1
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Joshi O, Skóra T, Yarema A, Rabbitt RD, Bidone TC. Contributions of the individual domains of α IIbβ 3 integrin to its extension: Insights from multiscale modeling. Cytoskeleton (Hoboken) 2024. [PMID: 38682753 DOI: 10.1002/cm.21865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 05/01/2024]
Abstract
The platelet integrin αIIbβ3 undergoes long-range conformational transitions between bent and extended conformations to regulate platelet aggregation during hemostasis and thrombosis. However, how exactly αIIbβ3 transitions between conformations remains largely elusive. Here, we studied how transitions across bent and extended-closed conformations of αIIbβ3 integrin are regulated by effective interactions between its functional domains. We first carried out μs-long equilibrium molecular dynamics (MD) simulations of full-length αIIbβ3 integrins in bent and intermediate conformations, the latter characterized by an extended headpiece and closed legs. Then, we built heterogeneous elastic network models, perturbed inter-domain interactions, and evaluated their relative contributions to the energy barriers between conformations. Results showed that integrin extension emerges from: (i) changes in interfaces between functional domains; (ii) allosteric coupling of the head and upper leg domains with flexible lower leg domains. Collectively, these results provide new insights into integrin conformational activation based on short- and long-range interactions between its functional domains and highlight the importance of the lower legs in the regulation of integrin allostery.
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Affiliation(s)
- Onkar Joshi
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah, USA
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah, USA
| | - Tomasz Skóra
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah, USA
| | - Anna Yarema
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah, USA
| | - Richard D Rabbitt
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah, USA
| | - Tamara C Bidone
- Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah, USA
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah, USA
- Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, Utah, USA
- Department of Biochemistry, University of Utah, Salt Lake City, Utah, USA
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2
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Huang Y, Huang C, Chen J, Chen S, Li B, Li J, Jin Z, Zhang Q, Pan P, Du W, Liu L, Liu Z. Inhibition of SARS-CoV-2 replication by a ssDNA aptamer targeting the nucleocapsid protein. Microbiol Spectr 2024; 12:e0341023. [PMID: 38376366 PMCID: PMC10986557 DOI: 10.1128/spectrum.03410-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/01/2024] [Indexed: 02/21/2024] Open
Abstract
The nucleocapsid protein of SARS-CoV-2 plays significant roles in viral assembly, immune evasion, and viral stability. Due to its immunogenicity, high expression levels during COVID-19, and conservation across viral strains, it represents an attractive target for antiviral treatment. In this study, we identified and characterized a single-stranded DNA aptamer, N-Apt17, which effectively disrupts the liquid-liquid phase separation (LLPS) mediated by the N protein. To enhance the aptamer's stability, a circular bivalent form, cb-N-Apt17, was designed and evaluated. Our findings demonstrated that cb-N-Apt17 exhibited improved stability, enhanced binding affinity, and superior inhibition of N protein LLPS; thus, it has the potential inhibition ability on viral replication. These results provide valuable evidence supporting the potential of cb-N-Apt17 as a promising candidate for the development of antiviral therapies against COVID-19.IMPORTANCEVariants of SARS-CoV-2 pose a significant challenge to currently available COVID-19 vaccines and therapies due to the rapid epitope changes observed in the viral spike protein. However, the nucleocapsid (N) protein of SARS-CoV-2, a highly conserved structural protein, offers promising potential as a target for inhibiting viral replication. The N protein forms complexes with genomic RNA, interacts with other viral structural proteins during virion assembly, and plays a critical role in evading host innate immunity by impairing interferon production during viral infection. In this investigation, we discovered a single-stranded DNA aptamer, designated as N-Apt17, exhibiting remarkable affinity and specificity for the N protein. Notably, N-Apt17 disrupts the liquid-liquid phase separation (LLPS) of the N protein. To enhance the stability and molecular recognition capabilities of N-Apt17, we designed a circular bivalent DNA aptamer termed cb-N-Apt17. In both in vivo and in vitro experiments, cb-N-Apt17 exhibited increased stability, enhanced binding affinity, and superior LLPS disrupting ability. Thus, our study provides essential proof-of-principle evidence supporting the further development of cb-N-Apt17 as a therapeutic candidate for COVID-19.
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Affiliation(s)
- Yanping Huang
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Virology Key Laboratory of Shiyan City, Shiyan, China
| | - Congcong Huang
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Virology Key Laboratory of Shiyan City, Shiyan, China
| | - Junkai Chen
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Virology Key Laboratory of Shiyan City, Shiyan, China
| | - Siwei Chen
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Virology Key Laboratory of Shiyan City, Shiyan, China
| | - Bei Li
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Virology Key Laboratory of Shiyan City, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Jian Li
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Virology Key Laboratory of Shiyan City, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Zhixiong Jin
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Virology Key Laboratory of Shiyan City, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Qiwei Zhang
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Pan Pan
- The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Weixing Du
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Long Liu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Virology Key Laboratory of Shiyan City, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Zhixin Liu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Institute of Virology, Virology Key Laboratory of Shiyan City, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
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3
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de Carvalho RSA, Rasel SI, Khandelwal NK, Tomasiak TM. Cryo-EM structure of the tetra-phosphorylated R-domain in Ycf1 reveals key interactions for transport regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583773. [PMID: 38496555 PMCID: PMC10942426 DOI: 10.1101/2024.03.06.583773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Many ATP-binding cassette (ABC) transporters are regulated by phosphorylation on long and disordered loops which present a challenge to visualize with structural methods. We have trapped an activated state of the regulatory domain (R-domain) of Yeast Cadmium Factor 1 (Ycf1) by enzymatically enriching the phosphorylated state. A 3.2 Å cryo-EM structure reveals an R-domain structure with four phosphorylated residues and a position for the entire R-domain. The structure reveals key R-domain interactions including a bridging interaction between NBD1 and NBD2 as well as an interaction with the R-insertion, another regulatory region. We systematically probe these interactions with a linker substitution strategy along the R-domain and find a close match with these interactions and survival under Ycf1-dependent growth conditions. We propose a model where four overlapping phosphorylation sites bridge several regions of Ycf1 to engage in a transport-competent state.
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Affiliation(s)
| | - Shamiul I Rasel
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
| | - Nitesh K Khandelwal
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
- Current Address: Department of Biochemistry and Biophysics, University of California - San Francisco, San Francisco, CA 94
| | - Thomas M Tomasiak
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721
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4
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McCullagh M, Zeczycki TN, Kariyawasam CS, Durie CL, Halkidis K, Fitzkee NC, Holt JM, Fenton AW. What is allosteric regulation? Exploring the exceptions that prove the rule! J Biol Chem 2024; 300:105672. [PMID: 38272229 PMCID: PMC10897898 DOI: 10.1016/j.jbc.2024.105672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
"Allosteric" was first introduced to mean the other site (i.e., a site distinct from the active or orthosteric site), an adjective for "regulation" to imply a regulatory outcome resulting from ligand binding at another site. That original idea outlines a system with two ligand-binding events at two distinct locations on a macromolecule (originally a protein system), which defines a four-state energy cycle. An allosteric energy cycle provides a quantifiable allosteric coupling constant and focuses our attention on the unique properties of the four equilibrated protein complexes that constitute the energy cycle. Because many observed phenomena have been referenced as "allosteric regulation" in the literature, the goal of this work is to use literature examples to explore which systems are and are not consistent with the two-ligand thermodynamic energy cycle-based definition of allosteric regulation. We emphasize the need for consistent language so comparisons can be made among the ever-increasing number of allosteric systems. Building on the mutually exclusive natures of an energy cycle definition of allosteric regulation versus classic two-state models, we conclude our discussion by outlining how the often-proposed Rube-Goldberg-like mechanisms are likely inconsistent with an energy cycle definition of allosteric regulation.
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Affiliation(s)
- Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Tonya N Zeczycki
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, USA
| | - Chathuri S Kariyawasam
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
| | - Clarissa L Durie
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Konstantine Halkidis
- Department of Hematologic Malignancies and Cellular Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas, USA; Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
| | - Jo M Holt
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Aron W Fenton
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA.
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5
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Lin X, Haller PR, Bavi N, Faruk N, Perozo E, Sosnick TR. Folding of prestin's anion-binding site and the mechanism of outer hair cell electromotility. eLife 2023; 12:RP89635. [PMID: 38054956 PMCID: PMC10699807 DOI: 10.7554/elife.89635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023] Open
Abstract
Prestin responds to transmembrane voltage fluctuations by changing its cross-sectional area, a process underlying the electromotility of outer hair cells and cochlear amplification. Prestin belongs to the SLC26 family of anion transporters yet is the only member capable of displaying electromotility. Prestin's voltage-dependent conformational changes are driven by the putative displacement of residue R399 and a set of sparse charged residues within the transmembrane domain, following the binding of a Cl- anion at a conserved binding site formed by the amino termini of the TM3 and TM10 helices. However, a major conundrum arises as to how an anion that binds in proximity to a positive charge (R399), can promote the voltage sensitivity of prestin. Using hydrogen-deuterium exchange mass spectrometry, we find that prestin displays an unstable anion-binding site, where folding of the amino termini of TM3 and TM10 is coupled to Cl- binding. This event shortens the TM3-TM10 electrostatic gap, thereby connecting the two helices, resulting in reduced cross-sectional area. These folding events upon anion binding are absent in SLC26A9, a non-electromotile transporter closely related to prestin. Dynamics of prestin embedded in a lipid bilayer closely match that in detergent micelle, except for a destabilized lipid-facing helix TM6 that is critical to prestin's mechanical expansion. We observe helix fraying at prestin's anion-binding site but cooperative unfolding of multiple lipid-facing helices, features that may promote prestin's fast electromechanical rearrangements. These results highlight a novel role of the folding equilibrium of the anion-binding site, and help define prestin's unique voltage-sensing mechanism and electromotility.
