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Mai M, Zazubovich V, Mansbach RA. Identification of Residues Potentially Involved in Optical Shifts in the Water-Soluble Chlorophyll a-Binding Protein through Molecular Dynamics Simulations. J Phys Chem B 2024; 128:1371-1384. [PMID: 38299975 PMCID: PMC10876061 DOI: 10.1021/acs.jpcb.3c06889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/02/2024]
Abstract
Reversible light and thermally induced spectral shifts are universally observed in a wide variety of pigment-protein complexes at temperatures ranging from cryogenic to ambient. In this paper, we employed large-scale molecular dynamics (MD) simulations of a prototypical pigment-protein complex to better understand these shifts at a molecular scale. Although multiple mechanisms have been proposed over the years, no verification of these proposals via MD simulations has thus far been performed; our work represents the first step in this direction. From simulations of the water-soluble chlorophyll-binding protein complex, we determined that rearrangements of long hydrogen bonds were unlikely to be the origin of the multiwell landscape features necessary to explain observed spectral shifts. We also assessed small motions of amino acid residues and identified side chain rotations of some of these residues as likely candidates for the origin of relevant multiwell landscape features. The protein free-energy landscapes associated with side chain rotations feature energy barriers of around 1100-1600 cm-1, in agreement with optical spectroscopy results, with the most promising residue type associated with experimental signatures being serine, which possesses a symmetric triple-well landscape and moment of inertia of a relevant magnitude.
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Affiliation(s)
- Martina Mai
- Department of Physics, Concordia
University, Montréal, Quebec H4B 1R6, Canada
| | - Valter Zazubovich
- Department of Physics, Concordia
University, Montréal, Quebec H4B 1R6, Canada
| | - Rachael A. Mansbach
- Department of Physics, Concordia
University, Montréal, Quebec H4B 1R6, Canada
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2
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Nguyen K, Chakraborty S, Mansbach RA, Korber B, Gnanakaran S. Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. Viruses 2021; 13:927. [PMID: 34067878 PMCID: PMC8156887 DOI: 10.3390/v13050927] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/03/2021] [Accepted: 05/07/2021] [Indexed: 01/01/2023] Open
Abstract
COVID-19 is a highly infectious respiratory disease caused by the novel coronavirus SARS-CoV-2. It has become a global pandemic and its frequent mutations may pose new challenges for vaccine design. During viral infection, the Spike RBD of SARS-CoV-2 binds the human host cell receptor ACE2, enabling the virus to enter the host cell. Both the Spike and ACE2 are densely glycosylated, and it is unclear how distinctive glycan types may modulate the interaction of RBD and ACE2. Detailed understanding of these determinants is key for the development of novel therapeutic strategies. To this end, we perform extensive all-atom simulations of the (i) RBD-ACE2 complex without glycans, (ii) RBD-ACE2 with oligomannose MAN9 glycans in ACE2, and (iii) RBD-ACE2 with complex FA2 glycans in ACE2. These simulations identify the key residues at the RBD-ACE2 interface that form contacts with higher probabilities, thus providing a quantitative evaluation that complements recent structural studies. Notably, we find that this RBD-ACE2 contact signature is not altered by the presence of different glycoforms, suggesting that RBD-ACE2 interaction is robust. Applying our simulated results, we illustrate how the recently prevalent N501Y mutation may alter specific interactions with host ACE2 that facilitate the virus-host binding. Furthermore, our simulations reveal how the glycan on Asn90 of ACE2 can play a distinct role in the binding and unbinding of RBD. Finally, an energetics analysis shows that MAN9 glycans on ACE2 decrease RBD-ACE2 affinity, while FA2 glycans lead to enhanced binding of the complex. Together, our results provide a more comprehensive picture of the detailed interplay between virus and human receptor, which is much needed for the discovery of effective treatments that aim at modulating the physical-chemical properties of this virus.
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Affiliation(s)
- Kien Nguyen
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (K.N.); (S.C.); (B.K.)
| | - Srirupa Chakraborty
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (K.N.); (S.C.); (B.K.)
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (K.N.); (S.C.); (B.K.)
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (K.N.); (S.C.); (B.K.)
