognize one specific pentapeptide motif; however, Streptococcus pyogenes sortase A (SpSrtA WT) recognizes LPETG, LPETA and LPKLG motifs. Here, we examined SpSrtA's flexible substrate specificity by investigating the role of the β7/β8 loop in determining substrate specificity. We exchanged the β7/β8 loop in SpSrtA with corresponding β7/β8 loops from Staphylococcus aureus (SaSrtA WT) and Bacillus anthracis (BaSrtA WT). While the BaSrtA‐derived variant showed no enzymatic activity toward either LPETG or LPETA substrates, the activity of the SaSrtA‐derived mutant toward the LPETA substrate was completely abolished. Instead, the mutant had an improved activity toward LPETG, the preferred substrate of SaSrtA WT.
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Affiliation(s)
- Magdalena Wójcik
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Kamil Szala
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Ronald van Merkerk
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Ykelien L Boersma
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
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11
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Dokholyan NV. Experimentally-driven protein structure modeling. J Proteomics 2020; 220:103777. [PMID: 32268219 PMCID: PMC7214187 DOI: 10.1016/j.jprot.2020.103777] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/17/2020] [Accepted: 04/02/2020] [Indexed: 11/25/2022]
Abstract
Revolutions in natural and exact sciences started at the dawn of last century have led to the explosion of theoretical, experimental, and computational approaches to determine structures of molecules, complexes, as well as their rich conformational dynamics. Since different experimental methods produce information that is attributed to specific time and length scales, corresponding computational methods have to be tailored to these scales and experiments. These methods can be then combined and integrated in scales, hence producing a fuller picture of molecular structure and motion from the "puzzle pieces" offered by various experiments. Here, we describe a number of computational approaches to utilize experimental data to glance into structure of proteins and understand their dynamics. We will also discuss the limitations and the resolution of the constraints-based modeling approaches. SIGNIFICANCE: Experimentally-driven computational structure modeling and determination is a rapidly evolving alternative to traditional approaches for molecular structure determination. These new hybrid experimental-computational approaches are proving to be a powerful microscope to glance into the structural features of intrinsically or partially disordered proteins, dynamics of molecules and complexes. In this review, we describe various approaches in the field of experimentally-driven computational structure modeling.
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Affiliation(s)
- Nikolay V Dokholyan
- Department of Pharmacology, Penn State University College of Medicine, Hershey, PA 17033, USA; Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA.; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.; Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
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12
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Liu X, Chen J. Residual Structures and Transient Long-Range Interactions of p53 Transactivation Domain: Assessment of Explicit Solvent Protein Force Fields. J Chem Theory Comput 2019; 15:4708-4720. [PMID: 31241933 DOI: 10.1021/acs.jctc.9b00397] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Molecular dynamics simulations using physics-based atomistic force fields have been increasingly used to characterize the heterogeneous structural ensembles of intrinsically disordered proteins (IDPs). To evaluate the accuracy of the latest atomistic explicit-solvent force fields in modeling larger IDPs with nontrivial structural features, we focus on the 61-residue N-terminal transactivation domain (TAD) of tumor suppressor p53, an important protein in cancer biology that has been extensively studied, and abundant experimental data is available for evaluation of simulated ensembles. We performed extensive replica exchange with solute tempering simulations, in excess of 1.0 μs/replica, to generate disordered structural ensembles of p53-TAD using six latest explicit solvent protein force fields. Multiple local and long-range structural properties, including chain dimension, residual secondary structures, and transient long-range contacts, were analyzed and compared against available experimental data. The results show that IDPs such as p53-TAD remain highly challenging for atomistic simulations due to conformational complexity and difficulty in achieving adequate convergence. Structural ensembles of p53-TAD generated using various force fields differ significantly from each other. The a99SB-disp force field demonstrates the best agreement with experimental data at all levels and proves to be suitable for simulating unbound p53-TAD and how its conformational properties may be modulated by phosphorylation and other cellular signals or cancer-associated mutations. Feasibility of such detailed structural characterization is a key step toward establishing the sequence-disordered ensemble-function-disease relationship of p53 and other biologically important IDPs.