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Affiliation(s)
- Xiaoxuan Lin
- Center for Mechanical Excitability, The University of ChicagoChicagoUnited States
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
| | - Patrick R Haller
- Center for Mechanical Excitability, The University of ChicagoChicagoUnited States
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
| | - Navid Bavi
- Center for Mechanical Excitability, The University of ChicagoChicagoUnited States
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
| | - Nabil Faruk
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
| | - Eduardo Perozo
- Center for Mechanical Excitability, The University of ChicagoChicagoUnited States
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
- Institute for Neuroscience, The University of ChicagoChicagoUnited States
- Institute for Biophysical Dynamics, The University of ChicagoChicagoUnited States
| | - Tobin R Sosnick
- Center for Mechanical Excitability, The University of ChicagoChicagoUnited States
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
- Institute for Biophysical Dynamics, The University of ChicagoChicagoUnited States
- Prizker School for Molecular Engineering, The University of ChicagoChicagoUnited States
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6
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Rak A, Isakova-Sivak I, Rudenko L. Overview of Nucleocapsid-Targeting Vaccines against COVID-19. Vaccines (Basel) 2023; 11:1810. [PMID: 38140214 PMCID: PMC10747980 DOI: 10.3390/vaccines11121810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
The new SARS-CoV-2 coronavirus, which emerged in late 2019, is a highly variable causative agent of COVID-19, a contagious respiratory disease with potentially severe complications. Vaccination is considered the most effective measure to prevent the spread and complications of this infection. Spike (S) protein-based vaccines were very successful in preventing COVID-19 caused by the ancestral SARS-CoV-2 strain; however, their efficacy was significantly reduced when coronavirus variants antigenically different from the original strain emerged in circulation. This is due to the high variability of this major viral antigen caused by escape from the immunity caused by the infection or vaccination with spike-targeting vaccines. The nucleocapsid protein (N) is a much more conserved SARS-CoV-2 antigen than the spike protein and has therefore attracted the attention of scientists as a promising target for broad-spectrum vaccine development. Here, we summarized the current data on various N-based COVID-19 vaccines that have been tested in animal challenge models or clinical trials. Despite the high conservatism of the N protein, escape mutations gradually occurring in the N sequence can affect its protective properties. During the three years of the pandemic, at least 12 mutations have arisen in the N sequence, affecting more than 40 known immunogenic T-cell epitopes, so the antigenicity of the N protein of recent SARS-CoV-2 variants may be altered. This fact should be taken into account as a limitation in the development of cross-reactive vaccines based on N-protein.
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Affiliation(s)
- Alexandra Rak
- Department of Virology, Institute of Experimental Medicine, St. Petersburg 197022, Russia; (I.I.-S.); (L.R.)
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7
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Breen ME, Joy ST, Baruti OJ, Beyersdorf MS, Henley MJ, De Salle SN, Ycas PD, Croskey A, Cierpicki T, Pomerantz WCK, Mapp AK. Garcinolic Acid Distinguishes Between GACKIX Domains and Modulates Interaction Networks. Chembiochem 2023; 24:e202300439. [PMID: 37525583 PMCID: PMC10870240 DOI: 10.1002/cbic.202300439] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/02/2023]
Abstract
Natural products are often uniquely suited to modulate protein-protein interactions (PPIs) due to their architectural and functional group complexity relative to synthetic molecules. Here we demonstrate that the natural product garcinolic acid allosterically blocks the CBP/p300 KIX PPI network and displays excellent selectivity over related GACKIX motifs. It does so via a strong interaction (KD 1 μM) with a non-canonical binding site containing a structurally dynamic loop in CBP/p300 KIX. Garcinolic acid engages full-length CBP in the context of the proteome and in doing so effectively inhibits KIX-dependent transcription in a leukemia model. As the most potent small-molecule KIX inhibitor yet reported, garcinolic acid represents an important step forward in the therapeutic targeting of CBP/p300.
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Affiliation(s)
- Meghan E Breen
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI-48109, USA
| | - Stephen T Joy
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI-48109, USA
| | - Omari J Baruti
- Program in Chemical Biology, Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI-48109, USA
| | - Matthew S Beyersdorf
- Program in Chemical Biology, Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI-48109, USA
| | - Madeleine J Henley
- Program in Chemical Biology, Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI-48109, USA
| | - Samantha N De Salle
- Program in Chemical Biology, Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI-48109, USA
| | - Peter D Ycas
- Department of Chemistry, University of Minnesota, 207 Pleasant St SE, Minneapolis, MN-55455, USA
| | - Ayza Croskey
- Program in Chemical Biology, Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI-48109, USA
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI-48109, USA
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant St SE, Minneapolis, MN-55455, USA
| | - Anna K Mapp
- Department of Chemistry and Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI-48109, USA
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8
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Posey AE, Ross KA, Bagheri M, Lanum EN, Khan MA, Jennings CE, Harwig MC, Kennedy NW, Hilser VJ, Harden JL, Hill RB. The variable domain from dynamin-related protein 1 promotes liquid-liquid phase separation that enhances its interaction with cardiolipin-containing membranes. Protein Sci 2023; 32:e4787. [PMID: 37743569 PMCID: PMC10578129 DOI: 10.1002/pro.4787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/26/2023]
Abstract
Dynamins are an essential superfamily of mechanoenzymes that remodel membranes and often contain a "variable domain" important for regulation. For the mitochondrial fission dynamin, dynamin-related protein 1, a regulatory role for the variable domain (VD) is demonstrated by gain- and loss-of-function mutations, yet the basis for this is unclear. Here, the isolated VD is shown to be intrinsically disordered and undergo a cooperative transition in the stabilizing osmolyte trimethylamine N-oxide. However, the osmolyte-induced state is not folded and surprisingly appears as a condensed state. Other co-solutes including known molecular crowder Ficoll PM 70, also induce a condensed state. Fluorescence recovery after photobleaching experiments reveal this state to be liquid-like indicating the VD undergoes a liquid-liquid phase separation under crowding conditions. These crowding conditions also enhance binding to cardiolipin, a mitochondrial lipid, which appears to promote phase separation. Since dynamin-related protein 1 is found assembled into discrete punctate structures on the mitochondrial surface, the inference from the present work is that these structures might arise from a condensed state involving the VD that may enable rapid tuning of mechanoenzyme assembly necessary for fission.
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Affiliation(s)
- Ammon E. Posey
- Program in Molecular BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
- Present address:
Department of Biomedical EngineeringWashington UniversitySt. LouisMissouriUSA
| | - Kyle A. Ross
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Mehran Bagheri
- Department of PhysicsUniversity of OttawaOttawaOntarioUSA
| | - Elizabeth N. Lanum
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Misha A. Khan
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | | | - Megan C. Harwig
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Nolan W. Kennedy
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Vincent J. Hilser
- Program in Molecular BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
| | | | - R. Blake Hill
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
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9
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Manley LJ, Lin MM. Kinetic and thermodynamic allostery in the Ras protein family. Biophys J 2023; 122:3882-3893. [PMID: 37598291 PMCID: PMC10560677 DOI: 10.1016/j.bpj.2023.08.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 07/20/2023] [Accepted: 08/14/2023] [Indexed: 08/21/2023] Open
Abstract
Allostery, the transfer of information between distant parts of a macromolecule, is a fundamental feature of protein function and regulation. However, allosteric mechanisms are usually not explained by protein structure, requiring information on correlated fluctuations uniquely accessible to molecular simulation. Existing work to extract allosteric pathways from molecular dynamics simulations has focused on thermodynamic correlations. Here, we show how kinetic correlations encode complementary information essential to explain observed variations in allosteric regulation. We applied kinetic and thermodynamic correlation analysis on atomistic simulations of H, K, and NRas isoforms in the apo, GTP, and GDP-bound states of Ras protein, with and without complexing to its downstream effector, Raf. We show that switch I and switch II are the primary components of thermodynamic and kinetic allosteric networks, consistent with the key roles of these two motifs. These networks connect the switches to an allosteric loop recently discovered from a crystal structure of HRas. This allosteric loop is inactive in KRas, but is coupled to the hydrolysis arm switch II in NRas and HRas. We find that the mechanism in the latter two isoforms are thermodynamic and kinetic, respectively. Binding of Raf-RBD further activates thermodynamic allostery in HRas and KRas but has limited effect on NRas. These results indicate that kinetic and thermodynamic correlations are both needed to explain protein function and allostery. These two distinct channels of allosteric regulation, and their combinatorial variability, may explain how subtle mutational differences can lead to diverse regulatory profiles among enzymatic proteins.
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Affiliation(s)
- Leigh J Manley
- Green Center for Systems Biology, Lyda Hill Department of Bioinformatics, Department of Biophysics, Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Milo M Lin
- Green Center for Systems Biology, Lyda Hill Department of Bioinformatics, Department of Biophysics, Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, Texas.
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10
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Lin X, Haller P, Bavi N, Faruk N, Perozo E, Sosnick TR. Folding of Prestin's Anion-Binding Site and the Mechanism of Outer Hair Cell Electromotility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530320. [PMID: 36909622 PMCID: PMC10002659 DOI: 10.1101/2023.02.27.530320] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Prestin responds to transmembrane voltage fluctuations by changing its cross-sectional area, a process underlying the electromotility of outer hair cells and cochlear amplification. Prestin belongs to the SLC26 family of anion transporters yet is the only member capable of displaying electromotility. Prestin's voltage-dependent conformational changes are driven by the putative displacement of residue R399 and a set of sparse charged residues within the transmembrane domain, following the binding of a Cl - anion at a conserved binding site formed by amino termini of the TM3 and TM10 helices. However, a major conundrum arises as to how an anion that binds in proximity to a positive charge (R399), can promote the voltage sensitivity of prestin. Using hydrogen-deuterium exchange mass spectrometry, we find that prestin displays an unstable anion-binding site, where folding of the amino termini of TM3 and TM10 is coupled to Cl - binding. This event shortens the TM3-TM10 electrostatic gap, thereby connecting the two helices, resulting in reduced cross-sectional area. These folding events upon anion-binding are absent in SLC26A9, a non-electromotile transporter closely related to prestin. Dynamics of prestin embedded in a lipid bilayer closely match that in detergent micelle, except for a destabilized lipid-facing helix TM6 that is critical to prestin's mechanical expansion. We observe helix fraying at prestin's anion-binding site but cooperative unfolding of multiple lipid-facing helices, features that may promote prestin's fast electromechanical rearrangements. These results highlight a novel role of the folding equilibrium of the anion-binding site, and helps define prestin's unique voltage-sensing mechanism and electromotility.
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11
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Abstract
A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.
