101
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Jia Y, Guo S, Han Q, Zhu J, Zhang X, Na N, Ouyang J. Target-triggered and controlled release plasmon-enhanced fluorescent AIE probe for conformational monitoring of insulin fibrillation. J Mater Chem B 2021; 9:5128-5135. [PMID: 34132315 DOI: 10.1039/d1tb00712b] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this work, we constructed a target-triggered and controlled-release plasmon-enhanced fluorescent AIE probe to realize the purpose of conformational monitoring of insulin fibrillation. We synthesized a novel water-soluble anthracene derivative, 4,4',4'',4'''-(anthracene-9,10-diylbis(ethene-2,1,1-triyl))tetrakis(N,N,N-trimethylbenzenaminium) iodide (BDVAI), with AIE properties, high biocompatibility and good self-assembly effect. Gold nanocages (AuNCs) were selected as the substrate for PEF, and the inner space of hollow AuNCs was filled with BDVAI. Thiol-modified DNA chains were bonded to the surface of AuNCs by Au-S bonds, and an insulin aptamer was combined with the sulfhydryl chain to seal the AuNCs. This PEF-AIE sensor produces different fluorescence signals when interacting with native insulin and fibrillar insulin; thus, monitoring conformational changes in insulin can be realized by detecting fluorescence intensity changes during insulin fibrillation. Based on this design, this system realized sensitive detection of fibrillar insulin with a detection limit of 23.6 pM. This AIE molecular-based PEF fluorescence enhancement system improves the optical properties of fluorescent substances, which is of great significance in improving the detection sensitivity of amyloid fibrils conformational changes and providing a reliable basis for further understanding the pathogenesis of amyloidosis.
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Affiliation(s)
- Yijing Jia
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
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102
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Verkhivker GM. Making the invisible visible: Toward structural characterization of allosteric states, interaction networks, and allosteric regulatory mechanisms in protein kinases. Curr Opin Struct Biol 2021; 71:71-78. [PMID: 34237520 DOI: 10.1016/j.sbi.2021.06.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/27/2021] [Accepted: 06/03/2021] [Indexed: 02/07/2023]
Abstract
Despite the established view of protein kinases as dynamic and versatile allosteric regulatory machines, our knowledge of allosteric functional states, allosteric interaction networks, and the intrinsic folding energy landscapes is surprisingly limited. We discuss the latest developments in structural characterization of allosteric molecular events underlying protein kinase dynamics and functions using structural, biophysical, and computational biology approaches. The recent studies highlighted progress in making the invisible aspects of protein kinase 'life' visible, including the determination of hidden allosteric states and mapping of allosteric energy landscapes, discovery of new mechanisms underlying ligand-induced modulation of allosteric activity, evolutionary adaptation of kinase allostery, and characterization of allosteric interaction networks as the intrinsic driver of kinase adaptability and signal transmission in the regulatory assemblies.
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Affiliation(s)
- Gennady M Verkhivker
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA, 92866, USA; Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, 9401 Jeronimo Road, Irvine, CA, 92618, USA.
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103
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Trozzi F, Wang F, Verkhivker G, Zoltowski BD, Tao P. Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE. PLoS Comput Biol 2021; 17:e1009168. [PMID: 34310591 PMCID: PMC8341706 DOI: 10.1371/journal.pcbi.1009168] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 08/05/2021] [Accepted: 06/10/2021] [Indexed: 11/19/2022] Open
Abstract
In Arabidopsis thaliana, the Light-Oxygen-Voltage (LOV) domain containing protein ZEITLUPE (ZTL) integrates light quality, intensity, and duration into regulation of the circadian clock. Recent structural and biochemical studies of ZTL indicate that the protein diverges from other members of the LOV superfamily in its allosteric mechanism, and that the divergent allosteric mechanism hinges upon conservation of two signaling residues G46 and V48 that alter dynamic motions of a Gln residue implicated in signal transduction in all LOV proteins. Here, we delineate the allosteric mechanism of ZTL via an integrated computational approach that employs atomistic simulations of wild type and allosteric variants of ZTL in the functional dark and light states, together with Markov state and supervised machine learning classification models. This approach has unveiled key factors of the ZTL allosteric mechanisms, and identified specific interactions and residues implicated in functional allosteric changes. The final results reveal atomic level insights into allosteric mechanisms of ZTL function that operate via a non-trivial combination of population-shift and dynamics-driven allosteric pathways.
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Affiliation(s)
- Francesco Trozzi
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, United States of America
| | - Feng Wang
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, United States of America
| | - Gennady Verkhivker
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Chapman University School of Pharmacy, Irvine, California, United States of America
| | - Brian D. Zoltowski
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, United States of America
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, United States of America
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104
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Long C, Dai L, E C, Da LT, Yu J. Allosteric regulation in CRISPR/Cas1-Cas2 protospacer acquisition mediated by DNA and Cas2. Biophys J 2021; 120:3126-3137. [PMID: 34197800 PMCID: PMC8390960 DOI: 10.1016/j.bpj.2021.06.007] [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: 01/06/2021] [Revised: 05/10/2021] [Accepted: 06/04/2021] [Indexed: 11/19/2022] Open
Abstract
Cas1 and Cas2 are highly conserved proteins across clustered-regularly-interspaced-short-palindromic-repeat-Cas systems and play a significant role in protospacer acquisition. Based on crystal structure of twofold symmetric Cas1-Cas2 in complex with dual-forked protospacer DNA (psDNA), we conducted all-atom molecular dynamics simulations to study the psDNA binding, recognition, and response to cleavage on the protospacer-adjacent-motif complementary sequence, or PAMc, of Cas1-Cas2. In the simulation, we noticed that two active sites of Cas1 and Cas1’ bind asymmetrically to two identical PAMc on the psDNA captured from the crystal structure. For the modified psDNA containing only one PAMc, as that to be recognized by Cas1-Cas2 in general, our simulations show that the non-PAMc association site of Cas1-Cas2 remains destabilized until after the stably bound PAMc being cleaved at the corresponding association site. Thus, long-range correlation appears to exist upon the PAMc cleavage between the two active sites (∼10 nm apart) on Cas1-Cas2, which can be allosterically mediated by psDNA and Cas2 and Cas2’ in bridging. To substantiate such findings, we conducted repeated runs and further simulated Cas1-Cas2 in complex with synthesized psDNA sequences psL and psH, which have been measured with low and high frequency in acquisition, respectively. Notably, such intersite correlation becomes even more pronounced for the Cas1-Cas2 in complex with psH but remains low for the Cas1-Cas2 in complex with psL. Hence, our studies demonstrate that PAMc recognition and cleavage at one active site of Cas1-Cas2 may allosterically regulate non-PAMc association or even cleavage at the other site, and such regulation can be mediated by noncatalytic Cas2 and DNA protospacer to possibly support the ensued psDNA acquisition.
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Affiliation(s)
- Chunhong Long
- School of Science, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Liqiang Dai
- Shenzhen JL Computational Science and Applied Research Institute, Shenzhen, China; Beijing Computational Science Research Center, Beijing, China
| | - Chao E
- Beijing Computational Science Research Center, Beijing, China
| | - Lin-Tai Da
- Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, Shanghai, China
| | - Jin Yu
- Departments of Physics and Astronomy and Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California.
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105
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Chatzigoulas A, Cournia Z. Rational design of allosteric modulators: Challenges and successes. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1529] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Alexios Chatzigoulas
- Biomedical Research Foundation Academy of Athens Athens Greece
- Department of Informatics and Telecommunications National and Kapodistrian University of Athens Athens Greece
| | - Zoe Cournia
- Biomedical Research Foundation Academy of Athens Athens Greece
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106
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Lopes TJS, Rios R, Nogueira T, Mello RF. Protein residue network analysis reveals fundamental properties of the human coagulation factor VIII. Sci Rep 2021; 11:12625. [PMID: 34135429 PMCID: PMC8209229 DOI: 10.1038/s41598-021-92201-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/08/2021] [Indexed: 11/09/2022] Open
Abstract
Hemophilia A is an X-linked inherited blood coagulation disorder caused by the production and circulation of defective coagulation factor VIII protein. People living with this condition receive either prophylaxis or on-demand treatment, and approximately 30% of patients develop inhibitor antibodies, a serious complication that limits treatment options. Although previous studies performed targeted mutations to identify important residues of FVIII, a detailed understanding of the role of each amino acid and their neighboring residues is still lacking. Here, we addressed this issue by creating a residue interaction network (RIN) where the nodes are the FVIII residues, and two nodes are connected if their corresponding residues are in close proximity in the FVIII protein structure. We studied the characteristics of all residues in this network and found important properties related to disease severity, interaction to other proteins and structural stability. Importantly, we found that the RIN-derived properties were in close agreement with in vitro and clinical reports, corroborating the observation that the patterns derived from this detailed map of the FVIII protein architecture accurately capture the biological properties of FVIII.