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3
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Lindsay RJ, Mansbach RA, Gnanakaran S, Shen T. Effects of pH on an IDP conformational ensemble explored by molecular dynamics simulation. Biophys Chem 2021; 271:106552. [PMID: 33581430 PMCID: PMC8024028 DOI: 10.1016/j.bpc.2021.106552] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 01/03/2023]
Abstract
The conformational ensemble of intrinsically disordered proteins, such as α-synuclein, are responsible for their function and malfunction. Misfolding of α-synuclein can lead to neurodegenerative diseases, and the ability to study their conformations and those of other intrinsically disordered proteins under varying physiological conditions can be crucial to understanding and preventing pathologies. In contrast to well-folded peptides, a consensus feature of IDPs is their low hydropathy and high charge, which makes their conformations sensitive to pH perturbation. We examine a prominent member of this subset of IDPs, α-synuclein, using a divide-and-conquer scheme that provides enhanced sampling of IDP structural ensembles. We constructed conformational ensembles of α-synuclein under neutral (pH ~ 7) and low (pH ~ 3) pH conditions and compared our results with available information obtained from smFRET, SAXS, and NMR studies. Specifically, α-synuclein has been found to in a more compact state at low pH conditions and the structural changes observed are consistent with those from experiments. We also characterize the conformational and dynamic differences between these ensembles and discussed the implication on promoting pathogenic fibril formation. We find that under low pH conditions, neutralization of negatively charged residues leads to compaction of the C-terminal portion of α-synuclein while internal reorganization allows α-synuclein to maintain its overall end-to-end distance. We also observe different levels of intra-protein interaction between three regions of α-synuclein at varying pH and a shift towards more hydrophilic interactions with decreasing pH.
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Affiliation(s)
- Richard J Lindsay
- UT- ORNL Graduate School of Genome Science and Technology, Knoxville, TN, 37996, USA.
| | - Rachael A Mansbach
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, 87544, USA; Department of Physics, Concordia University, Montreal, Quebec, Canada.
| | - S Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, 87544, USA.
| | - Tongye Shen
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.
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4
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Mansbach RA, Chakraborty S, Nguyen K, Montefiori DC, Korber B, Gnanakaran S. The SARS-CoV-2 Spike variant D614G favors an open conformational state. Sci Adv 2021; 7:eabf3671. [PMID: 33863729 PMCID: PMC8051874 DOI: 10.1126/sciadv.abf3671] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 03/03/2021] [Indexed: 05/21/2023]
Abstract
The COVID-19 (coronavirus disease 2019) pandemic underwent a rapid transition with the emergence of a dominant viral variant (from the "D-form" to the "G-form") that carried an amino acid substitution D614G in its "Spike" protein. The G-form is more infectious in vitro and is associated with increased viral loads in the upper airways. To gain insight into the molecular-level underpinnings of these characteristics, we used microsecond all-atom simulations. We show that changes in the protein energetics favor a higher population of infection-capable states in the G-form through release of asymmetry present in the D-form inter-protomer interactions. Thus, the increased infectivity of the G-form is likely due to a higher rate of profitable binding encounters with the host receptor. It is also predicted to be more neutralization sensitive owing to enhanced exposure of the receptor binding domain, a key target region for neutralizing antibodies. These results are critical for vaccine design.