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Affiliation(s)
- Ke-Wei Chen
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tian-Yu Sun
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yun-Dong Wu
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518132, China
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12
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Padmanabhan S, Manjithaya R. Leaderless secretory proteins of the neurodegenerative diseases via TNTs: a structure-function perspective. Front Mol Neurosci 2023; 16:983108. [PMID: 37396786 PMCID: PMC10308029 DOI: 10.3389/fnmol.2023.983108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 05/26/2023] [Indexed: 07/04/2023] Open
Abstract
Neurodegenerative disease-causing proteins such as alpha-synuclein, tau, and huntingtin are known to traverse across cells via exosomes, extracellular vesicles and tunneling nanotubes (TNTs). There seems to be good synergy between exosomes and TNTs in intercellular communication. Interestingly, many of the known major neurodegenerative proteins/proteolytic products are leaderless and are also reported to be secreted out of the cell via unconventional protein secretion. Such classes contain intrinsically disordered proteins and regions (IDRs) within them. The dynamic behavior of these proteins is due to their heterogenic conformations that is exhibited owing to various factors that occur inside the cells. The amino acid sequence along with the chemical modifications has implications on the functional roles of IDRs inside the cells. Proteins that form aggregates resulting in neurodegeneration become resistant to degradation by the processes of autophagy and proteasome system thus leading to Tunneling nanotubes, TNT formation. The proteins that traverse across TNTs may or may not be dependent on the autophagy machinery. It is not yet clear whether the conformation of the protein plays a crucial role in its transport from one cell to another without getting degraded. Although there is some experimental data, there are many grey areas which need to be revisited. This review provides a different perspective on the structural and functional aspects of these leaderless proteins that get secreted outside the cell. In this review, attention has been focused on the characteristic features that lead to aggregation of leaderless secretory proteins (from structural-functional aspect) with special emphasis on TNTs.
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13
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Posey AE, Bagheri M, Ross KA, Lanum EN, Khan MA, Jennings CM, Harwig MC, Kennedy NW, Hilser VJ, Harden JL, Hill RB. The variable domain from the mitochondrial fission mechanoenzyme Drp1 promotes liquid-liquid phase separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.542732. [PMID: 37398258 PMCID: PMC10312466 DOI: 10.1101/2023.05.29.542732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Dynamins are an essential superfamily of mechanoenzymes that remodel membranes and often contain a "variable domain" (VD) important for regulation. For the mitochondrial fission dynamin, Drp1, a regulatory role for the VD is demonstrated by mutations that can elongate, or fragment, mitochondria. How the VD encodes inhibitory and stimulatory activity is unclear. Here, isolated VD is shown to be intrinsically disordered (ID) yet undergoes a cooperative transition in the stabilizing osmolyte TMAO. However, the TMAO stabilized state is not folded and surprisingly appears as a condensed state. Other co-solutes including known molecular crowder Ficoll PM 70, also induce a condensed state. Fluorescence recovery after photobleaching experiments reveal this state to be liquid-like indicating the VD undergoes a liquid-liquid phase separation under crowding conditions. These crowding conditions also enhance binding to cardiolipin, a mitochondrial lipid, raising the possibility that phase separation may enable rapid tuning of Drp1 assembly necessary for fission.
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14
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Zheng LL, Li JZ, Wen M, Xi D, Zhu Y, Wei Q, Zhang XB, Ke G, Xia F, Gao ZF. Enthalpy and entropy synergistic regulation-based programmable DNA motifs for biosensing and information encryption. SCIENCE ADVANCES 2023; 9:eadf5868. [PMID: 37196083 DOI: 10.1126/sciadv.adf5868] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/13/2023] [Indexed: 05/19/2023]
Abstract
Deoxyribonucleic acid (DNA) provides a collection of intelligent tools for the development of information cryptography and biosensors. However, most conventional DNA regulation strategies rely solely on enthalpy regulation, which suffers from unpredictable stimuli-responsive performance and unsatisfactory accuracy due to relatively large energy fluctuations. Here, we report an enthalpy and entropy synergistic regulation-based pH-responsive A+/C DNA motif for programmable biosensing and information encryption. In the DNA motif, the variation in loop length alters entropic contribution, and the number of A+/C bases regulates enthalpy, which is verified through thermodynamic characterizations and analyses. On the basis of this straightforward strategy, the performances, such as pKa, of the DNA motif can be precisely and predictably tuned. The DNA motifs are finally successfully applied for glucose biosensing and crypto-steganography systems, highlighting their potential in the field of biosensing and information encryption.
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Affiliation(s)
- Lin Lin Zheng
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Jin Ze Li
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Mei Wen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Dongmei Xi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Yanxi Zhu
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
- Central Laboratory of Linyi People's Hospital, Linyi 276003, P. R. China
| | - Qin Wei
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, 388 Lumo Road, Wuhan 430074, P. R. China
| | - Zhong Feng Gao
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
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15
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Lee KY, Lee BJ. Dynamics-Based Regulatory Switches of Type II Antitoxins: Insights into New Antimicrobial Discovery. Antibiotics (Basel) 2023; 12:antibiotics12040637. [PMID: 37106997 PMCID: PMC10135005 DOI: 10.3390/antibiotics12040637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
Type II toxin-antitoxin (TA) modules are prevalent in prokaryotes and are involved in cell maintenance and survival under harsh environmental conditions, including nutrient deficiency, antibiotic treatment, and human immune responses. Typically, the type II TA system consists of two protein components: a toxin that inhibits an essential cellular process and an antitoxin that neutralizes its toxicity. Antitoxins of type II TA modules typically contain the structured DNA-binding domain responsible for TA transcription repression and an intrinsically disordered region (IDR) at the C-terminus that directly binds to and neutralizes the toxin. Recently accumulated data have suggested that the antitoxin's IDRs exhibit variable degrees of preexisting helical conformations that stabilize upon binding to the corresponding toxin or operator DNA and function as a central hub in regulatory protein interaction networks of the type II TA system. However, the biological and pathogenic functions of the antitoxin's IDRs have not been well discussed compared with those of IDRs from the eukaryotic proteome. Here, we focus on the current state of knowledge about the versatile roles of IDRs of type II antitoxins in TA regulation and provide insights into the discovery of new antibiotic candidates that induce toxin activation/reactivation and cell death by modulating the regulatory dynamics or allostery of the antitoxin.
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Affiliation(s)
- Ki-Young Lee
- College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Pocheon-si 11160, Republic of Korea
| | - Bong-Jin Lee
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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16
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Gurumoorthy V, Shrestha UR, Zhang Q, Pingali SV, Boder ET, Urban VS, Smith JC, Petridis L, O'Neill H. Disordered Domain Shifts the Conformational Ensemble of the Folded Regulatory Domain of the Multidomain Oncoprotein c-Src. Biomacromolecules 2023; 24:714-723. [PMID: 36692364 DOI: 10.1021/acs.biomac.2c01158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
c-Src kinase is a multidomain non-receptor tyrosine kinase that aberrantly phosphorylates several signaling proteins in cancers. Although the structural properties of the regulatory domains (SH3-SH2) and the catalytic kinase domain have been extensively characterized, there is less knowledge about the N-terminal disordered region (SH4UD) and its interactions with the other c-Src domains. Here, we used domain-selective isotopic labeling combined with the small-angle neutron scattering contrast matching technique to study SH4UD interactions with SH3-SH2. Our results show that in the presence of SH4UD, the radius of gyration (Rg) of SH3-SH2 increases, indicating that it has a more extended conformation. Hamiltonian replica exchange molecular dynamics simulations provide a detailed molecular description of the structural changes in SH4UD-SH3-SH2 and show that the regulatory loops of SH3 undergo significant conformational changes in the presence of SH4UD, while SH2 remains largely unchanged. Overall, this study highlights how a disordered region can drive a folded region of a multidomain protein to become flexible, which may be important for allosteric interactions with binding partners. This may help in the design of therapeutic interventions that target the regulatory domains of this important family of kinases.
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Affiliation(s)
- Viswanathan Gurumoorthy
- UT/ORNL Graduate School of Genome and Science Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Utsab R Shrestha
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Sai Venkatesh Pingali
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Eric T Boder
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Volker S Urban
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Loukas Petridis
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hugh O'Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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17
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Panigrahi R, Kailasam S. Mapping allosteric pathway in NIa-Pro using computational approach. QUANTITATIVE BIOLOGY 2023. [DOI: 10.15302/j-qb-022-0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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18
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Intrinsically Disordered Proteins: An Overview. Int J Mol Sci 2022; 23:ijms232214050. [PMID: 36430530 PMCID: PMC9693201 DOI: 10.3390/ijms232214050] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Many proteins and protein segments cannot attain a single stable three-dimensional structure under physiological conditions; instead, they adopt multiple interconverting conformational states. Such intrinsically disordered proteins or protein segments are highly abundant across proteomes, and are involved in various effector functions. This review focuses on different aspects of disordered proteins and disordered protein regions, which form the basis of the so-called "Disorder-function paradigm" of proteins. Additionally, various experimental approaches and computational tools used for characterizing disordered regions in proteins are discussed. Finally, the role of disordered proteins in diseases and their utility as potential drug targets are explored.
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19
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Wen B, Zhang W, Zhang Y, Lei H, Cao Y, Li W, Wang W. Self-Effected Allosteric Coupling and Cooperativity in Hypoxic Response Regulation with Disordered Proteins. J Phys Chem Lett 2022; 13:9201-9209. [PMID: 36170455 DOI: 10.1021/acs.jpclett.2c02065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Hypersensitive regulation of cellular hypoxic response relies on cooperative displacement of one disordered protein (HIF-1α) by another disordered protein (CITED2) from the target in a negative feedback loop. Considering the weak intramolecule coupling in disordered proteins, the molecular mechanism of high cooperativity in the molecular displacement event remains elusive. Herein, we show that disordered proteins utilize a "self-effected allostery" mechanism to achieve high binding cooperativity. Different from the conventional allostery mechanisms shown by many structured or disordered proteins, this mechanism utilizes one part of the disordered protein as the effector to trigger the allosteric coupling and enhance the binding of the remaining part of the same disordered protein, contributing to high cooperativity of the displacement event. The conserved charge motif of CITED2 is the key determinant of the molecular displacement event by serving as the effector of allosteric coupling. Such self-effected allostery provides an efficient strategy to achieve high cooperativity in the molecular events involving disordered proteins.