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Affiliation(s)
- Tiago J S Lopes
- Department of Reproductive Biology, Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.
| | - Ricardo Rios
- Department of Computer Science, Federal University of Bahia, Salvador, Brazil.,Institute of Mathematics and Computer Science, University of São Paulo, São Paulo, Brazil
| | - Tatiane Nogueira
- Department of Computer Science, Federal University of Bahia, Salvador, Brazil.,Institute of Mathematics and Computer Science, University of São Paulo, São Paulo, Brazil
| | - Rodrigo F Mello
- Institute of Mathematics and Computer Science, University of São Paulo, São Paulo, Brazil.,Itaú Unibanco, Av. Eng. Armando de Arruda Pereira, 707, Jabaquara, São Paulo, 04309-010, Brazil
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107
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Remington JM, McKay KT, Ferrell JB, Schneebeli ST, Li J. Enhanced sampling protocol to elucidate fusion peptide opening of SARS-CoV-2 spike protein. Biophys J 2021; 120:2848-2858. [PMID: 34087207 PMCID: PMC8169235 DOI: 10.1016/j.bpj.2021.05.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 04/14/2021] [Accepted: 05/05/2021] [Indexed: 12/20/2022] Open
Abstract
Large-scale conformational transitions in the spike protein S2 domain are required during host-cell infection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Although conventional molecular dynamics simulations have been extensively used to study therapeutic targets of SARS-CoV-2, it is still challenging to gain molecular insight into the key conformational changes because of the size of the spike protein and the long timescale required to capture these transitions. In this work, we have developed an efficient simulation protocol that leverages many short simulations, a dynamic selection algorithm, and Markov state models to interrogate the structural changes of the S2 domain. We discovered that the conformational flexibility of the dynamic region upstream of the fusion peptide in S2 is coupled to the proteolytic cleavage state of the spike protein. These results suggest that opening of the fusion peptide likely occurs on a submicrosecond timescale after cleavage at the S2' site. Building on the structural and dynamical information gained to date about S2 domain dynamics, we provide proof of principle that a small molecule bound to a seam neighboring the fusion peptide can slow the opening of the fusion peptide, leading to a new inhibition strategy for experiments to confirm. In aggregate, these results will aid the development of drug cocktails to inhibit infections caused by SARS-CoV-2 and other coronaviruses.
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Affiliation(s)
| | - Kyle T McKay
- Department of Chemistry, University of Vermont, Burlington, Vermont
| | | | | | - Jianing Li
- Department of Chemistry, University of Vermont, Burlington, Vermont.
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108
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Nierzwicki Ł, Arantes PR, Saha A, Palermo G. Establishing the allosteric mechanism in CRISPR-Cas9. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2021; 11:e1503. [PMID: 34322166 PMCID: PMC8315640 DOI: 10.1002/wcms.1503] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 08/26/2020] [Indexed: 12/18/2022]
Abstract
Allostery is a fundamental property of proteins, which regulates biochemical information transfer between spatially distant sites. Here, we report on the critical role of molecular dynamics (MD) simulations in discovering the mechanism of allosteric communication within CRISPR-Cas9, a leading genome editing machinery with enormous promises for medicine and biotechnology. MD revealed how allostery intervenes during at least three steps of the CRISPR-Cas9 function: affecting DNA recognition, mediating the cleavage and interfering with the off-target activity. An allosteric communication that activates concerted DNA cleavages was found to led through the L1/L2 loops, which connect the HNH and RuvC catalytic domains. The identification of these "allosteric transducers" inspired the development of novel variants of the Cas9 protein with improved specificity, opening a new avenue for controlling the CRISPR-Cas9 activity. Discussed studies also highlight the critical role of the recognition lobe in the conformational activation of the catalytic HNH domain. Specifically, the REC3 region was found to modulate the dynamics of HNH by sensing the formation of the RNA:DNA hybrid. The role of REC3 was revealed to be particularly relevant in the presence of DNA mismatches. Indeed, interference of REC3 with the RNA:DNA hybrid containing mismatched pairs at specific positions resulted in locking HNH in an inactive "conformational checkpoint" conformation, thereby hampering off-target cleavages. Overall, MD simulations established the fundamental mechanisms underlying the allosterism of CRISPR-Cas9, aiding engineering strategies to develop new CRISPR-Cas9 variants for improved genome editing.
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Affiliation(s)
- Łukasz Nierzwicki
- Department of Bioengineering, University of California Riverside, Riverside, California
| | - Pablo Ricardo Arantes
- Department of Bioengineering, University of California Riverside, Riverside, California
| | - Aakash Saha
- Department of Bioengineering, University of California Riverside, Riverside, California
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California Riverside, Riverside, California
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109
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Abstract
The spectroscopic response of and structural dynamics around all azido-modified alanine residues (AlaN3) in lysozyme are characterized. It is found that AlaN3 is a positionally sensitive probe for the local dynamics, covering a frequency range of ∼15 cm-1 for the center frequency of the line shape. This is consistent with findings from selective replacements of amino acids in PDZ2, which reported a frequency span of ∼10 cm-1 for replacements of Val, Ala, or Glu by azidohomoalanine. For the frequency fluctuation correlation functions, the long-time decay constants τ2 range from ∼1 to ∼10 ps, which compares with experimentally measured correlation times of 3 ps. Attaching azide to alanine residues can yield dynamics that decays to zero on the few ps time scale (i.e., static component Δ0 ∼ 0 ps-1) or to a remaining, static contribution of ∼0.5 ps-1 (corresponding to 2.5 cm-1), depending on the local environment on the 10 ps time scale. The magnitude of the static component correlates qualitatively with the degree of hydration of the spectroscopic probe. Although attaching azide to alanine residues is found to be structurally minimally invasive with respect to the overall protein structure, analysis of the local hydrophobicity indicates that the hydration around the modification site differs for modified and unmodified alanine residues, respectively.
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Affiliation(s)
- Seyedeh Maryam Salehi
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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110
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Das N, Khan T, Subba N, Sen P. Correlating Bromelain's activity with its structure and active-site dynamics and the medium's physical properties in a hydrated deep eutectic solvent. Phys Chem Chem Phys 2021; 23:9337-9346. [PMID: 33885064 DOI: 10.1039/d1cp00046b] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Deep eutectic solvents (DESs) are emerging as new media of choice for biocatalysis due to their environmentally friendly nature, fine-tunability, and potential biocompatibility. This work deciphers the behaviour of bromelain in a ternary DES composed of acetamide, urea, and sorbitol at mole fractions of 0.5, 0.3, and 0.2, respectively (0.5Ac/0.3Ur/0.2Sor), with various degrees of hydration. Bromelain is an essential industrial proteolytic enzyme, and the chosen DES is non-ionic and liquid at room temperature. This provides us with a unique opportunity to contemplate protein behaviour in a non-ionic DES for the very first time. Our results infer that at a low DES concentration (up to 30% V/V DES), bromelain adopts a more compact structural conformation, whereas at higher DES concentrations, it becomes somewhat elongated. The microsecond conformational fluctuation time around the active site of bromelain gradually increases with increasing DES concentration, especially beyond 30% V/V. Interestingly, bromelain retains most of its enzymatic activity in the DES, and at some concentrations, the activity is even higher compared with its native state. Furthermore, we correlate the activity of bromelain with its structure, its active-site dynamics, and the physical properties of the medium. Our results demonstrate that the compact structural conformation and flexibility of the active site of bromelain favour its proteolytic activity. Similarly, a medium with increased polarity and decreased viscosity is favourable for its activity. The presented physical insights into how enzymatic activity depends on the protein structure and dynamics and the physical properties of the medium might provide useful guidelines for the rational design of DESs as biocatalytic media.
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Affiliation(s)
- Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur - 208 016, UP, India.
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111
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Zhang M, Chen S, Hu J, Ding Q, Li L, Lü S, Long M. Mapping the morphological identifiers of distinct conformations via the protein translocation current in nanopores. NANOSCALE 2021; 13:6053-6065. [PMID: 33683247 DOI: 10.1039/d0nr07413f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Conformational changes of proteins play a vital role in implementing their functions and revealing the underlying mechanisms in various biological processes. It is still challenging to monitor protein conformations with temporal fingerprints of current-resistance pulses in the nanopore technique. Here the low-resolution morphologies of different conformations of a typical integrin, αxβ2, were estimated via relative blockade currents simulated from all-atom molecular dynamics (MD). Distinct conformational states of αxβ2 were directly explained by the volume and shape identifiers. Protein modulation in ionic current was analyzed from the conductivity distribution inside the protein-blocked nanopore. Combining a discrete model with spheroidal approximation, a MD-based approach was developed to theoretically predict the volume and shape of the nanopore for sensing αxβ2. This method was also applicable in specifying morphological identifiers of six other proteins, and the theoretical predictions are in good agreement with the experimental measurements. These results potentiated the validity of this method for the conformational identification of proteins in nanopores.
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Affiliation(s)
- Mingkun Zhang
- Center of Biomechanics and Bioengineering, Key Laboratory of Microgravity (National Microgravity Laboratory), Beijing Key Laboratory of Engineered Construction and Mechanobiology, and CAS Center for Excellence in Complex System Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing, 100190, China.
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112
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Ghosh S, Banerjee-Ghosh K, Levy D, Riven I, Naaman R, Haran G. Substrates Modulate Charge-Reorganization Allosteric Effects in Protein-Protein Association. J Phys Chem Lett 2021; 12:2805-2808. [PMID: 33710900 PMCID: PMC8041378 DOI: 10.1021/acs.jpclett.1c00437] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Protein function may be modulated by an event occurring far away from the functional site, a phenomenon termed allostery. While classically allostery involves conformational changes, we recently observed that charge redistribution within an antibody can also lead to an allosteric effect, modulating the kinetics of binding to target antigen. In the present work, we study the association of a polyhistidine tagged enzyme (phosphoglycerate kinase, PGK) to surface-immobilized anti-His antibodies, finding a significant Charge-Reorganization Allostery (CRA) effect. We further observe that PGK's negatively charged nucleotide substrates modulate CRA substantially, even though they bind far away from the His-tag-antibody interaction interface. In particular, binding of ATP reduces CRA by more than 50%. The results indicate that CRA is affected by the binding of charged molecules to a protein and provide further insight into the significant role that charge redistribution can play in protein function.