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13
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Chang CEA. Tuning Free Energy by Backbone Conformational Entropy: A Strategy from Disordered Proteins. Biophys J 2019; 114:2757-2758. [PMID: 29925011 DOI: 10.1016/j.bpj.2018.05.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 05/12/2018] [Accepted: 05/15/2018] [Indexed: 12/19/2022] Open
Affiliation(s)
- Chia-En A Chang
- Department of Chemistry, University of California, Riverside, Riverside, California.
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14
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Ahuja LG, Taylor SS, Kornev AP. Tuning the "violin" of protein kinases: The role of dynamics-based allostery. IUBMB Life 2019; 71:685-696. [PMID: 31063633 PMCID: PMC6690483 DOI: 10.1002/iub.2057] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 04/12/2019] [Indexed: 12/17/2022]
Abstract
The intricacies of allosteric regulation of protein kinases continue to engage the research community. Allostery, or control from a distance, is seen as a fundamental biomolecular mechanism for proteins. From the traditional methods of conformational selection and induced fit, the field has grown to include the role of protein motions in defining a dynamics-based allosteric approach. Harnessing of these continuous motions in the protein to exert allosteric effects can be defined by a "violin" model that focuses on distributions of protein vibrations as opposed to concerted pathways. According to this model, binding of an allosteric modifier causes global redistribution of dynamics in the protein kinase domain that leads to changes in its catalytic properties. This model is consistent with the "entropy-driven allostery" mechanism proposed by Cooper and Dryden in 1984 and does not require, but does not exclude, any major structural changes. We provide an overview of practical implementation of the violin model and how it stands amidst the other known models of protein allostery. Protein kinases have been described as the biomolecules of interest. © 2019 IUBMB Life, 71(6):685-696, 2019.
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Affiliation(s)
- Lalima G. Ahuja
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Susan S. Taylor
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Alexandr P. Kornev
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
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15
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Giorgino T, Mattioni D, Hassan A, Milani M, Mastrangelo E, Barbiroli A, Verhelle A, Gettemans J, Barzago MM, Diomede L, de Rosa M. Nanobody interaction unveils structure, dynamics and proteotoxicity of the Finnish-type amyloidogenic gelsolin variant. Biochim Biophys Acta Mol Basis Dis 2019; 1865:648-660. [DOI: 10.1016/j.bbadis.2019.01.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/11/2018] [Accepted: 01/04/2019] [Indexed: 02/06/2023]
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16
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Yu M, Chen Y, Wang ZL, Liu Z. Fluctuation correlations as major determinants of structure- and dynamics-driven allosteric effects. Phys Chem Chem Phys 2019; 21:5200-5214. [DOI: 10.1039/c8cp07859a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Both structure- and dynamics-driven allosteric effects are determined by the correlation of distance fluctuations in proteins.
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Affiliation(s)
- Miao Yu
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- China
| | - Yixin Chen
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- China
| | - Zi-Le Wang
- Department of Physics
- Tsinghua University
- Beijing 100084
- China
| | - Zhirong Liu
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- China
- Center for Quantitative Biology
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17
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Wang X, Chen JL, Otting G, Su XC. Conversion of an amide to a high-energy thioester by Staphylococcus aureus sortase A is powered by variable binding affinity for calcium. Sci Rep 2018; 8:16371. [PMID: 30401805 PMCID: PMC6219580 DOI: 10.1038/s41598-018-34752-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/25/2018] [Indexed: 12/21/2022] Open
Abstract
Thioesters are key intermediates in biology, which often are generated from less energy-rich amide precursors. Staphylococcus aureus sortase A (SrtA) is an enzyme widely used in biotechnology for peptide ligation. The reaction proceeds in two steps, where the first step involves the conversion of an amide bond of substrate peptide into a thioester intermediate with the enzyme. Here we show that the free energy required for this step is matched by an about 30-fold increase in binding affinity of a calcium ion at the calcium binding site of SrtA, which is remote from the thioester bond. The magnitude of this allosteric effect highlights the importance of calcium for the activity of SrtA. The increase in calcium binding affinity upon binding of substrate not only achieves catalytic formation of an energy-rich intermediate in the absence of nucleotide triphosphates or any tight non-covalent enzyme-substrate interactions, but is also accompanied by accumulation of the labile thioester intermediate, which makes it directly observable in nuclear magnetic resonance (NMR) spectra.