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Affiliation(s)
- Rachael A Mansbach
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Srirupa Chakraborty
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Kien Nguyen
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - David C Montefiori
- Department of Surgery, Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - S Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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5
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Mansbach RA, Chakraborty S, Nguyen K, Montefiori DC, Korber B, Gnanakaran G. The SARS-CoV-2 Spike Variant D614G Favors an Open Conformational State. Biophys J 2021. [PMCID: PMC7879737 DOI: 10.1016/j.bpj.2020.11.1904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Mansbach RA, Chakraborty S, Nguyen K, Montefiori D, Korber B, Gnanakaran S. The SARS-CoV-2 Spike Variant D614G Favors an Open Conformational State. bioRxiv 2020. [PMID: 32743581 DOI: 10.1101/2020.07.26.219741] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The COVID-19 pandemic underwent a rapid transition with the emergence of a SARS-CoV-2 variant that carried the amino acid substitution D614G in the Spike protein that became globally prevalent. The G-form is both more infectious in vitro and associated with increased viral loads in infected people. To gain insight into the mechanism underlying these distinctive characteristics, we employed multiple replicas of microsecond all-atom simulations to probe the molecular-level impact of this substitution on Spike closed and open states. The open state enables Spike interactions with its human cellular receptor, ACE2. Here we show that changes in the inter-protomer energetics due to the D614G substitution favor a higher population of infection-capable (open) states. The inter-protomer interactions between S1 and S2 subunits in the open state of the D-form are asymmetric. This asymmetry is resolved in the G-form due to the release of tensile hydrogen bonds resulting in an increased population of open conformations. Thus, the increased infectivity of the G-form is likely due to a higher rate of profitable binding encounters with the host receptor. It is also predicted to be more neutralization sensitive due to enhanced exposure of the receptor binding domain, a key target region for neutralizing antibodies.
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7
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Mansbach RA, Leus IV, Mehla J, Lopez CA, Walker JK, Rybenkov VV, Hengartner NW, Zgurskaya HI, Gnanakaran S. Machine Learning Algorithm Identifies an Antibiotic Vocabulary for Permeating Gram-Negative Bacteria. J Chem Inf Model 2020; 60:2838-2847. [PMID: 32453589 DOI: 10.1021/acs.jcim.0c00352] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Drug discovery faces a crisis. The industry has used up the "obvious" space in which to find novel drugs for biomedical applications, and productivity is declining. One strategy to combat this is rational approaches to expand the search space without relying on chemical intuition, to avoid rediscovery of similar spaces. In this work, we present proof of concept of an approach to rationally identify a "chemical vocabulary" related to a specific drug activity of interest without employing known rules. We focus on the pressing concern of multidrug resistance in Pseudomonas aeruginosa by searching for submolecules that promote compound entry into this bacterium. By synergizing theory, computation, and experiment, we validate our approach, explain the molecular mechanism behind identified fragments promoting compound entry, and select candidate compounds from an external library that display good permeation ability.
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Affiliation(s)
- Rachael A Mansbach
- Department of Theoretical Biology and Biophysics, Los Alamos National Lab, MS-K710, P.O. Box 1663, Los Alamos, New Mexico 87545-0001, United States
| | - Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, SLSRC, Rm 1000, Norman, Oklahoma 73019-5251, United States
| | - Jitender Mehla
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, SLSRC, Rm 1000, Norman, Oklahoma 73019-5251, United States
| | - Cesar A Lopez
- Department of Theoretical Biology and Biophysics, Los Alamos National Lab, MS-K710, P.O. Box 1663, Los Alamos, New Mexico 87545-0001, United States
| | - John K Walker
- Pharmacology and Physiological Science, School of Medicine, Saint Louis University, Schwitalla Hall, Room M362, St. Louis, Missouri 63104, United States
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, SLSRC, Rm 1000, Norman, Oklahoma 73019-5251, United States
| | - Nicolas W Hengartner
- Department of Theoretical Biology and Biophysics, Los Alamos National Lab, MS-K710, P.O. Box 1663, Los Alamos, New Mexico 87545-0001, United States
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, SLSRC, Rm 1000, Norman, Oklahoma 73019-5251, United States
| | - S Gnanakaran
- Department of Theoretical Biology and Biophysics, Los Alamos National Lab, MS-K710, P.O. Box 1663, Los Alamos, New Mexico 87545-0001, United States
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8
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Mansbach RA, Chakraborty S, Travers T, Gnanakaran S. Graph-Directed Approach for Downselecting Toxins for Experimental Structure Determination. Mar Drugs 2020; 18:E256. [PMID: 32422972 PMCID: PMC7281422 DOI: 10.3390/md18050256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/24/2020] [Accepted: 05/09/2020] [Indexed: 11/29/2022] Open
Abstract
Conotoxins are short, cysteine-rich peptides of great interest as novel therapeutic leads and of great concern as lethal biological agents due to their high affinity and specificity for various receptors involved in neuromuscular transmission. Currently, of the approximately 6000 known conotoxin sequences, only about 3% have associated structural characterization, which leads to a bottleneck in rapid high-throughput screening (HTS) for identification of potential leads or threats. In this work, we combine a graph-based approach with homology modeling to expand the library of conotoxin structures and to identify those conotoxin sequences that are of the greatest value for experimental structural characterization. The latter would allow for the rapid expansion of the known structural space for generating high quality template-based models. Our approach generalizes to other evolutionarily-related, short, cysteine-rich venoms of interest. Overall, we present and validate an approach for venom structure modeling and experimental guidance and employ it to produce a 290%-larger library of approximate conotoxin structures for HTS. We also provide a set of ranked conotoxin sequences for experimental structure determination to further expand this library.