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113
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Thompson CJ, Vu VH, Leckband DE, Schwartz DK. Cadherin cis and trans interactions are mutually cooperative. Proc Natl Acad Sci U S A 2021; 118:e2019845118. [PMID: 33658369 PMCID: PMC7958404 DOI: 10.1073/pnas.2019845118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Cadherin transmembrane proteins are responsible for intercellular adhesion in all biological tissues and modulate tissue morphogenesis, cell motility, force transduction, and macromolecular transport. The protein-mediated adhesions consist of adhesive trans interactions and lateral cis interactions. Although theory suggests cooperativity between cis and trans bonds, direct experimental evidence of such cooperativity has not been demonstrated. Here, the use of superresolution microscopy, in conjunction with intermolecular single-molecule Förster resonance energy transfer, demonstrated the mutual cooperativity of cis and trans interactions. Results further demonstrate the consequent assembly of large intermembrane junctions, using a biomimetic lipid bilayer cell adhesion model. Notably, the presence of cis interactions resulted in a nearly 30-fold increase in trans-binding lifetimes between epithelial-cadherin extracellular domains. In turn, the presence of trans interactions increased the lifetime of cis bonds. Importantly, comparison of trans-binding lifetimes of small and large cadherin clusters suggests that this cooperativity is primarily due to allostery. The direct quantitative demonstration of strong mutual cooperativity between cis and trans interactions at intermembrane adhesions provides insights into the long-standing controversy of how weak cis and trans interactions act in concert to create strong macroscopic cell adhesions.
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Affiliation(s)
- Connor J Thompson
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80309
| | - Vinh H Vu
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801
| | - Deborah E Leckband
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801
| | - Daniel K Schwartz
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80309;
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114
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Incorporation of sensing modalities into de novo designed fluorescence-activating proteins. Nat Commun 2021; 12:856. [PMID: 33558528 PMCID: PMC7870846 DOI: 10.1038/s41467-020-18911-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/10/2020] [Indexed: 01/07/2023] Open
Abstract
Through the efforts of many groups, a wide range of fluorescent protein reporters and sensors based on green fluorescent protein and its relatives have been engineered in recent years. Here we explore the incorporation of sensing modalities into de novo designed fluorescence-activating proteins, called mini-fluorescence-activating proteins (mFAPs), that bind and stabilize the fluorescent cis-planar state of the fluorogenic compound DFHBI. We show through further design that the fluorescence intensity and specificity of mFAPs for different chromophores can be tuned, and the fluorescence made sensitive to pH and Ca2+ for real-time fluorescence reporting. Bipartite split mFAPs enable real-time monitoring of protein-protein association and (unlike widely used split GFP reporter systems) are fully reversible, allowing direct readout of association and dissociation events. The relative ease with which sensing modalities can be incorporated and advantages in smaller size and photostability make de novo designed fluorescence-activating proteins attractive candidates for optical sensor engineering.
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115
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Gupta M, Venkatramani R, Ainavarapu SRK. Role of Ligand Binding Site in Modulating the Mechanical Stability of Proteins with β-Grasp Fold. J Phys Chem B 2021; 125:1009-1019. [PMID: 33492970 DOI: 10.1021/acs.jpcb.0c08085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite many studies on ligand-modulated protein mechanics, a comparative analysis of the role of ligand binding site on any specific protein fold is yet to be made. In this study, we explore the role of ligand binding site on the mechanical properties of β-grasp fold proteins, namely, ubiquitin and small ubiquitin related modifier 1 (SUMO1). The terminal segments directly connected through hydrogen bonds constitute the β-clamp geometry (or mechanical clamp), which confers high mechanical resilience to the β-grasp fold. Here, we study ubiquitin complexed with CUE2-1, a ubiquitin-binding domain (UBD) from yeast endonuclease protein Cue2, using a combination of single-molecule force spectroscopy (SMFS) and steered molecular dynamics (SMD) simulations. Our study reveals that CUE2-1 does not alter the mechanical properties of ubiquitin, despite directly interacting with its β-clamp. To explore the role of ligand binding site, we compare the mechanical properties of the ubiquitin/CUE2-1 complex with that of previously studied SUMO1/S12, another β-grasp protein complex, using SMD simulations. Simulations on the SUMO1/S12 complex corroborate previous experimentally observed enhancement in the mechanical stability of SUMO1, even though S12 binds away from the β-clamp. Differences in ligand binding-induced structural impact at the transition state of the two complexes explain the differences in ligand modulated protein mechanics. Contrary to previous reports, our study demonstrates that direct binding of ligands to the mechanical clamp does not necessarily alter the mechanical stability of β-grasp fold proteins. Rather, binding interactions away from the clamp can reinforce protein stability provided by the β-grasp fold. Our study highlights the importance of binding site and binding modes of ligands in modulating the mechanical stability of β-grasp fold proteins.
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Affiliation(s)
- Mona Gupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr Homi Bhabha Road, Colaba, Mumbai 400005, India
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116
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Perras FA, Paterson AL, Kobayashi T. Phase-sensitive γ-encoded recoupling of heteronuclear dipolar interactions and 1H chemical shift anisotropy. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2021; 111:101712. [PMID: 33450713 DOI: 10.1016/j.ssnmr.2020.101712] [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: 11/11/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
γ-encoded recoupling sequences are known to produce strong amplitude modulations that lead to sharp doublets when Fourier transformed. These doublets depend very little on the recoupled tensor asymmetry and thus enable for the straightforward determination of dynamic order parameters. It can, however, be difficult to measure small anisotropies, or small order parameters, using such sequences; the resonances from the doublet may overlap with each other, or with the zero-frequency glitch. This limitation has prevented the widespread use of 1H chemical shift anisotropy (CSA) for the measurement of dynamics, particularly for CH protons which typically have CSAs of only a few ppm when immobile. Here, we introduce a simple modification to the traditional 1H CSA and proton-detected local field pulse sequences that enables the acquisition of a hypercomplex dataset and the removal of the uncorrelated magnetization that results in the zero-frequency glitch. These new sequences then yield a frequency shift in the indirect dimension, rather than a splitting, which is easily identifiable even in cases of weak interactions.
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117
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Verkhivker GM, Di Paola L. Dynamic Network Modeling of Allosteric Interactions and Communication Pathways in the SARS-CoV-2 Spike Trimer Mutants: Differential Modulation of Conformational Landscapes and Signal Transmission via Cascades of Regulatory Switches. J Phys Chem B 2021; 125:850-873. [PMID: 33448856 PMCID: PMC7839160 DOI: 10.1021/acs.jpcb.0c10637] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/08/2021] [Indexed: 12/13/2022]
Abstract
The rapidly growing body of structural and biochemical studies of the SARS-CoV-2 spike glycoprotein has revealed a variety of distinct functional states with radically different arrangements of the receptor-binding domain, highlighting a remarkable function-driven conformational plasticity and adaptability of the spike proteins. In this study, we examined molecular mechanisms underlying conformational and dynamic changes in the SARS-CoV-2 spike mutant trimers through the lens of dynamic analysis of allosteric interaction networks and atomistic modeling of signal transmission. Using an integrated approach that combined coarse-grained molecular simulations, protein stability analysis, and perturbation-based modeling of residue interaction networks, we examined how mutations in the regulatory regions of the SARS-CoV-2 spike protein can differentially affect dynamics and allosteric signaling in distinct functional states. The results of this study revealed key functional regions and regulatory centers that govern collective dynamics, allosteric interactions, and control signal transmission in the SARS-CoV-2 spike proteins. We found that the experimentally confirmed regulatory hotspots that dictate dynamic switching between conformational states of the SARS-CoV-2 spike protein correspond to the key hinge sites and global mediating centers of the allosteric interaction networks. The results of this study provide a novel insight into allosteric regulatory mechanisms of SARS-CoV-2 spike proteins showing that mutations at the key regulatory positions can differentially modulate distribution of states and determine topography of signal communication pathways operating through state-specific cascades of control switch points. This analysis provides a plausible strategy for allosteric probing of the conformational equilibrium and therapeutic intervention by targeting specific hotspots of allosteric interactions and communications in the SARS-CoV-2 spike proteins.
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Affiliation(s)
- Gennady M. Verkhivker
- Keck
Center for Science and Engineering, Schmid College of Science and
Technology, Chapman University, One University Drive, Orange, California 92866, United States
- Department
of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
| | - Luisa Di Paola
- Unit
of Chemical-Physics Fundamentals in Chemical Engineering, Department
of Engineering, Università Campus
Bio-Medico di Roma, via
Álvaro del Portillo 21, 00128 Rome, Italy
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118
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Lim JPL, Braza MKE, Nellas RB. The effect of ligand affinity to the contact dynamics of the ligand binding domain of thyroid hormone receptor - retinoid X receptor. J Mol Graph Model 2021; 104:107829. [PMID: 33450664 DOI: 10.1016/j.jmgm.2020.107829] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/19/2020] [Accepted: 12/21/2020] [Indexed: 11/19/2022]
Abstract
Ligand-based allostery has been gaining attention for its importance in protein regulation and implication in drug design. One of the interesting cases of protein allostery is the thyroid hormone receptor - retinoid x receptor (TR:RXR), which regulates the gene expression of important physiological processes, such as development and metabolism. It is regulated by the TR native ligand triiodothyronine (T3), which displays anticooperative behavior to the RXR ligand 9-cis retinoic acid (9C). In contrast to this anticooperative behavior, 9C has been shown to increase the activity of TR:RXR. Here we probed the influence of the affinity and the interactions of the TR ligand to the allostery of the TR:RXR through contact dynamics and residue networks. The TR ligand analogs were designed to have higher (G2) and lower (N1) binding energies than T3 when docked to the TR:RXR(9C) complex. The aqueous TR(N1/T3/G2):RXR(9C) complexes were subjected to 30 ns all-atom simulations using theNAMD. The program CAMERRA was used to capture the subtle perturbations of TR:RXR by mapping the residue contact dynamics. Various parts of the TR ligands; including the hydrophilic head, the iodine substituents, and the ligand tail; have been probed for their significance in ligand affinity. The results on the T3 and G2 complexes suggest that ligand affinity can be utilized as a predictor for anticooperative systems on which ligand is more likely to dissociate or remain bound. All 3 complexes also display distinct contact networks for cross-dimer signalling and ligand communication. Understanding ligand-based allostery could potentially unveil secrets of ligand-regulated protein dynamics, a foundation for the design of better and more efficient allosteric drugs.