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Affiliation(s)
- Xiao Wang
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, College of Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin, 300071, China
| | - Jia-Liang Chen
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, College of Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin, 300071, China
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, College of Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin, 300071, China.
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18
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Ca2+ binding induced sequential allosteric activation of sortase A: An example for ion-triggered conformational selection. PLoS One 2018; 13:e0205057. [PMID: 30321208 PMCID: PMC6188747 DOI: 10.1371/journal.pone.0205057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 09/19/2018] [Indexed: 12/11/2022] Open
Abstract
The allosteric activation of the intrinsically disordered enzyme Staphylococcus aureus sortase A is initiated via binding of a Ca2+ ion. Although Ca2+ binding was shown to initiate structural changes inducing disorder-to-order transitions, the details of the allosteric activation mechanism remain elusive. We performed long-term molecular dynamics simulations of sortase A without (3 simulations of 1.6 μs) and with bound Ca2+ (simulations of 1.6 μs, 1.8 μs, and 2.5 μs). Our results show that Ca2+ binding causes not only ordering of the disordered β6/β7 loop of the protein, but also modulates hinge motions in the dynamic β7/β8 loop, which is important for the catalytic activity of the enzyme. Cation binding triggers signal transmission from the Ca2+ binding site to the dynamic β7/β8 loop via the repetitive folding/unfolding of short helical stretches of the disordered β6/β7 loop. These correlated structural rearrangements lead to several distinct conformational states of the binding groove, which show optimal binding features for the sorting signal motif and feature binding energies up to 20 kcal/mol more favorable than observed for the sortase A without Ca2+. The presented results indicate a highly correlated, conformational selection-based activation mechanism of the enzyme triggered by cation binding. They also demonstrate the importance of the dynamics of intrinsically disordered regions for allosteric regulation.
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19
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Hicks A, Zhou HX. Temperature-induced collapse of a disordered peptide observed by three sampling methods in molecular dynamics simulations. J Chem Phys 2018; 149:072313. [PMID: 30134733 DOI: 10.1063/1.5027409] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The conformational ensembles of a disordered peptide, polyglutamine Q15, over a wide temperature range were sampled using multiple replicates of conventional molecular dynamics (cMD) simulations as well as two enhanced sampling methods, temperature replica exchange (TREMD) and replica exchange with solute tempering (REST). The radius of gyration, asphericity, secondary structure, and hydrogen bonding patterns were used for the comparison of the sampling methods. Overall, the three sampling methods generated similar conformational ensembles, with progressive collapse at higher temperatures. Although accumulating the longest simulation time (90 μs), cMD at room temperature missed a small subspace that was sampled by both TREMD and REST. This subspace was high in α-helical content and separated from the main conformational space by an energy barrier. REST used less simulation time than TREMD (36 μs versus 42 μs), and this gap is expected to widen significantly for larger disordered proteins. We conclude that REST is the method of choice for conformational sampling of intrinsically disordered proteins.
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Affiliation(s)
- Alan Hicks
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
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20
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Arefi HH, Yamamoto T. Communication: Self-assembly of a model supramolecular polymer studied by replica exchange with solute tempering. J Chem Phys 2017; 147:211102. [PMID: 29221407 DOI: 10.1063/1.5008275] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Conventional molecular-dynamics (cMD) simulation has a well-known limitation in accessible time and length scales, and thus various enhanced sampling techniques have been proposed to alleviate the problem. In this paper, we explore the utility of replica exchange with solute tempering (REST) (i.e., a variant of Hamiltonian replica exchange methods) to simulate the self-assembly of a supramolecular polymer in explicit solvent and compare the performance with temperature-based replica exchange MD (T-REMD) as well as cMD. As a test system, we consider a relatively simple all-atom model of supramolecular polymerization (namely, benzene-1,3,5-tricarboxamides in methylcyclohexane solvent). Our results show that both REST and T-REMD are able to predict highly ordered polymer structures with helical H-bonding patterns, in contrast to cMD which completely fails to obtain such a structure for the present model. At the same time, we have also experienced some technical challenge (i.e., aggregation-dispersion transition and the resulting bottleneck for replica traversal), which is illustrated numerically. Since the computational cost of REST scales more moderately than T-REMD, we expect that REST will be useful for studying the self-assembly of larger systems in solution with enhanced rearrangement of monomers.
