1
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Bock A, Irannejad R, Scott JD. cAMP signaling: a remarkably regional affair. Trends Biochem Sci 2024; 49:305-317. [PMID: 38310024 PMCID: PMC11175624 DOI: 10.1016/j.tibs.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/22/2023] [Accepted: 01/10/2024] [Indexed: 02/05/2024]
Abstract
Louis Pasteur once famously said 'in the fields of observation chance favors only the prepared mind'. Much of chance is being in the right place at the right time. This is particularly true in the crowded molecular environment of the cell where being in the right place is often more important than timing. Although Brownian motion argues that enzymes will eventually bump into substrates, this probability is greatly enhanced if both molecules reside in the same subcellular compartment. However, activation of cell signaling enzymes often requires the transmission of chemical signals from extracellular stimuli to intracellular sites of action. This review highlights new developments in our understanding of cAMP generation and the 3D utilization of this second messenger inside cells.
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Affiliation(s)
- Andreas Bock
- Rudolf Boehm Institute of Pharmacology and Toxicology, Medical Faculty, Leipzig University, 04107 Leipzig, Germany.
| | - Roshanak Irannejad
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - John D Scott
- Department of Pharmacology, University of Washington Medical Center, Seattle, WA 98195, USA.
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2
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Alderson TR, Pritišanac I, Kolarić Đ, Moses AM, Forman-Kay JD. Systematic identification of conditionally folded intrinsically disordered regions by AlphaFold2. Proc Natl Acad Sci U S A 2023; 120:e2304302120. [PMID: 37878721 PMCID: PMC10622901 DOI: 10.1073/pnas.2304302120] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 08/30/2023] [Indexed: 10/27/2023] Open
Abstract
The AlphaFold Protein Structure Database contains predicted structures for millions of proteins. For the majority of human proteins that contain intrinsically disordered regions (IDRs), which do not adopt a stable structure, it is generally assumed that these regions have low AlphaFold2 confidence scores that reflect low-confidence structural predictions. Here, we show that AlphaFold2 assigns confident structures to nearly 15% of human IDRs. By comparison to experimental NMR data for a subset of IDRs that are known to conditionally fold (i.e., upon binding or under other specific conditions), we find that AlphaFold2 often predicts the structure of the conditionally folded state. Based on databases of IDRs that are known to conditionally fold, we estimate that AlphaFold2 can identify conditionally folding IDRs at a precision as high as 88% at a 10% false positive rate, which is remarkable considering that conditionally folded IDR structures were minimally represented in its training data. We find that human disease mutations are nearly fivefold enriched in conditionally folded IDRs over IDRs in general and that up to 80% of IDRs in prokaryotes are predicted to conditionally fold, compared to less than 20% of eukaryotic IDRs. These results indicate that a large majority of IDRs in the proteomes of human and other eukaryotes function in the absence of conditional folding, but the regions that do acquire folds are more sensitive to mutations. We emphasize that the AlphaFold2 predictions do not reveal functionally relevant structural plasticity within IDRs and cannot offer realistic ensemble representations of conditionally folded IDRs.