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Affiliation(s)
- James Peter L Lim
- Institute of Chemistry, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | - Mac Kevin E Braza
- Institute of Chemistry, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | - Ricky B Nellas
- Institute of Chemistry, College of Science, University of the Philippines Diliman, Quezon City, Philippines.
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119
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Paterson AL, Liu DJ, Kanbur U, Sadow AD, Perras FA. Observing the three-dimensional dynamics of supported metal complexes. Inorg Chem Front 2021. [DOI: 10.1039/d0qi01241f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dynamics of heterogeneous catalysts are linked to their activity and selectivity but are poorly understood. NMR enables for the determination of high-resolution dynamic structures for such sites and the mapping of accessible conformations.
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120
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Liu Y, Vashisth H. Allosteric Pathways Originating at Cysteine Residues in Regulators of G-Protein Signaling Proteins. Biophys J 2020; 120:517-526. [PMID: 33347886 PMCID: PMC7895990 DOI: 10.1016/j.bpj.2020.12.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/07/2020] [Accepted: 12/14/2020] [Indexed: 12/23/2022] Open
Abstract
Regulators of G-protein signaling (RGS) proteins play a central role in modulating signaling via G-protein coupled receptors (GPCRs). Specifically, RGS proteins bind to activated Gα subunits in G-proteins, accelerate the GTP hydrolysis, and thereby rapidly dampen GPCR signaling. Therefore, covalent molecules targeting conserved cysteine residues among RGS proteins have emerged as potential candidates to inhibit the RGS/Gα protein-protein interaction and enhance GPCR signaling. Although these inhibitors bind to conserved cysteine residues among RGS proteins, we have previously suggested [J. Am. Chem. Soc. 2018;140:3454–3460] that their potencies and specificities are related to differential protein dynamics among RGS proteins. Using data from all-atom molecular dynamics simulations, we reveal these differences in dynamics of RGS proteins by partitioning the protein structural space into a network of communities that allow allosteric signals to propagate along unique pathways originating at inhibitor binding sites and terminating at the RGS/Gα protein-protein interface.
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Affiliation(s)
- Yong Liu
- Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire.
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121
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Bozovic O, Jankovic B, Hamm P. Sensing the allosteric force. Nat Commun 2020; 11:5841. [PMID: 33203849 PMCID: PMC7673989 DOI: 10.1038/s41467-020-19689-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/27/2020] [Indexed: 12/20/2022] Open
Abstract
Allosteric regulation is an innate control in most metabolic and signalling cascades that enables living organisms to adapt to the changing environment by tuning the affinity and regulating the activity of target proteins. For a microscopic understanding of this process, a protein system has been designed in such a way that allosteric communication between the binding and allosteric site can be observed in both directions. To that end, an azobenzene-derived photoswitch has been linked to the α3-helix of the PDZ3 domain, arguably the smallest allosteric protein with a clearly identifiable binding and allosteric site. Photo-induced trans-to-cis isomerisation of the photoswitch increases the binding affinity of a small peptide ligand to the protein up to 120-fold, depending on temperature. At the same time, ligand binding speeds up the thermal cis-to-trans back-isomerisation rate of the photoswitch. Based on the energetics of the four states of the system (cis vs trans and ligand-bound vs free), the concept of an allosteric force is introduced, which can be used to drive chemical reactions.
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Affiliation(s)
- Olga Bozovic
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | | | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland.
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122
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Rogers DM. Protein Conformational States-A First Principles Bayesian Method. ENTROPY 2020; 22:e22111242. [PMID: 33287010 PMCID: PMC7712966 DOI: 10.3390/e22111242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/23/2020] [Accepted: 10/29/2020] [Indexed: 12/19/2022]
Abstract
Automated identification of protein conformational states from simulation of an ensemble of structures is a hard problem because it requires teaching a computer to recognize shapes. We adapt the naïve Bayes classifier from the machine learning community for use on atom-to-atom pairwise contacts. The result is an unsupervised learning algorithm that samples a ‘distribution’ over potential classification schemes. We apply the classifier to a series of test structures and one real protein, showing that it identifies the conformational transition with >95% accuracy in most cases. A nontrivial feature of our adaptation is a new connection to information entropy that allows us to vary the level of structural detail without spoiling the categorization. This is confirmed by comparing results as the number of atoms and time-samples are varied over 1.5 orders of magnitude. Further, the method’s derivation from Bayesian analysis on the set of inter-atomic contacts makes it easy to understand and extend to more complex cases.
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Affiliation(s)
- David M Rogers
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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123
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Giampà M, Sgobba E. Insight to Functional Conformation and Noncovalent Interactions of Protein-Protein Assembly Using MALDI Mass Spectrometry. Molecules 2020; 25:E4979. [PMID: 33126406 PMCID: PMC7662314 DOI: 10.3390/molecules25214979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 11/16/2022] Open
Abstract
Noncovalent interactions are the keys to the structural organization of biomolecule e.g., proteins, glycans, lipids in the process of molecular recognition processes e.g., enzyme-substrate, antigen-antibody. Protein interactions lead to conformational changes, which dictate the functionality of that protein-protein complex. Besides biophysics techniques, noncovalent interaction and conformational dynamics, can be studied via mass spectrometry (MS), which represents a powerful tool, due to its low sample consumption, high sensitivity, and label-free sample. In this review, the focus will be placed on Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) and its role in the analysis of protein-protein noncovalent assemblies exploring the relationship within noncovalent interaction, conformation, and biological function.
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Affiliation(s)
- Marco Giampà
- MR Cancer Group, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Olav Kyrres Gate 9, 7030 Trondheim, Norway
| | - Elvira Sgobba
- Genetics and Plant Physiology, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden;
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124
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Haran G, Mazal H. How fast are the motions of tertiary-structure elements in proteins? J Chem Phys 2020; 153:130902. [PMID: 33032421 DOI: 10.1063/5.0024972] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Protein motions occur on multiple time and distance scales. Large-scale motions of protein tertiary-structure elements, i.e., domains, are particularly intriguing as they are essential for the catalytic activity of many enzymes and for the functional cycles of protein machines and motors. Theoretical estimates suggest that domain motions should be very fast, occurring on the nanosecond or microsecond time scales. Indeed, free-energy barriers for domain motions are likely to involve salt bridges, which can break in microseconds. Experimental methods that can directly probe domain motions on fast time scales have appeared only in recent years. This Perspective discusses briefly some of these techniques, including nuclear magnetic resonance and single-molecule fluorescence spectroscopies. We introduce a few recent studies that demonstrate ultrafast domain motions and discuss their potential roles. Particularly surprising is the observation of tertiary-structure element dynamics that are much faster than the functional cycles in some protein machines. These swift motions can be rationalized on a case-by-case basis. For example, fast domain closure in multi-substrate enzymes may be utilized to optimize relative substrate orientation. Whether a large mismatch in time scales of conformational dynamics vs functional cycles is a general design principle in proteins remains to be determined.
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Affiliation(s)
- Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Hisham Mazal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
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125
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Real-time observation of ligand-induced allosteric transitions in a PDZ domain. Proc Natl Acad Sci U S A 2020; 117:26031-26039. [PMID: 33020277 DOI: 10.1073/pnas.2012999117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
While allostery is of paramount importance for protein regulation, the underlying dynamical process of ligand (un)binding at one site, resulting time evolution of the protein structure, and change of the binding affinity at a remote site are not well understood. Here the ligand-induced conformational transition in a widely studied model system of allostery, the PDZ2 domain, is investigated by transient infrared spectroscopy accompanied by molecular dynamics simulations. To this end, an azobenzene-derived photoswitch is linked to a peptide ligand in a way that its binding affinity to the PDZ2 domain changes upon switching, thus initiating an allosteric transition in the PDZ2 domain protein. The subsequent response of the protein, covering four decades of time, ranging from ∼1 ns to ∼μs, can be rationalized by a remodeling of its rugged free-energy landscape, with very subtle shifts in the populations of a small number of structurally well-defined states. It is proposed that structurally and dynamically driven allostery, often discussed as limiting scenarios of allosteric communication, actually go hand-in-hand, allowing the protein to adapt its free-energy landscape to incoming signals.
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126
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Functional plasticity and evolutionary adaptation of allosteric regulation. Proc Natl Acad Sci U S A 2020; 117:25445-25454. [PMID: 32999067 DOI: 10.1073/pnas.2002613117] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Allostery is a fundamental regulatory mechanism of protein function. Despite notable advances, understanding the molecular determinants of allostery remains an elusive goal. Our current knowledge of allostery is principally shaped by a structure-centric view, which makes it difficult to understand the decentralized character of allostery. We present a function-centric approach using deep mutational scanning to elucidate the molecular basis and underlying functional landscape of allostery. We show that allosteric signaling exhibits a high degree of functional plasticity and redundancy through myriad mutational pathways. Residues critical for allosteric signaling are surprisingly poorly conserved while those required for structural integrity are highly conserved, suggesting evolutionary pressure to preserve fold over function. Our results suggest multiple solutions to the thermodynamic conditions of cooperativity, in contrast to the common view of a finely tuned allosteric residue network maintained under selection.