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Affiliation(s)
- Bin Wen
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Weiwei Zhang
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Yangyang Zhang
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Hai Lei
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Yi Cao
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wenfei Li
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wei Wang
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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20
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Bonin JP, Sapienza PJ, Lee AL. Dynamic allostery in substrate binding by human thymidylate synthase. eLife 2022; 11:79915. [PMID: 36200982 PMCID: PMC9536839 DOI: 10.7554/elife.79915] [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: 05/02/2022] [Accepted: 08/31/2022] [Indexed: 11/25/2022] Open
Abstract
Human thymidylate synthase (hTS) is essential for DNA replication and therefore a therapeutic target for cancer. Effective targeting requires knowledge of the mechanism(s) of regulation of this 72 kDa homodimeric enzyme. Here, we investigate the mechanism of binding cooperativity of the nucleotide substrate. We have employed exquisitely sensitive methyl-based CPMG and CEST NMR experiments enabling us to identify residues undergoing bifurcated linear 3-state exchange, including concerted switching between active and inactive conformations in the apo enzyme. The inactive state is populated to only ~1.3%, indicating that conformational selection contributes negligibly to the cooperativity. Instead, methyl rotation axis order parameters, determined by 2H transverse relaxation rates, suggest that rigidification of the enzyme upon substrate binding is responsible for the entropically-driven cooperativity. Lack of the rigidification in product binding and substrate binding to an N-terminally truncated enzyme, both non-cooperative, support this idea. In addition, the lack of this rigidification in the N-terminal truncation indicates that interactions between the flexible N-terminus and the rest of the protein, which are perturbed by substrate binding, play a significant role in the cooperativity—a novel mechanism of dynamic allostery. Together, these findings yield a rare depth of insight into the substrate binding cooperativity of an essential enzyme.
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Affiliation(s)
- Jeffrey P Bonin
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina
| | - Paul J Sapienza
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina
| | - Andrew L Lee
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina
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21
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Zhang Y, Liu X, Chen J. Toward Accurate Coarse-Grained Simulations of Disordered Proteins and Their Dynamic Interactions. J Chem Inf Model 2022; 62:4523-4536. [PMID: 36083825 PMCID: PMC9910785 DOI: 10.1021/acs.jcim.2c00974] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) play crucial roles in cellular regulatory networks and are now recognized to often remain highly dynamic even in specific interactions and assemblies. Accurate description of these dynamic interactions is extremely challenging using atomistic simulations because of the prohibitive computational cost. Efficient coarse-grained approaches could offer an effective solution to overcome this bottleneck if they could provide an accurate description of key local and global properties of IDPs in both unbound and bound states. The recently developed hybrid-resolution (HyRes) protein model has been shown to be capable of providing a semiquantitative description of the secondary structure propensities of IDPs. Here, we show that greatly improved description of global structures and transient interactions can be achieved by introducing a solvent-accessible surface area-based implicit solvent term followed by reoptimization of effective interaction strengths. The new model, termed HyRes II, can semiquantitatively reproduce a wide range of local and global structural properties of a set of IDPs of various lengths and complexities. It can also distinguish the level of compaction between folded proteins and IDPs. In particular, applied to the disordered N-terminal transactivation domain (TAD) of tumor suppressor p53, HyRes II is able to recapitulate various nontrivial structural properties compared to experimental results, some of them to a level of accuracy that is almost comparable to results from atomistic explicit solvent simulations. Furthermore, we demonstrate that HyRes II can be used to simulate the dynamic interactions of TAD with the DNA-binding domain of p53, generating structural ensembles that are highly consistent with existing NMR data. We anticipate that HyRes II will provide an efficient and relatively reliable tool toward accurate coarse-grained simulations of dynamic protein interactions.
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Affiliation(s)
- Yumeng Zhang
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Xiaorong Liu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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22
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A modular approach to map out the conformational landscapes of unbound intrinsically disordered proteins. Proc Natl Acad Sci U S A 2022; 119:e2113572119. [PMID: 35658083 PMCID: PMC9191344 DOI: 10.1073/pnas.2113572119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceIntrinsically disordered proteins have the unique ability to morph in response to multiple partners and thereby process sophisticated inputs and outputs. It is, however, a mystery whether their response is passive, that is, entirely determined by the partner, or controlled via an internal, yet unknown, folding mechanism. Here we introduce an approach to examine this key question and demonstrate its potential by dissecting the conformational properties of the partially disordered protein NCBD and obtaining important clues about how it performs its biological function.
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23
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Camacho-Zarco AR, Schnapka V, Guseva S, Abyzov A, Adamski W, Milles S, Jensen MR, Zidek L, Salvi N, Blackledge M. NMR Provides Unique Insight into the Functional Dynamics and Interactions of Intrinsically Disordered Proteins. Chem Rev 2022; 122:9331-9356. [PMID: 35446534 PMCID: PMC9136928 DOI: 10.1021/acs.chemrev.1c01023] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Intrinsically disordered
proteins are ubiquitous throughout all
known proteomes, playing essential roles in all aspects of cellular
and extracellular biochemistry. To understand their function, it is
necessary to determine their structural and dynamic behavior and to
describe the physical chemistry of their interaction trajectories.
Nuclear magnetic resonance is perfectly adapted to this task, providing
ensemble averaged structural and dynamic parameters that report on
each assigned resonance in the molecule, unveiling otherwise inaccessible
insight into the reaction kinetics and thermodynamics that are essential
for function. In this review, we describe recent applications of NMR-based
approaches to understanding the conformational energy landscape, the
nature and time scales of local and long-range dynamics and how they
depend on the environment, even in the cell. Finally, we illustrate
the ability of NMR to uncover the mechanistic basis of functional
disordered molecular assemblies that are important for human health.
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Affiliation(s)
| | - Vincent Schnapka
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Serafima Guseva
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Anton Abyzov
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Wiktor Adamski
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Sigrid Milles
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | | | - Lukas Zidek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 82500 Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Kamenice 5, 82500 Brno, Czech Republic
| | - Nicola Salvi
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
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24
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Peiffer AL, Garlick JM, Joy ST, Mapp AK, Brooks CL. Allostery in the dynamic coactivator domain KIX occurs through minor conformational micro-states. PLoS Comput Biol 2022; 18:e1009977. [PMID: 35452454 PMCID: PMC9067669 DOI: 10.1371/journal.pcbi.1009977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 05/04/2022] [Accepted: 02/27/2022] [Indexed: 12/16/2022] Open
Abstract
The coactivator KIX of CBP uses two binding surfaces to recognize multiple activators and exhibits allostery in ternary complex formation. Activator•coactivator interactions are central to transcriptional regulation, yet the microscopic origins of allostery in dynamic proteins like KIX are largely unknown. Here, we investigate the molecular recognition and allosteric manifestations involved in two KIX ternary systems c-Myb•KIX•MLL and pKID•KIX•MLL. Exploring the hypothesis that binary complex formation prepays an entropic cost for positive cooperativity, we utilize molecular dynamics simulations, side chain methyl order parameters, and differential scanning fluorimetry (DSF) to explore conformational entropy changes in KIX. The protein's configurational micro-states from structural clustering highlight the utility of protein plasticity in molecular recognition and allostery. We find that apo KIX occupies a wide distribution of lowly-populated configurational states. Each binding partner has its own suite of KIX states that it selects, building a model of molecular recognition fingerprints. Allostery is maximized with MLL pre-binding, which corresponds to the observation of a significant reduction in KIX micro-states observed when MLL binds. With all binding partners, the changes in KIX conformational entropy arise predominantly from changes in the most flexible loop. Likewise, we find that a small molecule and mutations allosterically inhibit/enhance activator binding by tuning loop dynamics, suggesting that loop-targeting chemical probes could be developed to alter KIX•activator interactions. Experimentally capturing KIX stabilization is challenging, particularly because of the disordered nature of particular activators. However, DSF melting curves allow for inference of relative entropic changes that occur across complexes, which we compare to our computed entropy changes using simulation methyl order parameters.
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Affiliation(s)
- Amanda L. Peiffer
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Julie M. Garlick
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Stephen T. Joy
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Anna K. Mapp
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Charles L. Brooks
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, United States of America
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25
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Bondos SE, Dunker AK, Uversky VN. Intrinsically disordered proteins play diverse roles in cell signaling. Cell Commun Signal 2022; 20:20. [PMID: 35177069 PMCID: PMC8851865 DOI: 10.1186/s12964-022-00821-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/11/2021] [Indexed: 11/29/2022] Open
Abstract
Abstract Signaling pathways allow cells to detect and respond to a wide variety of chemical (e.g. Ca2+ or chemokine proteins) and physical stimuli (e.g., sheer stress, light). Together, these pathways form an extensive communication network that regulates basic cell activities and coordinates the function of multiple cells or tissues. The process of cell signaling imposes many demands on the proteins that comprise these pathways, including the abilities to form active and inactive states, and to engage in multiple protein interactions. Furthermore, successful signaling often requires amplifying the signal, regulating or tuning the response to the signal, combining information sourced from multiple pathways, all while ensuring fidelity of the process. This sensitivity, adaptability, and tunability are possible, in part, due to the inclusion of intrinsically disordered regions in many proteins involved in cell signaling. The goal of this collection is to highlight the many roles of intrinsic disorder in cell signaling. Following an overview of resources that can be used to study intrinsically disordered proteins, this review highlights the critical role of intrinsically disordered proteins for signaling in widely diverse organisms (animals, plants, bacteria, fungi), in every category of cell signaling pathway (autocrine, juxtacrine, intracrine, paracrine, and endocrine) and at each stage (ligand, receptor, transducer, effector, terminator) in the cell signaling process. Thus, a cell signaling pathway cannot be fully described without understanding how intrinsically disordered protein regions contribute to its function. The ubiquitous presence of intrinsic disorder in different stages of diverse cell signaling pathways suggest that more mechanisms by which disorder modulates intra- and inter-cell signals remain to be discovered. Graphical abstract ![]()
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Affiliation(s)
- Sarah E Bondos
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX, 77843, USA.