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Affiliation(s)
- Rachael A. Mansbach
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (R.A.M.); (S.C.); (T.T.)
| | - Srirupa Chakraborty
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (R.A.M.); (S.C.); (T.T.)
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Timothy Travers
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (R.A.M.); (S.C.); (T.T.)
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - S. Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (R.A.M.); (S.C.); (T.T.)
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9
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Shmilovich K, Mansbach RA, Sidky H, Dunne OE, Panda SS, Tovar JD, Ferguson AL. Discovery of Self-Assembling π-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation. J Phys Chem B 2020; 124:3873-3891. [PMID: 32180410 DOI: 10.1021/acs.jpcb.0c00708] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Electronically active organic molecules have demonstrated great promise as novel soft materials for energy harvesting and transport. Self-assembled nanoaggregates formed from π-conjugated oligopeptides composed of an aromatic core flanked by oligopeptide wings offer emergent optoelectronic properties within a water-soluble and biocompatible substrate. Nanoaggregate properties can be controlled by tuning core chemistry and peptide composition, but the sequence-structure-function relations remain poorly characterized. In this work, we employ coarse-grained molecular dynamics simulations within an active learning protocol employing deep representational learning and Bayesian optimization to efficiently identify molecules capable of assembling pseudo-1D nanoaggregates with good stacking of the electronically active π-cores. We consider the DXXX-OPV3-XXXD oligopeptide family, where D is an Asp residue and OPV3 is an oligophenylenevinylene oligomer (1,4-distyrylbenzene), to identify the top performing XXX tripeptides within all 203 = 8000 possible sequences. By direct simulation of only 2.3% of this space, we identify molecules predicted to exhibit superior assembly relative to those reported in prior work. Spectral clustering of the top candidates reveals new design rules governing assembly. This work establishes new understanding of DXXX-OPV3-XXXD assembly, identifies promising new candidates for experimental testing, and presents a computational design platform that can be generically extended to other peptide-based and peptide-like systems.
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Affiliation(s)
- Kirill Shmilovich
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Rachael A Mansbach
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Hythem Sidky
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Olivia E Dunne
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Sayak Subhra Panda
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Institute of NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - John D Tovar
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Institute of NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
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Travers T, Kanagy WK, Mansbach RA, Jhamba E, Cleyrat C, Goldstein B, Lidke DS, Wilson BS, Gnanakaran S. Combinatorial diversity of Syk recruitment driven by its multivalent engagement with FcεRIγ. Mol Biol Cell 2019; 30:2331-2347. [PMID: 31216232 PMCID: PMC6743456 DOI: 10.1091/mbc.e18-11-0722] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 05/17/2019] [Accepted: 06/10/2019] [Indexed: 12/14/2022] Open
Abstract
Syk/Zap70 family kinases are essential for signaling via multichain immune-recognition receptors such as tetrameric (αβγ2) FcεRI. Syk activation is generally attributed to cis binding of its tandem SH2 domains to dual phosphotyrosines within FcεRIγ-ITAMs (immunoreceptor tyrosine-based activation motifs). However, the mechanistic details of Syk docking on γ homodimers are unresolved. Here, we estimate that multivalent interactions for WT Syk improve cis-oriented binding by three orders of magnitude. We applied molecular dynamics (MD), hybrid MD/worm-like chain polymer modeling, and live cell imaging to evaluate relative binding and signaling output for all possible cis and trans Syk-FcεRIγ configurations. Syk binding is likely modulated during signaling by autophosphorylation on Y130 in interdomain A, since a Y130E phosphomimetic form of Syk is predicted to lead to reduced helicity of interdomain A and alter Syk's bias for cis binding. Experiments in reconstituted γ-KO cells, whose γ subunits are linked by disulfide bonds, as well as in cells expressing monomeric ITAM or hemITAM γ-chimeras, support model predictions that short distances between γ ITAM pairs are required for trans docking. We propose that the full range of docking configurations improves signaling efficiency by expanding the combinatorial possibilities for Syk recruitment, particularly under conditions of incomplete ITAM phosphorylation.