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127
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Carofiglio F, Trisciuzzi D, Gambacorta N, Leonetti F, Stefanachi A, Nicolotti O. Bcr-Abl Allosteric Inhibitors: Where We Are and Where We Are Going to. Molecules 2020; 25:E4210. [PMID: 32937901 PMCID: PMC7570842 DOI: 10.3390/molecules25184210] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 12/12/2022] Open
Abstract
The fusion oncoprotein Bcr-Abl is an aberrant tyrosine kinase responsible for chronic myeloid leukemia and acute lymphoblastic leukemia. The auto-inhibition regulatory module observed in the progenitor kinase c-Abl is lost in the aberrant Bcr-Abl, because of the lack of the N-myristoylated cap able to bind the myristoyl binding pocket also conserved in the Bcr-Abl kinase domain. A way to overcome the occurrence of resistance phenomena frequently observed for Bcr-Abl orthosteric drugs is the rational design of allosteric ligands approaching the so-called myristoyl binding pocket. The discovery of these allosteric inhibitors although very difficult and extremely challenging, represents a valuable option to minimize drug resistance, mostly due to the occurrence of mutations more frequently affecting orthosteric pockets, and to enhance target selectivity with lower off-target effects. In this perspective, we will elucidate at a molecular level the structural bases behind the Bcr-Abl allosteric control and will show how artificial intelligence can be effective to drive the automated de novo design towards off-patent regions of the chemical space.
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Affiliation(s)
- Francesca Carofiglio
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Daniela Trisciuzzi
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
- Molecular Horizon srl, Via Montelino 32, 06084 Bettona, Italy
| | - Nicola Gambacorta
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Francesco Leonetti
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Angela Stefanachi
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Orazio Nicolotti
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
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128
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Lee CM, Wilderman PR, Park JW, Murphy TJ, Morgan ET. Tyrosine Nitration Contributes to Nitric Oxide-Stimulated Degradation of CYP2B6. Mol Pharmacol 2020; 98:267-279. [PMID: 32817462 PMCID: PMC7469253 DOI: 10.1124/molpharm.120.000020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/25/2020] [Indexed: 12/27/2022] Open
Abstract
Human cytochrome P450 (P450) CYP2B6 undergoes nitric oxide (NO)-dependent proteasomal degradation in response to the NO donor dipropylenetriamine NONOate (DPTA) and biologic NO in HeLa and HuH7 cell lines. CYP2B6 is also downregulated by NO in primary human hepatocytes. We hypothesized that NO or derivative reactive nitrogen species may generate adducts of tyrosine and/or cysteine residues, causing CYP2B6 downregulation, and selected Tyr and Cys residues for mutation based on predicted solvent accessibility. CYP2B6V5-Y317A, -Y380A, and -Y190A mutant proteins expressed in HuH7 cells were less sensitive than wild-type (WT) enzyme to degradation evoked by DPTA, suggesting that these tyrosines are targets for NO-dependent downregulation. The Y317A or Y380A mutants did not show increases in high molecular mass (HMM) species after treatment with DPTA or bortezomib + DPTA, in contrast to the WT enzyme. Carbon monoxide-releasing molecule 2 treatment caused rapid suppression of 2B6 enzyme activity, significant HMM species generation, and ubiquitination of CYP2B6 protein but did not stimulate CYP2B6 degradation. The CYP2B6 inhibitor 4-(4-chlorophenyl)imidazole blocked NO-dependent CYP2B6 degradation, suggesting that NO access to the active site is important. Molecular dynamics simulations predicted that tyrosine nitrations of CYP2B6 would cause significant destabilizing perturbations of secondary structure and remove correlated motions likely required for enzyme function. We propose that cumulative nitrations of Y190, Y317, and Y380 by reactive nitrogen species cause destabilization of CYP2B6, which may act synergistically with heme nitrosylation to target the enzyme for degradation. SIGNIFICANCE STATEMENT: This work provides novel insight into the mechanisms by which nitric oxide, which is produced in hepatocytes in response to inflammation, triggers the ubiquitin-dependent proteasomal degradation of the cytochrome P450 (P450) enzyme CYP2B6. Our data demonstrate that both nitration of specific tyrosine residues and interaction of nitric oxide (NO) with the P450 heme are necessary for NO to trigger ubiquitination and protein degradation.
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Affiliation(s)
- Choon-Myung Lee
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, Georgia (C.-m.L., J.W.P., T.J.M., E.T.M.) and University of Connecticut School of Pharmacy, Storrs, Connecticut (P.R.W.)
| | - P Ross Wilderman
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, Georgia (C.-m.L., J.W.P., T.J.M., E.T.M.) and University of Connecticut School of Pharmacy, Storrs, Connecticut (P.R.W.)
| | - Ji Won Park
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, Georgia (C.-m.L., J.W.P., T.J.M., E.T.M.) and University of Connecticut School of Pharmacy, Storrs, Connecticut (P.R.W.)
| | - Thomas J Murphy
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, Georgia (C.-m.L., J.W.P., T.J.M., E.T.M.) and University of Connecticut School of Pharmacy, Storrs, Connecticut (P.R.W.)
| | - Edward T Morgan
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, Georgia (C.-m.L., J.W.P., T.J.M., E.T.M.) and University of Connecticut School of Pharmacy, Storrs, Connecticut (P.R.W.)
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129
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Osuna S. The challenge of predicting distal active site mutations in computational enzyme design. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1502] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Sílvia Osuna
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química Universitat de Girona Girona Spain
- ICREA Barcelona Spain
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130
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Liu L, Zhou S, Deng Y. The 3-ketoacyl-CoA thiolase: an engineered enzyme for carbon chain elongation of chemical compounds. Appl Microbiol Biotechnol 2020; 104:8117-8129. [PMID: 32830293 DOI: 10.1007/s00253-020-10848-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/09/2020] [Accepted: 08/17/2020] [Indexed: 01/03/2023]
Abstract
Because of their function of catalyzing the rearrangement of the carbon chains, thiolases have attracted increasing attentions over the past decades. The 3-ketoacyl-CoA thiolase (KAT) is a member of the thiolase, which is capable of catalyzing the Claisen condensation reaction between the two acyl-CoAs, thereby achieving carbon chain elongation. In this way, diverse value-added compounds might be synthesized starting from simple small CoA thioesters. However, most KATs are hampered by low stability and poor substrate specificity, which has hindered the development of large-scale biosynthesis. In this review, the common characteristics in the three-dimensional structure of KATs from different sources are summarized. Moreover, structure-guided rational engineering is discussed as a strategy for enhancing the performance of KATs. Finally, we reviewed the metabolic engineering applications of KATs for producing various energy-storage molecules, such as n-butanol, fatty acids, dicarboxylic acids, and polyhydroxyalkanoates. KEY POINTS: • Summarize the structural characteristics and catalyzation mechanisms of KATs. • Review on the rational engineering to enhance the performance of KATs. • Discuss the applications of KATs for producing energy-storage molecules.
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Affiliation(s)
- Lixia Liu
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China. .,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China.
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131
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Dhusia K, Su Z, Wu Y. Understanding the Impacts of Conformational Dynamics on the Regulation of Protein-Protein Association by a Multiscale Simulation Method. J Chem Theory Comput 2020; 16:5323-5333. [PMID: 32667783 PMCID: PMC10829009 DOI: 10.1021/acs.jctc.0c00439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Complexes formed among diverse proteins carry out versatile functions in nearly all physiological processes. Association rates which measure how fast proteins form various complexes are of fundamental importance to characterize their functions. The association rates are not only determined by the energetic features at binding interfaces of a protein complex but also influenced by the intrinsic conformational dynamics of each protein in the complex. Unfortunately, how this conformational effect regulates protein association has never been calibrated on a systematic level. To tackle this problem, we developed a multiscale strategy to incorporate the information on protein conformational variations from Langevin dynamic simulations into a kinetic Monte Carlo algorithm of protein-protein association. By systematically testing this approach against a large-scale benchmark set, we found the association of a protein complex with a relatively rigid structure tends to be reduced by its conformational fluctuations. With specific examples, we further show that higher degrees of structural flexibility in various protein complexes can facilitate the searching and formation of intermolecular interactions and thereby accelerate their associations. In general, the integration of conformational dynamics can improve the correlation between experimentally measured association rates and computationally derived association probabilities. Finally, we analyzed the statistical distributions of different secondary structural types on protein-protein binding interfaces and their preference to the change of association rates. Our study, to the best of our knowledge, is the first computational method that systematically estimates the impacts of protein conformational dynamics on protein-protein association. It throws lights on the molecular mechanisms of how protein-protein recognition is kinetically modulated.
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Affiliation(s)
- Kalyani Dhusia
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
| | - Zhaoqian Su
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461
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132
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Harder-Viddal C, Roshko RM, Stetefeld J. Energy flow and intersubunit signalling in GSAM: A non-equilibrium molecular dynamics study. Comput Struct Biotechnol J 2020; 18:1651-1663. [PMID: 32670505 PMCID: PMC7338781 DOI: 10.1016/j.csbj.2020.06.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 06/14/2020] [Accepted: 06/16/2020] [Indexed: 12/11/2022] Open
Abstract
Non-equilibrium molecular dynamics simulations of vibrational energy flow induced by the imposition of a thermal gradient have been performed on the μ2-dimeric enzyme glutamate-1-semialdehyde aminomutase (GSAM), the key enzyme in the biosynthesis of chlorophyll, in order to identify energy transport pathways and to elucidate their role as potential allosteric communication networks for coordinating functional dynamics, specifically the negative cooperativity observed in the motion of the two active site gating loops. Fully atomistic MD simulations of thermal diffusion were executed with a GROMACS simulation package on a fully solvated GSAM enzyme by heating various active site target ligands (initially, catalytic intermediates and cofactors) to 300K while holding the remainder of the protein and the solvent bath at 10K and monitoring the temperature T(t) of all the enzyme residues as a function of time over a 1ns observation window. Energy is observed to be deposited in a relatively small number of discrete chains of residues most of which contribute to specific structural or biochemical functionality. Thermal linkages between all thermally active chains were established by isolating a specific pair of chains and performing a thermal diffusion simulation on the pair, one held at 300K and the other at 10K, with the rest of the protein frozen in its initial atomic configuration and thus thermally unresponsive. Proceeding in this way, it was possible to map out multiple pathways of vibrational energy flow leading from one of the active sites through a network of contiguous residues, many of which were evolutionarily conserved and linked by hydrogen bonds, into the other active site and ultimately to the other gating loop.