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.,Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, Russia, 142290
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Ledoux J, Trouvé A, Tchertanov L. The Inherent Coupling of Intrinsically Disordered Regions in the Multidomain Receptor Tyrosine Kinase KIT. Int J Mol Sci 2022; 23:ijms23031589. [PMID: 35163518 PMCID: PMC8835827 DOI: 10.3390/ijms23031589] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
RTK KIT regulates a variety of crucial cellular processes via its cytoplasmic domain (CD), which is composed of the tyrosine kinase domain, crowned by the highly flexible domains—the juxtamembrane region, kinase insertion domain, and C-tail, which are key recruitment regions for downstream signalling proteins. To prepare a structural basis for the characterization of the interactions of KIT with its signalling proteins (KIT INTERACTOME), we generated the 3D model of the full-length CD attached to the transmembrane helix. This generic model of KIT in inactive state was studied by molecular dynamics simulation under conditions mimicking the natural environment of KIT. With the accurate atomistic description of the multidomain KIT dynamics, we explained its intrinsic (intra-domain) and extrinsic (inter-domain) disorder and represented the conformational assemble of KIT through free energy landscapes. Strongly coupled movements within each domain and between distant domains of KIT prove the functional interdependence of these regions, described as allosteric regulation, a phenomenon widely observed in many proteins. We suggested that KIT, in its inactive state, encodes all properties of the active protein and its post-transduction events.
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27
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Chin AF, Wrabl JO, Hilser VJ. A thermodynamic atlas of proteomes reveals energetic innovation across the tree of life. Mol Biol Evol 2022; 39:6509521. [PMID: 35038744 PMCID: PMC8896757 DOI: 10.1093/molbev/msac010] [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] [Indexed: 11/12/2022] Open
Abstract
Protein stability is a fundamental molecular property enabling organisms to adapt to their biological niches. How this is facilitated and whether there are kingdom specific or more general universal strategies is not known. A principal obstacle to addressing this issue is that the vast majority of proteins lack annotation, specifically thermodynamic annotation, beyond the amino acid and chromosome information derived from genome sequencing. To address this gap and facilitate future investigation into large-scale patterns of protein stability and dynamics within and between organisms, we applied a unique ensemble-based thermodynamic characterization of protein folds to a substantial portion of extant sequenced genomes. Using this approach, we compiled a database resource focused on the position-specific variation in protein stability. Interrogation of the database reveals; 1) domains of life exhibit distinguishing thermodynamic features, with eukaryotes particularly different from both archaea and bacteria, 2) the optimal growth temperature of an organism is proportional to the average apolar enthalpy of its proteome, 3) intrinsic disorder content is also proportional to the apolar enthalpy (but unexpectedly not the predicted stability at 25 °C), and 4) secondary structure and global stability information of individual proteins is extractable. We hypothesize that wider access to residue-specific thermodynamic information of proteomes will result in deeper understanding of mechanisms driving functional adaptation and protein evolution. Our database is free for download at https://afc-science.github.io/thermo-env-atlas/.
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Affiliation(s)
- Alexander F Chin
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - James O Wrabl
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Vincent J Hilser
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA.,T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
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28
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Timsit Y, Grégoire SP. Towards the Idea of Molecular Brains. Int J Mol Sci 2021; 22:ijms222111868. [PMID: 34769300 PMCID: PMC8584932 DOI: 10.3390/ijms222111868] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/24/2021] [Accepted: 10/28/2021] [Indexed: 02/06/2023] Open
Abstract
How can single cells without nervous systems perform complex behaviours such as habituation, associative learning and decision making, which are considered the hallmark of animals with a brain? Are there molecular systems that underlie cognitive properties equivalent to those of the brain? This review follows the development of the idea of molecular brains from Darwin’s “root brain hypothesis”, through bacterial chemotaxis, to the recent discovery of neuron-like r-protein networks in the ribosome. By combining a structural biology view with a Bayesian brain approach, this review explores the evolutionary labyrinth of information processing systems across scales. Ribosomal protein networks open a window into what were probably the earliest signalling systems to emerge before the radiation of the three kingdoms. While ribosomal networks are characterised by long-lasting interactions between their protein nodes, cell signalling networks are essentially based on transient interactions. As a corollary, while signals propagated in persistent networks may be ephemeral, networks whose interactions are transient constrain signals diffusing into the cytoplasm to be durable in time, such as post-translational modifications of proteins or second messenger synthesis. The duration and nature of the signals, in turn, implies different mechanisms for the integration of multiple signals and decision making. Evolution then reinvented networks with persistent interactions with the development of nervous systems in metazoans. Ribosomal protein networks and simple nervous systems display architectural and functional analogies whose comparison could suggest scale invariance in information processing. At the molecular level, the significant complexification of eukaryotic ribosomal protein networks is associated with a burst in the acquisition of new conserved aromatic amino acids. Knowing that aromatic residues play a critical role in allosteric receptors and channels, this observation suggests a general role of π systems and their interactions with charged amino acids in multiple signal integration and information processing. We think that these findings may provide the molecular basis for designing future computers with organic processors.
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Affiliation(s)
- Youri Timsit
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
- Correspondence:
| | - Sergeant-Perthuis Grégoire
- Institut de Mathématiques de Jussieu—Paris Rive Gauche (IMJ-PRG), UMR 7586, CNRS-Université Paris Diderot, 75013 Paris, France;
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29
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The sequence-ensemble relationship in fuzzy protein complexes. Proc Natl Acad Sci U S A 2021; 118:2020562118. [PMID: 34504009 DOI: 10.1073/pnas.2020562118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2021] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) interact with globular proteins through a variety of mechanisms, resulting in the structurally heterogeneous ensembles known as fuzzy complexes. While there exists a reasonable comprehension on how IDP sequence determines the unbound IDP ensemble, little is known about what shapes the structural characteristics of IDPs bound to their targets. Using a statistical thermodynamic model, we show that the target-bound ensembles are determined by a simple code that combines the IDP sequence and the distribution of IDP-target interaction hotspots. These two parameters define the conformational space of target-bound IDPs and rationalize the observed structural heterogeneity of fuzzy complexes. The presented model successfully reproduces the dynamical signatures of target-bound IDPs from the NMR relaxation experiments as well as the changes of interaction affinity and the IDP helicity induced by mutations. The model explains how the target-bound IDP ensemble adapts to mutations in order to achieve an optimal balance between conformational freedom and interaction energy. Taken together, the presented sequence-ensemble relationship of fuzzy complexes explains the different manifestations of IDP disorder in folding-upon-binding processes.
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30
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Babel L, Nguyen MH, Mittelheisser C, Martin M, Fromm KM, Walker O, Hologne M. NMR reveals the interplay between SilE and SilB model peptides in the context of silver resistance. Chem Commun (Camb) 2021; 57:8726-8729. [PMID: 34396382 PMCID: PMC8686694 DOI: 10.1039/d1cc02597j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
SilE and SilB are both proteins involved in the silver efflux pump found in Gram-negative bacteria such as S. typhimurium. Using model peptides along with NMR and CD experiments, we show how SilE may store silver ions prior to delivery and we hypothesize for the first time the interplay between SilB and SilE. Illustrative sketch representative of the interplay between the SilB and SilE proteins in the context of silver bacteria resistance. In case of an excess of silver, SilE plays the role of a regulator and avoids a collapse of the silver efflux pump.![]()
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Affiliation(s)
- Lucille Babel
- University of Fribourg, Department of Chemistry, chemin du musée 9, Fribourg 1700, Switzerland
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31
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Cho B, Choi J, Kim R, Yun JN, Choi Y, Lee HH, Koh J. Thermodynamic Models for Assembly of Intrinsically Disordered Protein Hubs with Multiple Interaction Partners. J Am Chem Soc 2021; 143:12509-12523. [PMID: 34362249 DOI: 10.1021/jacs.1c00811] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Prevalent in diverse protein interactomes, intrinsically disordered proteins or regions (IDPs or IDRs) often drive assembly of higher-order macromolecular complexes, using multiple target-binding motifs. Such IDP hubs are suggested to process various cellular signals and coordinate relevant biological processes. However, the mechanism of assembly and functional regulation of IDP hubs remains elusive due to the challenges in dissecting their intricate protein-protein interaction networks. Here we present basic thermodynamic models for the assembly of simple IDP hubs with multiple target proteins, constructing partition functions from fundamental binding parameters. We combined these basic functions to develop advanced thermodynamic models to analyze the assembly of the Nup153 hubs interacting with multiple karyopherin β1 (Kap) molecules, critical components of nucleocytoplasmic transport. The thermodynamic analysis revealed a complex organization of the Kap binding sites within the C-terminal IDR of Nup153 including a high-affinity 1:1 interaction site and a series of low-affinity sites for binding of multiple Kaps with negative cooperativity. The negative cooperativity arises from the overlapping nature of the low-affinity sites where Kap occupies multiple dipeptide motifs. The quantitative dissection culminated in construction of the Nup153 hub ensemble, elucidating how distribution among various Kap-bound states is modulated by Kap concentration and competing nuclear proteins. In particular, the Kap occupancy of the IDR can be fine-tuned by varying the location of competition within the overlapping sites, suggesting coupling of specific nuclear processes to distinct transport activities. In general, our results demonstrate the feasibility and a potential mechanism for manifold regulation of IDP functions by diverse cellular signals.
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Affiliation(s)
- ByeongJin Cho
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jaejun Choi
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - RyeongHyeon Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jean Nyoung Yun
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yuri Choi
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyung Ho Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Junseock Koh
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
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32
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Stabilization Effect of Intrinsically Disordered Regions on Multidomain Proteins: The Case of the Methyl-CpG Protein 2, MeCP2. Biomolecules 2021; 11:biom11081216. [PMID: 34439881 PMCID: PMC8391517 DOI: 10.3390/biom11081216] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/04/2021] [Accepted: 08/13/2021] [Indexed: 12/14/2022] Open
Abstract
Intrinsic disorder plays an important functional role in proteins. Disordered regions are linked to posttranslational modifications, conformational switching, extra/intracellular trafficking, and allosteric control, among other phenomena. Disorder provides proteins with enhanced plasticity, resulting in a dynamic protein conformational/functional landscape, with well-structured and disordered regions displaying reciprocal, interdependent features. Although lacking well-defined conformation, disordered regions may affect the intrinsic stability and functional properties of ordered regions. MeCP2, methyl-CpG binding protein 2, is a multifunctional transcriptional regulator associated with neuronal development and maturation. MeCP2 multidomain structure makes it a prototype for multidomain, multifunctional, intrinsically disordered proteins (IDP). The methyl-binding domain (MBD) is one of the key domains in MeCP2, responsible for DNA recognition. It has been reported previously that the two disordered domains flanking MBD, the N-terminal domain (NTD) and the intervening domain (ID), increase the intrinsic stability of MBD against thermal denaturation. In order to prove unequivocally this stabilization effect, ruling out any artifactual result from monitoring the unfolding MBD with a local fluorescence probe (the single tryptophan in MBD) or from driving the protein unfolding by temperature, we have studied the MBD stability by differential scanning calorimetry (reporting on the global unfolding process) and chemical denaturation (altering intramolecular interactions by a different mechanism compared to thermal denaturation).