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Affiliation(s)
- Timothy Travers
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - William K. Kanagy
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
| | - Rachael A. Mansbach
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Elton Jhamba
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
| | - Cedric Cleyrat
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
| | - Byron Goldstein
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Diane S. Lidke
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
| | - Bridget S. Wilson
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
| | - S. Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
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Mansbach RA, Travers T, McMahon BH, Fair JM, Gnanakaran S. Snails In Silico: A Review of Computational Studies on the Conopeptides. Mar Drugs 2019; 17:E145. [PMID: 30832207 PMCID: PMC6471681 DOI: 10.3390/md17030145] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 12/26/2022] Open
Abstract
Marine cone snails are carnivorous gastropods that use peptide toxins called conopeptides both as a defense mechanism and as a means to immobilize and kill their prey. These peptide toxins exhibit a large chemical diversity that enables exquisite specificity and potency for target receptor proteins. This diversity arises in terms of variations both in amino acid sequence and length, and in posttranslational modifications, particularly the formation of multiple disulfide linkages. Most of the functionally characterized conopeptides target ion channels of animal nervous systems, which has led to research on their therapeutic applications. Many facets of the underlying molecular mechanisms responsible for the specificity and virulence of conopeptides, however, remain poorly understood. In this review, we will explore the chemical diversity of conopeptides from a computational perspective. First, we discuss current approaches used for classifying conopeptides. Next, we review different computational strategies that have been applied to understanding and predicting their structure and function, from machine learning techniques for predictive classification to docking studies and molecular dynamics simulations for molecular-level understanding. We then review recent novel computational approaches for rapid high-throughput screening and chemical design of conopeptides for particular applications. We close with an assessment of the state of the field, emphasizing important questions for future lines of inquiry.
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Affiliation(s)
- Rachael A Mansbach
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Timothy Travers
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Benjamin H McMahon
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Jeanne M Fair
- Biosecurity and Public Health Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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Affiliation(s)
- Rachael A. Mansbach
- Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Andrew L. Ferguson
- Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
- Department of Materials Science and Engineering, University of Illinois at Urbana−Champaign, 1304 W Green Street, Urbana, Illinois 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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13
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Song Z, Mansbach RA, He H, Shih KC, Baumgartner R, Zheng N, Ba X, Huang Y, Mani D, Liu Y, Lin Y, Nieh MP, Ferguson AL, Yin L, Cheng J. Modulation of polypeptide conformation through donor-acceptor transformation of side-chain hydrogen bonding ligands. Nat Commun 2017; 8:92. [PMID: 28733648 PMCID: PMC5522480 DOI: 10.1038/s41467-017-00079-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/31/2017] [Indexed: 01/07/2023] Open
Abstract
Synthetic polypeptides have received increasing attention due to their ability to form higher ordered structures similar to proteins. The control over their secondary structures, which enables dynamic conformational changes, is primarily accomplished by tuning the side-chain hydrophobic or ionic interactions. Herein we report a strategy to modulate the conformation of polypeptides utilizing donor-acceptor interactions emanating from side-chain H-bonding ligands. Specifically, 1,2,3-triazole groups, when incorporated onto polypeptide side-chains, serve as both H-bond donors and acceptors at neutral pH and disrupt the α-helical conformation. When protonated, the resulting 1,2,3-triazolium ions lose the ability to act as H-bond acceptors, and the polypeptides regain their α-helical structure. The conformational change of triazole polypeptides in response to the donor-acceptor pattern was conclusively demonstrated using both experimental-based and simulation-based methods. We further showed the utility of this transition by designing smart, cell-penetrating polymers that undergo acid-activated endosomal escape in living cells.Hydrogen bonding plays a major role in determining the tridimensional structure of biopolymers. Here, the authors show that control over a polypeptide conformation can be achieved by altering the donor-acceptor properties of side-chain triazole units via protonation-deprotonation.