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Affiliation(s)
- C Harder-Viddal
- Department of Chemistry and Physics, Canadian Mennonite University, 500 Shaftesbury Blvd, Winnipeg, Manitoba, Canada
| | - R M Roshko
- Department of Physics and Astronomy, University of Manitoba, 30A Sifton Rd, Winnipeg, Manitoba, Canada
| | - J Stetefeld
- Department of Chemistry, University of Manitoba, 144 Dysart Rd, Winnipeg, Manitoba, Canada.,Center for Oil and Gas Research and Development (COGRAD), Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, Canada.,Department of Human Anatomy and Cell Science, University of Manitoba, Canada
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133
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Verkhivker GM, Agajanian S, Hu G, Tao P. Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning. Front Mol Biosci 2020; 7:136. [PMID: 32733918 PMCID: PMC7363947 DOI: 10.3389/fmolb.2020.00136] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022] Open
Abstract
Allosteric regulation is a common mechanism employed by complex biomolecular systems for regulation of activity and adaptability in the cellular environment, serving as an effective molecular tool for cellular communication. As an intrinsic but elusive property, allostery is a ubiquitous phenomenon where binding or disturbing of a distal site in a protein can functionally control its activity and is considered as the "second secret of life." The fundamental biological importance and complexity of these processes require a multi-faceted platform of synergistically integrated approaches for prediction and characterization of allosteric functional states, atomistic reconstruction of allosteric regulatory mechanisms and discovery of allosteric modulators. The unifying theme and overarching goal of allosteric regulation studies in recent years have been integration between emerging experiment and computational approaches and technologies to advance quantitative characterization of allosteric mechanisms in proteins. Despite significant advances, the quantitative characterization and reliable prediction of functional allosteric states, interactions, and mechanisms continue to present highly challenging problems in the field. In this review, we discuss simulation-based multiscale approaches, experiment-informed Markovian models, and network modeling of allostery and information-theoretical approaches that can describe the thermodynamics and hierarchy allosteric states and the molecular basis of allosteric mechanisms. The wealth of structural and functional information along with diversity and complexity of allosteric mechanisms in therapeutically important protein families have provided a well-suited platform for development of data-driven research strategies. Data-centric integration of chemistry, biology and computer science using artificial intelligence technologies has gained a significant momentum and at the forefront of many cross-disciplinary efforts. We discuss new developments in the machine learning field and the emergence of deep learning and deep reinforcement learning applications in modeling of molecular mechanisms and allosteric proteins. The experiment-guided integrated approaches empowered by recent advances in multiscale modeling, network science, and machine learning can lead to more reliable prediction of allosteric regulatory mechanisms and discovery of allosteric modulators for therapeutically important protein targets.
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Affiliation(s)
- Gennady M. Verkhivker
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA, United States
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, United States
| | - Steve Agajanian
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA, United States
| | - Guang Hu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Peng Tao
- Department of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4), Center for Scientific Computation, Southern Methodist University, Dallas, TX, United States
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134
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Allosteric changes in HDM2 by the ATM phosphomimetic S395D mutation: implications on HDM2 function. Biochem J 2020; 476:3401-3411. [PMID: 31652301 PMCID: PMC6857739 DOI: 10.1042/bcj20190687] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 11/17/2022]
Abstract
Allosteric changes imposed by post-translational modifications regulate and differentiate the functions of proteins with intrinsic disorder regions. HDM2 is a hub protein with a large interactome and with different cellular functions. It is best known for its regulation of the p53 tumour suppressor. Under normal cellular conditions, HDM2 ubiquitinates and degrades p53 by the 26S proteasome but after DNA damage, HDM2 switches from a negative to a positive regulator of p53 by binding to p53 mRNA to promote translation of the p53 mRNA. This change in activity is governed by the ataxia telangiectasia mutated kinase via phosphorylation on serine 395 and is mimicked by the S395D phosphomimetic mutant. Here we have used different approaches to show that this event is accompanied by a specific change in the HDM2 structure that affects the HDM2 interactome, such as the N-termini HDM2–p53 protein–protein interaction. These data will give a better understanding of how HDM2 switches from a negative to a positive regulator of p53 and gain new insights into the control of the HDM2 structure and its interactome under different cellular conditions and help identify interphases as potential targets for new drug developments.
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135
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Das N, Sen P. Shape-Dependent Macromolecular Crowding on the Thermodynamics and Microsecond Conformational Dynamics of Protein Unfolding Revealed at the Single-Molecule Level. J Phys Chem B 2020; 124:5858-5871. [DOI: 10.1021/acs.jpcb.0c03897] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP India
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136
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Zhang M, Jang H, Nussinov R. PI3K inhibitors: review and new strategies. Chem Sci 2020; 11:5855-5865. [PMID: 32953006 PMCID: PMC7472334 DOI: 10.1039/d0sc01676d] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/18/2020] [Indexed: 12/16/2022] Open
Abstract
The search is on for effective specific inhibitors for PI3Kα mutants. PI3Kα, a critical lipid kinase, has two subunits, catalytic and inhibitory. PIK3CA, the gene that encodes the p110α catalytic subunit is a highly mutated protein in cancer. Dysregulation of PI3Kα signalling is commonly associated with tumorigenesis and drug resistance. Despite its vast importance, only recently the FDA approved the first drug (alpelisib by Novartis) for breast cancer. A second (GDC0077), classified as PI3Kα isoform-specific, is undergoing clinical trials. Not surprisingly, these ATP-competitive drugs commonly elicit severe concentration-dependent side effects. Here we briefly review PI3Kα mutations, focus on PI3K drug repertoire and propose new, to-date unexplored PI3Kα therapeutic strategies. These include (1) an allosteric and orthosteric inhibitor combination and (2) taking advantage of allosteric rescue mutations to guide drug discovery.
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Affiliation(s)
- Mingzhen Zhang
- Computational Structural Biology Section , Frederick National Laboratory for Cancer Research , National Cancer Institute at Frederick , Frederick , MD 21702 , USA . ; Tel: +1-301-846-5579
| | - Hyunbum Jang
- Computational Structural Biology Section , Frederick National Laboratory for Cancer Research , National Cancer Institute at Frederick , Frederick , MD 21702 , USA . ; Tel: +1-301-846-5579
| | - Ruth Nussinov
- Computational Structural Biology Section , Frederick National Laboratory for Cancer Research , National Cancer Institute at Frederick , Frederick , MD 21702 , USA . ; Tel: +1-301-846-5579
- Department of Human Molecular Genetics and Biochemistry , Sackler School of Medicine , Tel Aviv University , Tel Aviv 69978 , Israel
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137
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Benabderrahmane M, Bureau R, Voisin-Chiret AS, Sopkova-de Oliveira Santos J. Insights into Mcl-1 Conformational States and Allosteric Inhibition Mechanism from Molecular Dynamics Simulations, Enhanced Sampling, and Pocket Crosstalk Analysis. J Chem Inf Model 2020; 60:3172-3187. [DOI: 10.1021/acs.jcim.0c00315] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mohammed Benabderrahmane
- Normandy Univ, UNICAEN, Centre d’Etude et Recherche sur le Médicament de Normandie (CERMN), 14000 Caen, France
| | - Ronan Bureau
- Normandy Univ, UNICAEN, Centre d’Etude et Recherche sur le Médicament de Normandie (CERMN), 14000 Caen, France
| | - Anne Sophie Voisin-Chiret
- Normandy Univ, UNICAEN, Centre d’Etude et Recherche sur le Médicament de Normandie (CERMN), 14000 Caen, France
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138
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Kruk D, Masiewicz E, Wojciechowski M, Florek-Wojciechowska M, Broche LM, Lurie DJ. Slow dynamics of solid proteins - Nuclear magnetic resonance relaxometry versus dielectric spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 314:106721. [PMID: 32276108 DOI: 10.1016/j.jmr.2020.106721] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 06/11/2023]
Abstract
1H Nuclear Magnetic Resonance (NMR) relaxometry and Dielectric Spectroscopy (DS) have been exploited to investigate the dynamics of solid proteins. The experiments have been carried out in the frequency range of about 10 kHz-40 MHz for NMR relaxometry and 10-2Hz-20 MHz for DS. The data sets have been analyzed in terms of theoretical models allowing for a comparison of the correlation times revealed by NMR relaxometry and DS. The 1H spin-lattice relaxation profiles have been decomposed into relaxation contributions associated with 1H-1H and 1H-14N dipole - dipole interactions. The 1H-1H relaxation contribution has been interpreted in terms of three dynamical processes of time scales of 10-6s, 10-7s and 10-8s. It has turned out that the correlation times do not differ much among proteins and they are only weakly dependent on temperature. The analysis of DS relaxation spectra has also revealed three motional processes characterized by correlation times that considerably depend on temperature in contrast to those obtained from the 1H relaxation. This finding suggest that for solid proteins there is a contribution to the 1H spin-lattice relaxation associated with a kind of motion that is not probed in DS as it does not lead to a reorientation of the electric dipole moment.