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Affiliation(s)
- T. Reid Alderson
- Department of Biochemistry, University of Toronto, Toronto, ONM5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ONM5S 1A8, Canada
| | - Iva Pritišanac
- Department of Cell and Systems Biology, University of Toronto, Toronto, ONM5S 35G, Canada
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ONM5G 0A4, Canada
- Department of Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz8010, Austria
| | - Đesika Kolarić
- Department of Molecular Biology and Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz8010, Austria
| | - Alan M. Moses
- Department of Cell and Systems Biology, University of Toronto, Toronto, ONM5S 35G, Canada
| | - Julie D. Forman-Kay
- Department of Biochemistry, University of Toronto, Toronto, ONM5S 1A8, Canada
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ONM5G 0A4, Canada
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3
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Escobedo A, Piccirillo J, Aranda J, Diercks T, Mateos B, Garcia-Cabau C, Sánchez-Navarro M, Topal B, Biesaga M, Staby L, Kragelund BB, García J, Millet O, Orozco M, Coles M, Crehuet R, Salvatella X. A glutamine-based single α-helix scaffold to target globular proteins. Nat Commun 2022; 13:7073. [PMID: 36400768 PMCID: PMC9674830 DOI: 10.1038/s41467-022-34793-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022] Open
Abstract
The binding of intrinsically disordered proteins to globular ones can require the folding of motifs into α-helices. These interactions offer opportunities for therapeutic intervention but their modulation with small molecules is challenging because they bury large surfaces. Linear peptides that display the residues that are key for binding can be targeted to globular proteins when they form stable helices, which in most cases requires their chemical modification. Here we present rules to design peptides that fold into single α-helices by instead concatenating glutamine side chain to main chain hydrogen bonds recently discovered in polyglutamine helices. The resulting peptides are uncharged, contain only natural amino acids, and their sequences can be optimized to interact with specific targets. Our results provide design rules to obtain single α-helices for a wide range of applications in protein engineering and drug design.
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Affiliation(s)
- Albert Escobedo
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain ,grid.473715.30000 0004 6475 7299Present Address: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jonathan Piccirillo
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain ,grid.428469.50000 0004 1794 1018Present Address: Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Juan Aranda
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Tammo Diercks
- grid.420161.0CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Borja Mateos
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Carla Garcia-Cabau
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Macarena Sánchez-Navarro
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina López Neyra (IPBLN-CSIC), Armilla, Granada Spain
| | - Busra Topal
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Mateusz Biesaga
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Lasse Staby
- grid.5254.60000 0001 0674 042XREPIN and Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Birthe B. Kragelund
- grid.5254.60000 0001 0674 042XREPIN and Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Jesús García
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Oscar Millet
- grid.420161.0CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Modesto Orozco
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain ,grid.5841.80000 0004 1937 0247Department of Biochemistry and Biomedicine, University of Barcelona, Avinguda Diagonal 645, 08028 Barcelona, Spain
| | - Murray Coles
- grid.419580.10000 0001 0942 1125Department of Protein Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076 Tubingen, Germany
| | - Ramon Crehuet
- grid.4711.30000 0001 2183 4846Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Xavier Salvatella
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain ,grid.425902.80000 0000 9601 989XICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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4
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Wilcox KG, Dingle ME, Saha A, Hore MJA, Morozova S. Persistence length of α-helical poly-L-lysine. SOFT MATTER 2022; 18:6550-6560. [PMID: 36039676 DOI: 10.1039/d2sm00921h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The α-helix has a significant role in protein function and structure because of its rigidity. In this study, we investigate the persistence length, lp, of α-helical poly-L-lysine, PLL, for two molecular weights. PLL experiences a random coil-helix transition as the pH is raised from 7 to 12. Using light scattering experiments to determine the radius of gyration (Rg), hydrodynamic radius, (Rh), the shape factor (Rg/Rh), and second virial coefficient (A2), and circular dichroism to determine the helical content, we find the structure and lp of PLL as a function of pH (7.4-11.4) and ionic strength (100-166 mM). With increasing pH, we find an increase in lp from 2 nm to 15-21 nm because of α-helix formation. We performed dissipative particle dynamics (DPD) simulations and found a similar increase in lp. While this lp is less than that predicted by molecular dynamics simulations, it is consistent with other experimental results, which quantify the mechanics of α-helices. By determining the mechanics of helical polypeptides like PLL, we can further understand their implications to protein function.
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Affiliation(s)
- Kathryn G Wilcox
- Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH, USA.
| | - Marlee E Dingle
- Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH, USA.
| | - Ankit Saha
- Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH, USA.
| | - Michael J A Hore
- Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH, USA.
| | - Svetlana Morozova
- Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH, USA.