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Affiliation(s)
- Ziyuan Song
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Rachael A Mansbach
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Hua He
- Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, 215123, China
| | - Kuo-Chih Shih
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut, 06269, USA
- Department of Agricultural Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Ryan Baumgartner
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Nan Zheng
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Xiaochu Ba
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Yinzhao Huang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Deepak Mani
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Yun Liu
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899, USA
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, 19716, USA
| | - Yao Lin
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut, 06269, USA
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, 06269, USA
| | - Mu-Ping Nieh
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut, 06269, USA
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, Connecticut, 06269, USA
| | - Andrew L Ferguson
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA.
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA.
| | - Lichen Yin
- Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, 215123, China.
| | - Jianjun Cheng
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA.
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Mansbach RA, Ferguson AL. Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides. J Phys Chem B 2017; 121:1684-1706. [DOI: 10.1021/acs.jpcb.6b10165] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Rachael A. Mansbach
- Department
of Physics, University of Illinois at Urbana-Champaign, 1110 W Green Street, Urbana, Illinois 61801, United States
| | - Andrew L. Ferguson
- Department
of Materials Science and Engineering, University of Illinois at Urbana-Champaign, 1304 W Green Street, Urbana, Illinois 61801, United States
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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15
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Abstract
Coarse-grained molecular simulations reveal the influence of pH and flow on the self-assembly of DFAG-OPV3-GAFD optoelectronic peptides.
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Affiliation(s)
| | - Andrew L. Ferguson
- Department of Materials Science and Engineering
- University of Illinois at Urbana-Champaign
- Urbana
- USA
- Department of Chemical and Biomolecular Engineering
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16
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Xiong M, Lee MW, Mansbach RA, Song Z, Bao Y, Peek RM, Yao C, Chen LF, Ferguson AL, Wong GCL, Cheng J. Helical antimicrobial polypeptides with radial amphiphilicity. Proc Natl Acad Sci U S A 2015; 112:13155-60. [PMID: 26460016 PMCID: PMC4629321 DOI: 10.1073/pnas.1507893112] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
α-Helical antimicrobial peptides (AMPs) generally have facially amphiphilic structures that may lead to undesired peptide interactions with blood proteins and self-aggregation due to exposed hydrophobic surfaces. Here we report the design of a class of cationic, helical homo-polypeptide antimicrobials with a hydrophobic internal helical core and a charged exterior shell, possessing unprecedented radial amphiphilicity. The radially amphiphilic structure enables the polypeptide to bind effectively to the negatively charged bacterial surface and exhibit high antimicrobial activity against both gram-positive and gram-negative bacteria. Moreover, the shielding of the hydrophobic core by the charged exterior shell decreases nonspecific interactions with eukaryotic cells, as evidenced by low hemolytic activity, and protects the polypeptide backbone from proteolytic degradation. The radially amphiphilic polypeptides can also be used as effective adjuvants, allowing improved permeation of commercial antibiotics in bacteria and enhanced antimicrobial activity by one to two orders of magnitude. Designing AMPs bearing this unprecedented, unique radially amphiphilic structure represents an alternative direction of AMP development; radially amphiphilic polypeptides may become a general platform for developing AMPs to treat drug-resistant bacteria.
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Affiliation(s)
- Menghua Xiong
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Michelle W Lee
- Department of Bioengineering, Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, CA 90095
| | - Rachael A Mansbach
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Ziyuan Song
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Yan Bao
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Richard M Peek
- Division of Gastroenterology, Department of Medicine and Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Catherine Yao
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Lin-Feng Chen
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Andrew L Ferguson
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Gerard C L Wong
- Department of Bioengineering, Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, CA 90095;
| | - Jianjun Cheng
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801;
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17
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Mansbach RA, Ferguson AL. Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics. J Chem Phys 2015; 142:105101. [DOI: 10.1063/1.4914144] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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