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Affiliation(s)
- Danuta Kruk
- Faculty of Mathematics and Computer Science, University of Warmia & Mazury in Olsztyn, Słoneczna 54, 10-710 Olsztyn, Poland.
| | - Elzbieta Masiewicz
- Faculty of Mathematics and Computer Science, University of Warmia & Mazury in Olsztyn, Słoneczna 54, 10-710 Olsztyn, Poland
| | - Milosz Wojciechowski
- Faculty of Mathematics and Computer Science, University of Warmia & Mazury in Olsztyn, Słoneczna 54, 10-710 Olsztyn, Poland
| | | | - Lionel M Broche
- Bio-Medical Physics, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, United Kingdom
| | - David J Lurie
- Bio-Medical Physics, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, United Kingdom
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139
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Amide temperature coefficients in characterizing the allosteric effects of ligand binding on local stability in proteins. Biochem Biophys Res Commun 2020; 524:677-682. [DOI: 10.1016/j.bbrc.2020.01.144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 01/25/2020] [Indexed: 01/23/2023]
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140
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Pu W, Zheng Y, Peng Y. Prolyl Isomerase Pin1 in Human Cancer: Function, Mechanism, and Significance. Front Cell Dev Biol 2020; 8:168. [PMID: 32296699 PMCID: PMC7136398 DOI: 10.3389/fcell.2020.00168] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/29/2020] [Indexed: 02/05/2023] Open
Abstract
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Pin1) is an evolutionally conserved and unique enzyme that specifically catalyzes the cis-trans isomerization of phosphorylated serine/threonine-proline (pSer/Thr-Pro) motif and, subsequently, induces the conformational change of its substrates. Mounting evidence has demonstrated that Pin1 is widely overexpressed and/or overactivated in cancer, exerting a critical influence on tumor initiation and progression via regulation of the biological activity, protein degradation, or nucleus-cytoplasmic distribution of its substrates. Moreover, Pin1 participates in the cancer hallmarks through activating some oncogenes and growth enhancers, or inactivating some tumor suppressors and growth inhibitors, suggesting that Pin1 could be an attractive target for cancer therapy. In this review, we summarize the findings on the dysregulation, mechanisms, and biological functions of Pin1 in cancer cells, and also discuss the significance and potential applications of Pin1 dysregulation in human cancer.
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Affiliation(s)
- Wenchen Pu
- Laboratory of Molecular Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yuanyuan Zheng
- Laboratory of Molecular Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yong Peng
- Laboratory of Molecular Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University Collaborative Innovation Center of Biotherapy, Chengdu, China
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141
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Abriata LA, Dal Peraro M. Will Cryo-Electron Microscopy Shift the Current Paradigm in Protein Structure Prediction? J Chem Inf Model 2020; 60:2443-2447. [PMID: 32134661 DOI: 10.1021/acs.jcim.0c00177] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protein dynamics is undoubtedly a pervasive ingredient in all biological functions. However, structural biology has been strongly driven by a static-centered view of protein architecture. We argue that the recent advances of cryo-electron microscopy (EM) have the potential to more broadly explore the conformational landscapes of protein complexes and therefore will enhance our ability to predict the diverse conformations of tertiary and quaternary protein structures that are functionally relevant in physiological conditions.
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Affiliation(s)
- Luciano A Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland
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142
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Huang Q, Li M, Lai L, Liu Z. Allostery of multidomain proteins with disordered linkers. Curr Opin Struct Biol 2020; 62:175-182. [PMID: 32151887 DOI: 10.1016/j.sbi.2020.01.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/18/2020] [Accepted: 01/31/2020] [Indexed: 02/07/2023]
Abstract
Intrinsically disordered regions are often involved in allosteric regulation of multidomain proteins. They can act as disordered linkers to connect and interact with domains, resulting in rather complex allosteric mechanism and novel protein behavior. Therefore, it is necessary to analyze the diverse functions of disordered linkers in order to better understand allostery and relevant regulation process. Here we summarize recent advances in understanding the function of linkers and the advantages of adopting mutlidomain architecture with disorder linkers. It was shown that linkers between domains enhance the local domain concentration and make the allosteric regulation of weakly interacting partners possible, while linkers with only one tethered end cause an entropy effect to reduce binding affinity and prevent aggregation.
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Affiliation(s)
- Qiaojing Huang
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Maodong Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China; Institute of Systems Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Luhua Lai
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Center for Quantitative Biology, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
| | - Zhirong Liu
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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143
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Bravi B, Ravasio R, Brito C, Wyart M. Direct coupling analysis of epistasis in allosteric materials. PLoS Comput Biol 2020; 16:e1007630. [PMID: 32119660 PMCID: PMC7067494 DOI: 10.1371/journal.pcbi.1007630] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/12/2020] [Accepted: 01/03/2020] [Indexed: 11/22/2022] Open
Abstract
In allosteric proteins, the binding of a ligand modifies function at a distant active site. Such allosteric pathways can be used as target for drug design, generating considerable interest in inferring them from sequence alignment data. Currently, different methods lead to conflicting results, in particular on the existence of long-range evolutionary couplings between distant amino-acids mediating allostery. Here we propose a resolution of this conundrum, by studying epistasis and its inference in models where an allosteric material is evolved in silico to perform a mechanical task. We find in our model the four types of epistasis (Synergistic, Sign, Antagonistic, Saturation), which can be both short or long-range and have a simple mechanical interpretation. We perform a Direct Coupling Analysis (DCA) and find that DCA predicts well the cost of point mutations but is a rather poor generative model. Strikingly, it can predict short-range epistasis but fails to capture long-range epistasis, in consistence with empirical findings. We propose that such failure is generic when function requires subparts to work in concert. We illustrate this idea with a simple model, which suggests that other methods may be better suited to capture long-range effects. Allostery in proteins is the property of highly specific responses to ligand binding at a distant site. To inform protocols of de novo drug design, it is fundamental to understand the impact of mutations on allosteric regulation and whether it can be predicted from evolutionary correlations. In this work we consider allosteric architectures artificially evolved to optimize the cooperativity of binding at allosteric and active site. We first characterize the emergent pattern of epistasis as well as the underlying mechanical phenomena, finding the four types of epistasis (Synergistic, Sign, Antagonistic, Saturation), which can be both short or long-range. The numerical evolution of these allosteric architectures allows us to benchmark Direct Coupling Analysis, a method which relies on co-evolution in sequence data to infer direct evolutionary couplings, in connection to allostery. We show that Direct Coupling Analysis predicts quantitatively point mutation costs but underestimates strong long-range epistasis. We provide an argument, based on a simplified model, illustrating the reasons for this discrepancy. Our analysis suggests neural networks as more promising tool to measure epistasis.
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Affiliation(s)
- Barbara Bravi
- Institute of Physics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- * E-mail: (BB); (MW)
| | - Riccardo Ravasio
- Institute of Physics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Carolina Brito
- Instituto de Fìsica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Matthieu Wyart
- Institute of Physics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- * E-mail: (BB); (MW)
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144
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Qin J, Shen X, Zhang J, Jia D. Allosteric inhibitors of the STAT3 signaling pathway. Eur J Med Chem 2020; 190:112122. [DOI: 10.1016/j.ejmech.2020.112122] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/04/2020] [Accepted: 02/04/2020] [Indexed: 01/13/2023]
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145
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Campitelli P, Modi T, Kumar S, Ozkan SB. The Role of Conformational Dynamics and Allostery in Modulating Protein Evolution. Annu Rev Biophys 2020; 49:267-288. [PMID: 32075411 DOI: 10.1146/annurev-biophys-052118-115517] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Advances in sequencing techniques and statistical methods have made it possible not only to predict sequences of ancestral proteins but also to identify thousands of mutations in the human exome, some of which are disease associated. These developments have motivated numerous theories and raised many questions regarding the fundamental principles behind protein evolution, which have been traditionally investigated horizontally using the tip of the phylogenetic tree through comparative studies of extant proteins within a family. In this article, we review a vertical comparison of the modern and resurrected ancestral proteins. We focus mainly on the dynamical properties responsible for a protein's ability to adapt new functions in response to environmental changes. Using the Dynamic Flexibility Index and the Dynamic Coupling Index to quantify the relative flexibility and dynamic coupling at a site-specific, single-amino-acid level, we provide evidence that the migration of hinges, which are often functionally critical rigid sites, is a mechanism through which proteins can rapidly evolve. Additionally, we show that disease-associated mutations in proteins often result in flexibility changes even at positions distal from mutational sites, particularly in the modulation of active site dynamics.
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Affiliation(s)
- Paul Campitelli
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona 85281, USA; , ,
| | - Tushar Modi
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona 85281, USA; , ,
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania 19122, USA; .,Department of Biology, Temple University, Philadelphia, Pennsylvania 19122, USA.,Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - S Banu Ozkan
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, Arizona 85281, USA; , ,
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146
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Woods KN, Pfeffer J. Conformational perturbation, allosteric modulation of cellular signaling pathways, and disease in P23H rhodopsin. Sci Rep 2020; 10:2657. [PMID: 32060349 PMCID: PMC7021821 DOI: 10.1038/s41598-020-59583-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/30/2020] [Indexed: 02/07/2023] Open
Abstract
In this investigation we use THz spectroscopy and MD simulation to study the functional dynamics and conformational stability of P23H rhodopsin. The P23H mutation of rod opsin is the most common cause of human binding autosomal dominant retinitis pigmentosa (ADRP), but the precise mechanism by which this mutation leads to photoreceptor cell degeneration has not yet been elucidated. Our measurements confirm conformational instability in the global modes of the receptor and an active-state that uncouples the torsional dynamics of the retinal with protein functional modes, indicating inefficient signaling in P23H and a drastically altered mechanism of activation when contrasted with the wild-type receptor. Further, our MD simulations indicate that P23H rhodopsin is not functional as a monomer but rather, due to the instability of the mutant receptor, preferentially adopts a specific homodimerization motif. The preferred homodimer configuration induces structural changes in the receptor tertiary structure that reduces the affinity of the receptor for the retinal and significantly modifies the interactions of the Meta-II signaling state. We conjecture that the formation of the specific dimerization motif of P23H rhodopsin represents a cellular-wide signaling perturbation that is directly tied with the mechanism of P23H disease pathogenesis. Our results also support a direct role for rhodopsin P23H dimerization in photoreceptor rod death.