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Affiliation(s)
- Hadi H Arefi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Takeshi Yamamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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21
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Liu X, Jia Z, Chen J. Enhanced Sampling of Intrinsic Structural Heterogeneity of the BH3-Only Protein Binding Interface of Bcl-xL. J Phys Chem B 2017; 121:9160-9168. [PMID: 28903561 DOI: 10.1021/acs.jpcb.7b06768] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Antiapoptotic Bcl-xL plays central roles in regulating programed cell death. Partial unfolding of Bcl-xL has been observed at the interface upon specific binding to the pro-apoptotic BH3-only protein PUMA, which in turn disrupts the interaction of Bcl-xL with tumor suppressor p53 and promotes apoptosis. Previous analysis of existing Bcl-xL structures and atomistic molecular dynamics (MD) simulations have suggested that substantial intrinsic structure heterogeneity exists at the BH3-only protein binding interface of Bcl-xL to facilitate its conformational transitions upon binding. In this study, enhanced sampling is applied to further characterize the interfacial conformations of unbound Bcl-xL in explicit solvent. Extensive replica exchange with solute tempering (REST) simulations, with a total accumulated time of 16 μs, were able to cover much wider conformational spaces for the interfacial region of Bcl-xL. The resulting structural ensembles are much better converged, with local and long-range structural features that are highly consistent with existing NMR data. These simulations further demonstrate that the BH3-only protein binding interface of Bcl-xL is intrinsically disordered and samples many rapidly interconverting conformations. Intriguingly, all previously observed conformers are well represented in the unbound structure ensemble. Such intrinsic structural heterogeneity and flexibility may be critical for Bcl-xL to undergo partial unfolding induced by PUMA binding, and likely provide a robust basis that allows Bcl-xL to respond sensitively to binding of various ligands in cellular signaling and regulation.
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Affiliation(s)
- Xiaorong Liu
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst , Amherst, Massachusetts 01003, United States
| | - Zhiguang Jia
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst , Amherst, Massachusetts 01003, United States
| | - Jianhan Chen
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst , Amherst, Massachusetts 01003, United States
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22
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Li M, Sun T, Jin F, Yu D, Liu Z. Dimension conversion and scaling of disordered protein chains. MOLECULAR BIOSYSTEMS 2017; 12:2932-40. [PMID: 27440558 DOI: 10.1039/c6mb00415f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
To extract protein dimension and energetics information from single-molecule fluorescence resonance energy transfer spectroscopy (smFRET) data, it is essential to establish the relationship between the distributions of the radius of gyration (Rg) and the end-to-end (donor-to-acceptor) distance (Ree). Here, we performed a coarse-grained molecular dynamics simulation to obtain a conformational ensemble of denatured proteins and intrinsically disordered proteins. For any disordered chain with fixed length, there is an excellent linear correlation between the average values of Rg and Ree under various solvent conditions, but the relationship deviates from the prediction of a Gaussian chain. A modified conversion formula was proposed to analyze smFRET data. The formula reduces the discrepancy between the results obtained from FRET and small-angle X-ray scattering (SAXS). The scaling law in a coil-globule transition process was examined where a significant finite-size effect was revealed, i.e., the scaling exponent may exceed the theoretical critical boundary [1/3, 3/5] and the prefactor changes notably during the transition. The Sanchez chain model was also tested and it was shown that the mean-field approximation works well for expanded chains.
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Affiliation(s)
- Maodong Li
- Center for Quantitative Biology, Peking University, Beijing 100871, China.
| | - Tanlin Sun
- Center for Quantitative Biology, Peking University, Beijing 100871, China.