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33
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Civera M, Moroni E, Sorrentino L, Vasile F, Sattin S. Chemical and Biophysical Approaches to Allosteric Modulation. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Monica Civera
- Department of Chemistry Università degli Studi di Milano via C. Golgi, 19 20133 Milan Italy
| | - Elisabetta Moroni
- Istituto di Scienze e Tecnologie Chimiche Giulio Natta, SCITEC Via Mario Bianco 9 20131 Milan Italy
| | - Luca Sorrentino
- Department of Chemistry Università degli Studi di Milano via C. Golgi, 19 20133 Milan Italy
| | - Francesca Vasile
- Department of Chemistry Università degli Studi di Milano via C. Golgi, 19 20133 Milan Italy
| | - Sara Sattin
- Department of Chemistry Università degli Studi di Milano via C. Golgi, 19 20133 Milan Italy
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34
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Sørensen M, Møller BL. Metabolic Engineering of Photosynthetic Cells – in Collaboration with Nature. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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35
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Schrag LG, Liu X, Thevarajan I, Prakash O, Zolkiewski M, Chen J. Cancer-Associated Mutations Perturb the Disordered Ensemble and Interactions of the Intrinsically Disordered p53 Transactivation Domain. J Mol Biol 2021; 433:167048. [PMID: 33984364 PMCID: PMC8286338 DOI: 10.1016/j.jmb.2021.167048] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 01/08/2023]
Abstract
Intrinsically disordered proteins (IDPs) are key components of regulatory networks that control crucial aspects of cell decision making. The intrinsically disordered transactivation domain (TAD) of tumor suppressor p53 mediates its interactions with multiple regulatory pathways to control the p53 homeostasis during the cellular response to genotoxic stress. Many cancer-associated mutations have been discovered in p53-TAD, but their structural and functional consequences are poorly understood. Here, by combining atomistic simulations, NMR spectroscopy, and binding assays, we demonstrate that cancer-associated mutations can significantly perturb the balance of p53 interactions with key activation and degradation regulators. Importantly, the four mutations studied in this work do not all directly disrupt the known interaction interfaces. Instead, at least three of these mutations likely modulate the disordered state of p53-TAD to perturb its interactions with regulators. Specifically, NMR and simulation analysis together suggest that these mutations can modulate the level of conformational expansion as well as rigidity of the disordered state. Our work suggests that the disordered conformational ensemble of p53-TAD can serve as a central conduit in regulating the response to various cellular stimuli at the protein-protein interaction level. Understanding how the disordered state of IDPs may be modulated by regulatory signals and/or disease associated perturbations will be essential in the studies on the role of IDPs in biology and diseases.
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Affiliation(s)
- Lynn G Schrag
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66505, USA
| | - Xiaorong Liu
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Indhujah Thevarajan
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66505, USA
| | - Om Prakash
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66505, USA.
| | - Michal Zolkiewski
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66505, USA.
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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36
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Ledoux J, Trouvé A, Tchertanov L. Folding and Intrinsic Disorder of the Receptor Tyrosine Kinase KIT Insert Domain Seen by Conventional Molecular Dynamics Simulations. Int J Mol Sci 2021; 22:ijms22147375. [PMID: 34298994 PMCID: PMC8307779 DOI: 10.3390/ijms22147375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022] Open
Abstract
The kinase insert domain (KID) of RTK KIT is the key recruitment region for downstream signalling proteins. KID, studied by molecular dynamics simulations as a cleaved polypeptide and as a native domain fused to KIT, showed intrinsic disorder represented by a set of heterogeneous conformations. The accurate atomistic models showed that the helical fold of KID is mainly sequence dependent. However, the reduced fold of the native KID suggests that its folding is allosterically controlled by the kinase domain. The tertiary structure of KID represents a compact array of highly variable α- and 310-helices linked by flexible loops playing a principal role in the conformational diversity. The helically folded KID retains a collapsed globule-like shape due to non-covalent interactions associated in a ternary hydrophobic core. The free energy landscapes constructed from first principles-the size, the measure of the average distance between the conformations, the amount of helices and the solvent-accessible surface area-describe the KID disorder through a collection of minima (wells), providing a direct evaluation of conformational ensembles. We found that the cleaved KID simulated with restricted N- and C-ends better reproduces the native KID than the isolated polypeptide. We suggest that a cyclic, generic KID would be best suited for future studies of KID f post-transduction effects.
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37
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Grasso EM, Majumdar A, Wrabl JO, Frueh DP, Hilser VJ. Conserved allosteric ensembles in disordered proteins using TROSY/anti-TROSY R 2-filtered spectroscopy. Biophys J 2021; 120:2498-2510. [PMID: 33901472 PMCID: PMC8390865 DOI: 10.1016/j.bpj.2021.04.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/11/2021] [Accepted: 04/16/2021] [Indexed: 11/22/2022] Open
Abstract
Defining the role of intrinsic disorder in proteins in the myriad of biological processes with which it is involved represents a significant goal in modern biophysics. Toward this end, NMR is uniquely suited for molecular studies of dynamic and disordered regions, but studying these regions in concert with their more structured domains and binding partners presents spectroscopic challenges. Here, we investigate the interactions between the structured and disordered regions of the human glucocorticoid receptor (GR). To do this, we developed an NMR strategy that relies on a novel relaxation filter for the simultaneous study of structured and unstructured regions. Using this approach, we conducted a comparative analysis of three translational isoforms of GR containing a folded DNA-binding domain (DBD) and two disordered regions that flank the DBD, one of which varies in size in the different isoforms. Notably, we were able to assign resonances that had previously been inaccessible because of the spectral complexity of the translational isoforms, which in turn allowed us to 1) identify a region of the structured DBD that undergoes significant changes in the local chemical environment in the presence of the disordered region and 2) determine differences in the conformational ensembles of the disordered regions of the translational isoforms. Furthermore, an ensemble-based thermodynamic analysis of the isoforms reveals conserved patterns of stability within the N-terminal domain of GR that persist despite low sequence conservation. These studies provide an avenue for further investigations of the mechanistic underpinnings of the functional relevance of the translational isoforms of GR while also providing a general NMR strategy for studying systems containing both structured and disordered regions.
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Affiliation(s)
- Emily M Grasso
- Department of Biology, Johns Hopkins University, Baltimore, Maryland; T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Ananya Majumdar
- The Biomolecular NMR Center, Johns Hopkins University, Baltimore, Maryland
| | - James O Wrabl
- Department of Biology, Johns Hopkins University, Baltimore, Maryland
| | - Dominique P Frueh
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Vincent J Hilser
- Department of Biology, Johns Hopkins University, Baltimore, Maryland; T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.
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38
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Bai Z, Cao Y, Liu W, Li J. The SARS-CoV-2 Nucleocapsid Protein and Its Role in Viral Structure, Biological Functions, and a Potential Target for Drug or Vaccine Mitigation. Viruses 2021; 13:v13061115. [PMID: 34200602 PMCID: PMC8227405 DOI: 10.3390/v13061115] [Citation(s) in RCA: 148] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/24/2021] [Accepted: 06/04/2021] [Indexed: 12/14/2022] Open
Abstract
The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the world is still expanding. Thus, there is an urgent need to better understand this novel virus and find a way to control its spread. Like other coronaviruses, the nucleocapsid (N) protein is one of the most crucial structural components of SARS-CoV-2. This protein shares 90% homology with the severe acute respiratory syndrome coronavirus N protein, implying functional significance. Based on the evolutionary conservation of the N protein in coronavirus, we reviewed the currently available knowledge regarding the SARS-CoV-2 N protein in terms of structure, biological functions, and clinical application as a drug target or vaccine candidate.
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Affiliation(s)
- Zhihua Bai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Z.B.); (Y.C.); (W.L.)
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Cao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Z.B.); (Y.C.); (W.L.)
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Wenjun Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Z.B.); (Y.C.); (W.L.)
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China
- Center for Biosafety Mega-Science, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Z.B.); (Y.C.); (W.L.)
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
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39
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White JT, Rives J, Tharp ME, Wrabl JO, Thompson EB, Hilser VJ. Tumor Susceptibility Gene 101 Regulates the Glucocorticoid Receptor through Disorder-Mediated Allostery. Biochemistry 2021; 60:1647-1657. [PMID: 34009973 DOI: 10.1021/acs.biochem.1c00079] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tumor susceptibility gene 101 (TSG101) is involved in endosomal maturation and has been implicated in the transcriptional regulation of several steroid hormone receptors, although a detailed characterization of such regulation has yet to be conducted. Here we directly measure binding of TSG101 to one steroid hormone receptor, the glucocorticoid receptor (GR). Using biophysical and cellular assays, we show that the coiled-coil domain of TSG101 (1) binds and folds the disordered N-terminal domain of the GR, (2) upon binding improves the DNA binding of the GR in vitro, and (3) enhances the transcriptional activity of the GR in vivo. Our findings suggest that TSG101 is a bona fide transcriptional co-regulator of the GR and reveal how the underlying thermodynamics affect the function of the GR.