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5
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De novo design of discrete, stable 3 10-helix peptide assemblies. Nature 2022; 607:387-392. [PMID: 35732733 DOI: 10.1038/s41586-022-04868-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/13/2022] [Indexed: 02/02/2023]
Abstract
The α-helix is pre-eminent in structural biology1 and widely exploited in protein folding2, design3 and engineering4. Although other helical peptide conformations do exist near to the α-helical region of conformational space-namely, 310-helices and π-helices5-these occur much less frequently in protein structures. Less favourable internal energies and reduced tendencies to pack into higher-order structures mean that 310-helices rarely exceed six residues in length in natural proteins, and that they tend not to form normal supersecondary, tertiary or quaternary interactions. Here we show that despite their absence in nature, synthetic peptide assemblies can be built from 310-helices. We report the rational design, solution-phase characterization and an X-ray crystal structure for water-soluble bundles of 310-helices with consolidated hydrophobic cores. The design uses six-residue repeats informed by analysing 310-helical conformations in known protein structures, and incorporates α-aminoisobutyric acid residues. Design iterations reveal a tipping point between α-helical and 310-helical folding, and identify features required for stabilizing assemblies of 310-helices. This work provides principles and rules to open opportunities for designing into this hitherto unexplored region of protein-structure space.
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6
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Kim H, Choi G, Suk ME, Kim TJ. Resource for FRET-Based Biosensor Optimization. Front Cell Dev Biol 2022; 10:885394. [PMID: 35794864 PMCID: PMC9251444 DOI: 10.3389/fcell.2022.885394] [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: 02/28/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
After the development of Cameleon, the first fluorescence resonance energy transfer (FRET)-based calcium indicator, a variety of FRET-based genetically encoded biosensors (GEBs) have visualized numerous target players to monitor their cell physiological dynamics spatiotemporally. Many attempts have been made to optimize GEBs, which require labor-intensive effort, novel approaches, and precedents to develop more sensitive and versatile biosensors. However, researchers face considerable trial and error in upgrading biosensors because examples and methods of improving FRET-based GEBs are not well documented. In this review, we organize various optimization strategies after assembling the existing cases in which the non-fluorescent components of biosensors are upgraded. In addition, promising areas to which optimized biosensors can be applied are briefly discussed. Therefore, this review could serve as a resource for researchers attempting FRET-based GEB optimization.
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Affiliation(s)
- Heonsu Kim
- Institute of Systems Biology, Pusan National University, Busan, South Korea
| | - Gyuho Choi
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Myung Eun Suk
- Department of Mechanical Engineering, IT Convergence College of Materials and Components Engineering, Dong-Eui University, Busan, South Korea
- *Correspondence: Myung Eun Suk, ; Tae-Jin Kim,
| | - Tae-Jin Kim
- Institute of Systems Biology, Pusan National University, Busan, South Korea
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
- Department of Biological Sciences, Pusan National University, Busan, South Korea
- *Correspondence: Myung Eun Suk, ; Tae-Jin Kim,
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7
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Lang EJM, Baker EG, Woolfson DN, Mulholland AJ. Generalized Born Implicit Solvent Models Do Not Reproduce Secondary Structures of De Novo Designed Glu/Lys Peptides. J Chem Theory Comput 2022; 18:4070-4076. [PMID: 35687842 PMCID: PMC9281390 DOI: 10.1021/acs.jctc.1c01172] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
We test a range of
standard generalized Born (GB) models and protein
force fields for a set of five experimentally characterized, designed
peptides comprising alternating blocks of glutamate and lysine, which
have been shown to differ significantly in α-helical content.
Sixty-five combinations of force fields and GB models are evaluated
in >800 μs of molecular dynamics simulations. GB models generally
do not reproduce the experimentally observed α-helical content,
and none perform well for all five peptides. These results illustrate
that these models are not usefully predictive in this context. These
peptides provide a useful test set for simulation methods.