| | - Fan Jin
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Daqi Yu
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhirong Liu
- Center for Quantitative Biology, Peking University, Beijing 100871, China. and College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing 100871, China
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23
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Unidirectional allostery in the regulatory subunit RIα facilitates efficient deactivation of protein kinase A. Proc Natl Acad Sci U S A 2016; 113:E6776-E6785. [PMID: 27791125 DOI: 10.1073/pnas.1610142113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The holoenzyme complex of protein kinase A is in an inactive state; activation involves ordered cAMP binding to two tandem domains of the regulatory subunit and release of the catalytic subunit. Deactivation has been less studied, during which the two cAMPs unbind from the regulatory subunit to allow association of the catalytic subunit to reform the holoenzyme complex. Unbinding of the cAMPs appears ordered as indicated by a large difference in unbinding rates from the two sites, but the cause has remained elusive given the structural similarity of the two tandem domains. Even more intriguingly, NMR data show that allosteric communication between the two domains is unidirectional. Here, we present a mechanism for the unidirectionality, developed from extensive molecular dynamics simulations of the tandem domains in different cAMP-bound forms. Disparate responses to cAMP releases from the two sites (A and B) in conformational flexibility and chemical shift perturbation confirmed unidirectional allosteric communication. Community analysis revealed that the A-site cAMP, by forming across-domain interactions, bridges an essential pathway for interdomain communication. The pathway is impaired when this cAMP is removed but remains intact when only the B-site cAMP is removed. Specifically, removal of the A-site cAMP leads to the separation of the two domains, creating room for binding the catalytic subunit. Moreover, the A-site cAMP, by maintaining interdomain coupling, retards the unbinding of the B-site cAMP and stalls an unproductive pathway of cAMP release. Our work expands the perspective on allostery and implicates functional importance for the directionality of allostery.
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24
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Schueler-Furman O, Wodak SJ. Computational approaches to investigating allostery. Curr Opin Struct Biol 2016; 41:159-171. [PMID: 27607077 DOI: 10.1016/j.sbi.2016.06.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 06/23/2016] [Indexed: 01/01/2023]
Abstract
Allosteric regulation plays a key role in many biological processes, such as signal transduction, transcriptional regulation, and many more. It is rooted in fundamental thermodynamic and dynamic properties of macromolecular systems that are still poorly understood and are moreover modulated by the cellular context. Here we review the computational approaches used in the investigation of allosteric processes in protein systems. We outline how the models of allostery have evolved from their initial formulation in the sixties to the current views, which more fully account for the roles of the thermodynamic and dynamic properties of the system. We then describe the major classes of computational approaches employed to elucidate the mechanisms of allostery, the insights they have provided, as well as their limitations. We complement this analysis by highlighting the role of computational approaches in promising practical applications, such as the engineering of regulatory modules and identifying allosteric binding sites.
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Affiliation(s)
- Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada (IMRIC), Hebrew University, Hadassah Medical School, POB 12272, Jerusalem 91120, Israel
| | - Shoshana J Wodak
- VIB Structural Biology Research Center, VUB, Pleinlaan 2, 1050 Brussels, Belgium.
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25
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Abstract
The functions of many proteins are regulated through allostery, whereby effector binding at a distal site changes the functional activity (e.g., substrate binding affinity or catalytic efficiency) at the active site. Most allosteric studies have focused on thermodynamic properties, in particular, substrate binding affinity. Changes in substrate binding affinity by allosteric effectors have generally been thought to be mediated by conformational transitions of the proteins or, alternatively, by changes in the broadness of the free energy basin of the protein conformational state without shifting the basin minimum position. When effector binding changes the free energy landscape of a protein in conformational space, the change affects not only thermodynamic properties but also dynamic properties, including the amplitudes of motions on different time scales and rates of conformational transitions. Here we assess the roles of conformational dynamics in allosteric regulation. Two cases are highlighted where NMR spectroscopy and molecular dynamics simulation have been used as complementary approaches to identify residues possibly involved in allosteric communication. Perspectives on contentious issues, for example, the relationship between picosecond-nanosecond local and microsecond-millisecond conformational exchange dynamics, are presented.
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Affiliation(s)
- Jingjing Guo
- School of Chemistry and Chemical Engineering, Henan Normal University , Xinxiang, Henan 453007, People's Republic of China
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
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26
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Chen J. Atomistic Glimpse of the Orderly Chaos of One Protein. Biophys J 2015; 109:1511-2. [PMID: 26488639 DOI: 10.1016/j.bpj.2015.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 08/31/2015] [Accepted: 09/01/2015] [Indexed: 10/22/2022] Open
Affiliation(s)
- Jianhan Chen
- Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas.
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