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Affiliation(s)
- Jordan T White
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - James Rives
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Marla E Tharp
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - James O Wrabl
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - E Brad Thompson
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Sealy Center for Structural Biology and Molecular Biophysics and Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, Texas 77555, United States
| | - Vincent J Hilser
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States.,T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
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40
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Tee WV, Tan ZW, Lee K, Guarnera E, Berezovsky IN. Exploring the Allosteric Territory of Protein Function. J Phys Chem B 2021; 125:3763-3780. [PMID: 33844527 DOI: 10.1021/acs.jpcb.1c00540] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
While the pervasiveness of allostery in proteins is commonly accepted, we further show the generic nature of allosteric mechanisms by analyzing here transmembrane ion-channel viroporin 3a and RNA-dependent RNA polymerase (RdRp) from SARS-CoV-2 along with metabolic enzymes isocitrate dehydrogenase 1 (IDH1) and fumarate hydratase (FH) implicated in cancers. Using the previously developed structure-based statistical mechanical model of allostery (SBSMMA), we share our experience in analyzing the allosteric signaling, predicting latent allosteric sites, inducing and tuning targeted allosteric response, and exploring the allosteric effects of mutations. This, yet incomplete list of phenomenology, forms a complex and unique allosteric territory of protein function, which should be thoroughly explored. We propose a generic computational framework, which not only allows one to obtain a comprehensive allosteric control over proteins but also provides an opportunity to approach the fragment-based design of allosteric effectors and drug candidates. The advantages of allosteric drugs over traditional orthosteric compounds, complemented by the emerging role of the allosteric effects of mutations in the expansion of the cancer mutational landscape and in the increased mutability of viral proteins, leave no choice besides further extensive studies of allosteric mechanisms and their biomedical implications.
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Affiliation(s)
- Wei-Ven Tee
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore.,Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117597, Singapore
| | - Zhen Wah Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | - Keene Lee
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | - Enrico Guarnera
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore.,Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117597, Singapore
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41
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Huihui J, Ghosh K. An analytical theory to describe sequence-specific inter-residue distance profiles for polyampholytes and intrinsically disordered proteins. J Chem Phys 2020; 152:161102. [PMID: 32357776 DOI: 10.1063/5.0004619] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Intrinsically Disordered Proteins (IDPs), unlike folded proteins, lack a unique folded structure and rapidly interconvert among ensembles of disordered states. However, they have specific conformational properties when averaged over their ensembles of disordered states. It is critical to develop a theoretical formalism to predict these ensemble average conformational properties that are encoded in the IDP sequence (the specific order in which amino acids/residues are linked). We present a general heteropolymer theory that analytically computes the ensemble average distance profiles (⟨Rij 2⟩) between any two (i, j) monomers (amino acids for IDPs) as a function of the sequence. Information rich distance profiles provide a detailed description of the IDP in contrast to typical metrics such as scaling exponents, radius of gyration, or end-to-end distance. This generalized formalism supersedes homopolymer-like models or models that are built only on the composition of amino acids but ignore sequence details. The prediction of these distance profiles for highly charged polyampholytes and naturally occurring IDPs unmasks salient features that are hidden in the sequence. Moreover, the model reveals strategies to modulate the entire distance map to achieve local or global swelling/compaction by subtle changes/modifications-such as phosphorylation, a biologically relevant process-in specific hotspots in the sequence. Sequence-specific distance profiles and their modulation have been benchmarked against all-atom simulations. Our new formalism also predicts residue-pair specific coil-globule transitions. The analytical nature of the theory will facilitate design of new sequences to achieve specific target distance profiles with broad applications in synthetic biology and polymer science.
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Affiliation(s)
- Jonathan Huihui
- Department of Physics and Astronomy, University of Denver, Denver, Colorado 80208, USA and Molecular and Cellular Biophysics, University of Denver, Denver, Colorado 80208, USA
| | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, Colorado 80208, USA and Molecular and Cellular Biophysics, University of Denver, Denver, Colorado 80208, USA
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42
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Ferraro M, Moroni E, Ippoliti E, Rinaldi S, Sanchez-Martin C, Rasola A, Pavarino LF, Colombo G. Machine Learning of Allosteric Effects: The Analysis of Ligand-Induced Dynamics to Predict Functional Effects in TRAP1. J Phys Chem B 2020; 125:101-114. [PMID: 33369425 PMCID: PMC8016192 DOI: 10.1021/acs.jpcb.0c09742] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Allosteric
molecules provide a powerful means to modulate protein
function. However, the effect of such ligands on distal orthosteric
sites cannot be easily described by classical docking methods. Here,
we applied machine learning (ML) approaches to expose the links between
local dynamic patterns and different degrees of allosteric inhibition
of the ATPase function in the molecular chaperone TRAP1. We focused
on 11 novel allosteric modulators with similar affinities to the target
but with inhibitory efficacy between the 26.3 and 76%. Using a set
of experimentally related local descriptors, ML enabled us to connect
the molecular dynamics (MD) accessible to ligand-bound (perturbed)
and unbound (unperturbed) systems to the degree of ATPase allosteric
inhibition. The ML analysis of the comparative perturbed ensembles
revealed a redistribution of dynamic states in the inhibitor-bound
versus inhibitor-free systems following allosteric binding. Linear
regression models were built to quantify the percentage of experimental
variance explained by the predicted inhibitor-bound TRAP1 states.
Our strategy provides a comparative MD–ML framework to infer
allosteric ligand functionality. Alleviating the time scale issues
which prevent the routine use of MD, a combination of MD and ML represents
a promising strategy to support in silico mechanistic
studies and drug design.
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Affiliation(s)
- Mariarosaria Ferraro
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC, Via Mario Bianco 9, 20131 Milano, Italy
| | - Elisabetta Moroni
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC, Via Mario Bianco 9, 20131 Milano, Italy
| | - Emiliano Ippoliti
- Institute for Advanced Simulation (IAS-5) and Institute of Neuroscience and Medicine (INM-9), Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany.,JARA-HPC, Forschungszentrum Jülich, D-54245 Jülich, Germany
| | - Silvia Rinaldi
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC, Via Mario Bianco 9, 20131 Milano, Italy
| | - Carlos Sanchez-Martin
- Dipartimento di Scienze Biomediche, Università di Padova, viale G. Colombo 3, 35131 Padova, Italy
| | - Andrea Rasola
- Dipartimento di Scienze Biomediche, Università di Padova, viale G. Colombo 3, 35131 Padova, Italy
| | - Luca F Pavarino
- Dipartimento di Matematica "F. Casorati", Università di Pavia, Via Ferrata 5, 27100 Pavia Italy
| | - Giorgio Colombo
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC, Via Mario Bianco 9, 20131 Milano, Italy.,Dipartimento di Chimica, Università di Pavia, via Taramelli 12, 27100 Pavia, Italy
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43
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Salladini E, Jørgensen MLM, Theisen FF, Skriver K. Intrinsic Disorder in Plant Transcription Factor Systems: Functional Implications. Int J Mol Sci 2020; 21:E9755. [PMID: 33371315 PMCID: PMC7767404 DOI: 10.3390/ijms21249755] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 01/07/2023] Open
Abstract
Eukaryotic cells are complex biological systems that depend on highly connected molecular interaction networks with intrinsically disordered proteins as essential components. Through specific examples, we relate the conformational ensemble nature of intrinsic disorder (ID) in transcription factors to functions in plants. Transcription factors contain large regulatory ID-regions with numerous orphan sequence motifs, representing potential important interaction sites. ID-regions may affect DNA-binding through electrostatic interactions or allosterically as for the bZIP transcription factors, in which the DNA-binding domains also populate ensembles of dynamic transient structures. The flexibility of ID is well-suited for interaction networks requiring efficient molecular adjustments. For example, Radical Induced Cell Death1 depends on ID in transcription factors for its numerous, structurally heterogeneous interactions, and the JAZ:MYC:MED15 regulatory unit depends on protein dynamics, including binding-associated unfolding, for regulation of jasmonate-signaling. Flexibility makes ID-regions excellent targets of posttranslational modifications. For example, the extent of phosphorylation of the NAC transcription factor SOG1 regulates target gene expression and the DNA-damage response, and phosphorylation of the AP2/ERF transcription factor DREB2A acts as a switch enabling heat-regulated degradation. ID-related phase separation is emerging as being important to transcriptional regulation with condensates functioning in storage and inactivation of transcription factors. The applicative potential of ID-regions is apparent, as removal of an ID-region of the AP2/ERF transcription factor WRI1 affects its stability and consequently oil biosynthesis. The highlighted examples show that ID plays essential functional roles in plant biology and has a promising potential in engineering.
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Affiliation(s)
| | | | | | - Karen Skriver
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark; (E.S.); (M.L.M.J.); (F.F.T.)
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44
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Zhao Z, Wang JCY, Segura CP, Hadden-Perilla JA, Zlotnick A. The Integrity of the Intradimer Interface of the Hepatitis B Virus Capsid Protein Dimer Regulates Capsid Self-Assembly. ACS Chem Biol 2020; 15:3124-3132. [PMID: 32459465 DOI: 10.1021/acschembio.0c00277] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
During the hepatitis B virus lifecycle, 120 copies of homodimeric capsid protein assemble around a copy of reverse transcriptase and viral RNA and go on to produce an infectious virion. Assembly needs to be tightly regulated by protein conformational change to ensure symmetry, fidelity, and reproducibility. Here, we show that structures at the intradimer interface regulate conformational changes at the distal interdimer interface and so regulate assembly. A pair of interacting charged residues, D78 from each monomer, conspicuously located at the top of a four-helix bundle that forms the intradimer interface, were mutated to serine to disrupt communication between the two monomers. The mutation slowed assembly and destabilized the dimer to thermal and chemical denaturation. Mutant dimers showed evidence of transient partial unfolding based on the appearance of new proteolytically sensitive sites. Though the mutant dimer was less stable, the resulting capsids were as stable as the wildtype, based on assembly and thermal denaturation studies. Cryo-EM image reconstructions of capsid indicated that the subunits adopted an "open" state more usually associated with a free dimer and that the spike tips were either disordered or highly flexible. Molecular dynamics simulations provide mechanistic explanations for these results, suggesting that D78 stabilizes helix 4a, which forms part of the intradimer interface, by capping its N-terminus and hydrogen-bonding to nearby residues, whereas the D78S mutation disrupts these interactions, leading to partial unwinding of helix 4a. This in turn weakens the connection from helix 4 and the intradimer interface to helix 5, which forms the interdimer interface.