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Affiliation(s)
- Kristina N Woods
- Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians-Universität, 80538, München, Germany.
| | - Jürgen Pfeffer
- Technical University of Munich, Bavarian School of Public Policy, 80333, München, Germany
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147
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Fogha J, Diharce J, Obled A, Aci-Sèche S, Bonnet P. Computational Analysis of Crystallization Additives for the Identification of New Allosteric Sites. ACS OMEGA 2020; 5:2114-2122. [PMID: 32064372 PMCID: PMC7016913 DOI: 10.1021/acsomega.9b02697] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 11/21/2019] [Indexed: 06/10/2023]
Abstract
Allosteric effect can modulate the biological activity of a protein. Thus, the discovery of new allosteric sites is very attractive for designing new modulators or inhibitors. Here, we propose an innovative way to identify allosteric sites, based on crystallization additives (CA), used to stabilize proteins during the crystallization process. Density and clustering analyses of CA, applied on protein kinase and nuclear receptor families, revealed that CA are not randomly distributed around protein structures, but they tend to aggregate near common sites. All orthosteric and allosteric cavities described in the literature are retrieved from the analysis of CA distribution. In addition, new sites were identified, which could be associated to putative allosteric sites. We proposed an efficient and easy way to use the structural information of CA to identify allosteric sites. This method could assist medicinal chemists for the design of new allosteric compounds targeting cavities of new drug targets.
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148
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Jia F, Schröder HV, Yang LP, von Essen C, Sobottka S, Sarkar B, Rissanen K, Jiang W, Schalley CA. Redox-Responsive Host-Guest Chemistry of a Flexible Cage with Naphthalene Walls. J Am Chem Soc 2020; 142:3306-3310. [PMID: 32013425 DOI: 10.1021/jacs.9b11685] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
"Naphthocage", a naphthalene-based organic cage, reveals very strong binding (up to 1010 M-1) to aromatic (di)cationic guests, i.e., the tetrathiafulvalene mono- and dication and methyl viologen. Intercalation of the guests between two naphthalene walls is mediated by C-H···O, C-H···π, and cation···π interactions. The guests can be switched into and out of the cage by redox processes with high binding selectivity. Oxidation of the flexible cage itself in the absence of a guest leads to a stable radical cation with the oxidized naphthalene intercalated between and stabilized by the other two. Encapsulated guest cations are released from the cavity upon cage oxidation, paving the way to future applications in redox-controlled guest release or novel stimuli-responsive materials.
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Affiliation(s)
- Fei Jia
- Institut für Chemie und Biochemie , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany.,Department of Chemistry and Shenzhen Grubbs Institute , Southern University of Science and Technology , Xueyuan Boulevard 1088 , Shenzhen 518055 , China
| | - Hendrik V Schröder
- Institut für Chemie und Biochemie , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany
| | - Liu-Pan Yang
- Department of Chemistry and Shenzhen Grubbs Institute , Southern University of Science and Technology , Xueyuan Boulevard 1088 , Shenzhen 518055 , China
| | - Carolina von Essen
- Department of Chemistry , University of Jyvaskyla , P.O. Box 35, 40014 Jyväskylä , Finland
| | - Sebastian Sobottka
- Institut für Chemie und Biochemie , Freie Universität Berlin , Fabeckstraße 34/36 , 14195 Berlin , Germany
| | - Biprajit Sarkar
- Institut für Chemie und Biochemie , Freie Universität Berlin , Fabeckstraße 34/36 , 14195 Berlin , Germany
| | - Kari Rissanen
- Department of Chemistry , University of Jyvaskyla , P.O. Box 35, 40014 Jyväskylä , Finland
| | - Wei Jiang
- Department of Chemistry and Shenzhen Grubbs Institute , Southern University of Science and Technology , Xueyuan Boulevard 1088 , Shenzhen 518055 , China
| | - Christoph A Schalley
- Institut für Chemie und Biochemie , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany
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149
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Sheik Amamuddy O, Veldman W, Manyumwa C, Khairallah A, Agajanian S, Oluyemi O, Verkhivker GM, Tastan Bishop Ö. Integrated Computational Approaches and Tools forAllosteric Drug Discovery. Int J Mol Sci 2020; 21:E847. [PMID: 32013012 PMCID: PMC7036869 DOI: 10.3390/ijms21030847] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 12/16/2022] Open
Abstract
Understanding molecular mechanisms underlying the complexity of allosteric regulationin proteins has attracted considerable attention in drug discovery due to the benefits and versatilityof allosteric modulators in providing desirable selectivity against protein targets while minimizingtoxicity and other side effects. The proliferation of novel computational approaches for predictingligand-protein interactions and binding using dynamic and network-centric perspectives has ledto new insights into allosteric mechanisms and facilitated computer-based discovery of allostericdrugs. Although no absolute method of experimental and in silico allosteric drug/site discoveryexists, current methods are still being improved. As such, the critical analysis and integration ofestablished approaches into robust, reproducible, and customizable computational pipelines withexperimental feedback could make allosteric drug discovery more efficient and reliable. In this article,we review computational approaches for allosteric drug discovery and discuss how these tools can beutilized to develop consensus workflows for in silico identification of allosteric sites and modulatorswith some applications to pathogen resistance and precision medicine. The emerging realization thatallosteric modulators can exploit distinct regulatory mechanisms and can provide access to targetedmodulation of protein activities could open opportunities for probing biological processes and insilico design of drug combinations with improved therapeutic indices and a broad range of activities.
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Affiliation(s)
- Olivier Sheik Amamuddy
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Wayde Veldman
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Colleen Manyumwa
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Afrah Khairallah
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Steve Agajanian
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA 92866, USA; (S.A.); (O.O.)
| | - Odeyemi Oluyemi
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA 92866, USA; (S.A.); (O.O.)
| | - Gennady M. Verkhivker
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA 92866, USA; (S.A.); (O.O.)
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
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150
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Narayanan C, Bernard DN, Létourneau M, Gagnon J, Gagné D, Bafna K, Calmettes C, Couture JF, Agarwal PK, Doucet N. Insights into Structural and Dynamical Changes Experienced by Human RNase 6 upon Ligand Binding. Biochemistry 2020; 59:755-765. [PMID: 31909602 DOI: 10.1021/acs.biochem.9b00888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Ribonuclease 6 (RNase 6) is one of eight catalytically active human pancreatic-type RNases that belong to a superfamily of rapidly evolving enzymes. Like some of its human homologues, RNase 6 exhibits host defense properties such as antiviral and antibacterial activities. Recently solved crystal structures of this enzyme in its nucleotide-free form show the conservation of the prototypical kidney-shaped fold preserved among vertebrate RNases, in addition to revealing the presence of a unique secondary active site. In this study, we determine the structural and conformational properties experienced by RNase 6 upon binding to substrate and product analogues. We present the first crystal structures of RNase 6 bound to a nucleotide ligand (adenosine 5'-monophosphate), in addition to RNase 6 bound to phosphate ions. While the enzyme preserves B2 subsite ligand preferences, our results show a lack of typical B2 subsite interactions normally observed in homologous ligand-bound RNases. A comparison of the dynamical properties of RNase 6 in its apo-, substrate-, and product-bound states highlight the unique dynamical properties experienced on time scales ranging from nano- to milliseconds. Overall, our results confirm the specific evolutionary adaptation of RNase 6 relative to its unique catalytic and biological activities.
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Affiliation(s)
- Chitra Narayanan
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , 531 Boulevard des Prairies , Laval , Quebec City H7V 1B7 , Canada
| | - David N Bernard
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , 531 Boulevard des Prairies , Laval , Quebec City H7V 1B7 , Canada
| | - Myriam Létourneau
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , 531 Boulevard des Prairies , Laval , Quebec City H7V 1B7 , Canada
| | - Jacinthe Gagnon
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , 531 Boulevard des Prairies , Laval , Quebec City H7V 1B7 , Canada
| | - Donald Gagné
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , 531 Boulevard des Prairies , Laval , Quebec City H7V 1B7 , Canada
| | - Khushboo Bafna
- Genome Science and Technology , University of Tennesse , Knoxville , Tennessee 37996 , United States
| | - Charles Calmettes
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , 531 Boulevard des Prairies , Laval , Quebec City H7V 1B7 , Canada.,PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications , Université Laval , 1045 Avenue de la Médecine , Quebec , Quebec G1V 0A6 , Canada
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology , University of Ottawa , 451 Smyth Road , Ottawa , Ontario K1H 8M5 , Canada
| | - Pratul K Agarwal
- Department of Biochemistry, Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie , Institut National de la Recherche Scientifique (INRS), Université du Québec , 531 Boulevard des Prairies , Laval , Quebec City H7V 1B7 , Canada.,PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications , Université Laval , 1045 Avenue de la Médecine , Quebec , Quebec G1V 0A6 , Canada
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