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Affiliation(s)
- Zhongchao Zhao
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana 47405, United States
| | - Joseph Che-Yen Wang
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana 47405, United States
- Indiana University Electron Microscopy Center, Indiana University, Bloomington, Indiana 47405, United States
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Carolina Pérez Segura
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Jodi A. Hadden-Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Adam Zlotnick
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana 47405, United States
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45
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Hong S, Choi S, Kim R, Koh J. Mechanisms of Macromolecular Interactions Mediated by Protein Intrinsic Disorder. Mol Cells 2020; 43:899-908. [PMID: 33243935 PMCID: PMC7700844 DOI: 10.14348/molcells.2020.0186] [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: 09/11/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 12/29/2022] Open
Abstract
Intrinsically disordered proteins or regions (IDPs or IDRs) are widespread in the eukaryotic proteome. Although lacking stable three-dimensional structures in the free forms, IDRs perform critical functions in various cellular processes. Accordingly, mutations and altered expression of IDRs are associated with many pathological conditions. Hence, it is of great importance to understand at the molecular level how IDRs interact with their binding partners. In particular, discovering the unique interaction features of IDRs originating from their dynamic nature may reveal uncharted regulatory mechanisms of specific biological processes. Here we discuss the mechanisms of the macromolecular interactions mediated by IDRs and present the relevant cellular processes including transcription, cell cycle progression, signaling, and nucleocytoplasmic transport. Of special interest is the multivalent binding nature of IDRs driving assembly of multicomponent macromolecular complexes. Integrating the previous theoretical and experimental investigations, we suggest that such IDR-driven multiprotein complexes can function as versatile allosteric switches to process diverse cellular signals. Finally, we discuss the future challenges and potential medical applications of the IDR research.
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Affiliation(s)
- Sunghyun Hong
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Sangmin Choi
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Ryeonghyeon Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Junseock Koh
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
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46
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Pelham JF, Dunlap JC, Hurley JM. Intrinsic disorder is an essential characteristic of components in the conserved circadian circuit. Cell Commun Signal 2020; 18:181. [PMID: 33176800 PMCID: PMC7656774 DOI: 10.1186/s12964-020-00658-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/06/2020] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION The circadian circuit, a roughly 24 h molecular feedback loop, or clock, is conserved from bacteria to animals and allows for enhanced organismal survival by facilitating the anticipation of the day/night cycle. With circadian regulation reportedly impacting as high as 80% of protein coding genes in higher eukaryotes, the protein-based circadian clock broadly regulates physiology and behavior. Due to the extensive interconnection between the clock and other cellular systems, chronic disruption of these molecular rhythms leads to a decrease in organismal fitness as well as an increase of disease rates in humans. Importantly, recent research has demonstrated that proteins comprising the circadian clock network display a significant amount of intrinsic disorder. MAIN BODY In this work, we focus on the extent of intrinsic disorder in the circadian clock and its potential mechanistic role in circadian timing. We highlight the conservation of disorder by quantifying the extent of computationally-predicted protein disorder in the core clock of the key eukaryotic circadian model organisms Drosophila melanogaster, Neurospora crassa, and Mus musculus. We further examine previously published work, as well as feature novel experimental evidence, demonstrating that the core negative arm circadian period drivers FREQUENCY (Neurospora crassa) and PERIOD-2 (PER2) (Mus musculus), possess biochemical characteristics of intrinsically disordered proteins. Finally, we discuss the potential contributions of the inherent biophysical principals of intrinsically disordered proteins that may explain the vital mechanistic roles they play in the clock to drive their broad evolutionary conservation in circadian timekeeping. CONCLUSION The pervasive conservation of disorder amongst the clock in the crown eukaryotes suggests that disorder is essential for optimal circadian timing from fungi to animals, providing vital homeostatic cellular maintenance and coordinating organismal physiology across phylogenetic kingdoms. Video abstract.
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Affiliation(s)
- Jacqueline F. Pelham
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180 USA
| | - Jay C. Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
| | - Jennifer M. Hurley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180 USA
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12018 USA
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47
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Tee WV, Guarnera E, Berezovsky IN. Disorder driven allosteric control of protein activity. Curr Res Struct Biol 2020; 2:191-203. [PMID: 34235479 PMCID: PMC8244471 DOI: 10.1016/j.crstbi.2020.09.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/27/2020] [Accepted: 09/02/2020] [Indexed: 12/23/2022] Open
Abstract
Studies of protein allostery increasingly reveal an involvement of the back and forth order-disorder transitions in this mechanism of protein activity regulation. Here, we investigate the allosteric mechanisms mediated by structural disorder using the structure-based statistical mechanical model of allostery (SBSMMA) that we have previously developed. We show that SBSMMA accounts for the energetics and causality of allosteric communication underlying dimerization of the BirA biotin repressor, activation of the sortase A enzyme, and inhibition of the Rac1 GTPase. Using the SBSMMA, we also show that introducing structural order or disorder in various regions of esterases can originate tunable allosteric modulation of the catalytic triad. On the basis of obtained results, we propose that operating with the order-disorder continuum allows one to establish an allosteric control scale for achieving desired modulation of the protein activity. Back and forth order-disorder transitions can induce allosteric signaling. Allosteric signaling originated by order/disorder follow universal rules. Allosteric control scale facilitates engineering of the protein activity regulation.
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Affiliation(s)
- Wei-Ven Tee
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A∗STAR), 30 Biopolis Street, #07-01, Matrix 138671, Singapore.,Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive 117597, Singapore
| | - Enrico Guarnera
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A∗STAR), 30 Biopolis Street, #07-01, Matrix 138671, Singapore
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A∗STAR), 30 Biopolis Street, #07-01, Matrix 138671, Singapore.,Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive 117597, Singapore
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48
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NFAT5, which protects against hypertonicity, is activated by that stress via structuring of its intrinsically disordered domain. Proc Natl Acad Sci U S A 2020; 117:20292-20297. [PMID: 32747529 DOI: 10.1073/pnas.1911680117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Nuclear Factor of Activated T cells 5 (NFAT5) is a transcription factor (TF) that mediates protection from adverse effects of hypertonicity by increasing transcription of genes, including those that lead to cellular accumulation of protective organic osmolytes. NFAT5 has three intrinsically ordered (ID) activation domains (ADs). Using the NFAT5 N-terminal domain (NTD), which contains AD1, as a model, we demonstrate by biophysical methods that the NTD senses osmolytes and hypertonicity, resulting in stabilization of its ID regions. In the presence of sufficient NaCl or osmolytes, trehalose and sorbitol, the NFAT5 NTD undergoes a disorder-to-order shift, adopting higher average secondary and tertiary structure. Thus, NFAT5 is activated by the stress that it protects against. In its salt and/or osmolyte-induced more ordered conformation, the NTD interacts with several proteins, including HMGI-C, which is known to protect against apoptosis. These findings raise the possibility that the increased intracellular ionic strength and elevated osmolytes caused by hypertonicity activate and stabilize NFAT5.
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49
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Jang H, Kwon S, Jeong CS, Lee CW, Hwang J, Jung KH, Lee JH, Park HH. Structural analysis of a novel substrate-free form of the aminoglycoside 6'-N-acetyltransferase from Enterococcus faecium. Acta Crystallogr F Struct Biol Commun 2020; 76:364-371. [PMID: 32744248 PMCID: PMC7397467 DOI: 10.1107/s2053230x20009735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/16/2020] [Indexed: 11/10/2022] Open
Abstract
Aminoglycoside acetyltransferases (AACs) catalyze the transfer of an acetyl group between acetyl-CoA and an aminoglycoside, producing CoA and an acetylated aminoglycoside. AAC(6')-Ii enzymes target the amino group linked to the 6' C atom in an aminoglycoside. Several structures of the AAC(6')-Ii from Enterococcus faecium [Ef-AAC(6')-Ii] have been reported to date. However, the detailed mechanism of its enzymatic function remains elusive. In this study, the crystal structure of Ef-AAC(6')-Ii was determined in a novel substrate-free form. Based on structural analysis, it is proposed that Ef-AAC(6')-Ii sequentially undergoes conformational selection and induced fit for substrate binding. These results therefore provide a novel viewpoint on the mechanism of action of Ef-AAC(6')-Ii.
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Affiliation(s)
- Hyunseok Jang
- College of Pharmacy, Chung-Ang University, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Sunghark Kwon
- College of Pharmacy, Chung-Ang University, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Chang-Sook Jeong
- Unit of Research for Practical Application, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Chang Woo Lee
- Unit of Research for Practical Application, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jisub Hwang
- Unit of Research for Practical Application, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Kyoung Ho Jung
- College of Pharmacy, Chung-Ang University, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Jun Hyuck Lee
- Unit of Research for Practical Application, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Dongjak-gu, Seoul 06974, Republic of Korea
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50
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Lagunes L, Bardwell L, Enciso GA. Effect of magnitude and variability of energy of activation in multisite ultrasensitive biochemical processes. PLoS Comput Biol 2020; 16:e1007966. [PMID: 32760072 PMCID: PMC7444825 DOI: 10.1371/journal.pcbi.1007966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 08/24/2020] [Accepted: 05/19/2020] [Indexed: 11/18/2022] Open
Abstract
Protein activity is often regulated by ligand binding or by post-translational modifications such as phosphorylation. Moreover, proteins that are regulated in this way often contain multiple ligand binding sites or modification sites, which can operate to create an ultrasensitive dose response. Here, we consider the contribution of the individual modification/binding sites to the activation process, and how their individual values affect the ultrasensitive behavior of the overall system. We use a generalized Monod-Wyman-Changeux (MWC) model that allows for variable conformational free energy contributions from distinct sites, and associate a so-called activation parameter to each site. Our analysis shows that the ultrasensitivity generally increases as the conformational free energy contribution from one or more sites is strengthened. Furthermore, ultrasensitivity depends on the mean of the activation parameters and not on their variability. In some cases, we find that the best way to maximize ultrasensitivity is to make the contribution from all sites as strong as possible. These results provide insights into the performance objectives of multiple modification/binding sites and thus help gain a greater understanding of signaling and its role in diseases.
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Affiliation(s)
- Leonila Lagunes
- Developmental and Cell Biology Department, University of California Irvine, California, United States of America
| | - Lee Bardwell
- Developmental and Cell Biology Department, University of California Irvine, California, United States of America
| | - German A. Enciso
- Developmental and Cell Biology Department, University of California Irvine, California, United States of America
- Mathematics Department, University of California Irvine, California, United States of America
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