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Affiliation(s)
- Eric J M Lang
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K.,School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K.,BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Emily G Baker
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K.,BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K.,BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K.,School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K.,School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
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8
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Touma AM, Tang W, Rasicci DV, Vang D, Rai A, Previs SB, Warshaw DM, Yengo CM, Sivaramakrishnan S. Nanosurfer Assay Dissects β-Cardiac Myosin and Cardiac Myosin-Binding Protein C Interactions. Biophys J 2022; 121:2449-2460. [PMID: 35591788 DOI: 10.1016/j.bpj.2022.05.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 04/13/2022] [Accepted: 05/13/2022] [Indexed: 11/02/2022] Open
Abstract
Cardiac myosin-binding protein C (cMyBP-C) modulates cardiac contractility through putative interactions with the myosin S2 tail and/or the thin filament. The relative contribution of these binding-partner interactions to cMyBP-C modulatory function remains unclear. Hence, we developed a "nanosurfer" assay as a model system to interrogate these cMyBP-C binding-partner interactions. Synthetic thick filaments were generated using recombinant human β-cardiac myosin subfragments (HMM or S1) attached to DNA nanotubes, with 14 or 28 nm spacing, corresponding to the 14.3 nm myosin spacing in native thick filaments. The nanosurfer assay consists of DNA nanotubes added to the in vitro motility assay so that myosins on the motility surface effectively deliver thin filaments to the DNA nanotubes, enhancing thin filament gliding probability on the DNA nanotubes. Thin filament velocities on nanotubes with either 14 or 28 nm myosin spacing were no different. We then characterized the effects of cMyBP-C on thin filament motility by alternating HMM and cMyBP-C N-terminal fragments (C0-C2 or C1-C2) on nanotubes every 14 nm. Both C0-C2 and C1-C2 reduced thin filament velocity 4-6 fold relative to HMM alone. Similar inhibition occurred using the myosin S1 construct, which lacks the myosin S2 region proposed to interact with cMyBP-C, suggesting that the cMyBP-C N-terminus must interact with other myosin head domains and/or actin to slow thin filament velocity. Thin filament velocity was unaffected by the C0-C1f fragment, which lacks the majority of the M-domain, supporting the importance of this domain for inhibitory interaction(s). A C0-C2 fragment with phosphomimetic replacement in the M-domain showed markedly less inhibition of thin filament velocity compared to its phosphonull counterpart, highlighting the modulatory role of M-domain phosphorylation on cMyBP-C function. Therefore, the nanosurfer assay provides a platform to precisely manipulate spatially dependent cMyBP-C binding partner interactions, shedding light on the molecular regulation of β-cardiac myosin contractility.
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Affiliation(s)
- Anja M Touma
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Wanjian Tang
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - David V Rasicci
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Duha Vang
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Ashim Rai
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Samantha B Previs
- Department of Molecular Physiology and Biophysics, Cardiovascular Research Institute, University of Vermont, Burlington, VT
| | - David M Warshaw
- Department of Molecular Physiology and Biophysics, Cardiovascular Research Institute, University of Vermont, Burlington, VT
| | - Christopher M Yengo
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA.
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9
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Zhao VY, Rodrigues JV, Lozovsky ER, Hartl DL, Shakhnovich EI. Switching an active site helix in dihydrofolate reductase reveals limits to subdomain modularity. Biophys J 2021; 120:4738-4750. [PMID: 34571014 PMCID: PMC8595743 DOI: 10.1016/j.bpj.2021.09.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/14/2021] [Accepted: 09/22/2021] [Indexed: 11/23/2022] Open
Abstract
To what degree are individual structural elements within proteins modular such that similar structures from unrelated proteins can be interchanged? We study subdomain modularity by creating 20 chimeras of an enzyme, Escherichia coli dihydrofolate reductase (DHFR), in which a catalytically important, 10-residue α-helical sequence is replaced by α-helical sequences from a diverse set of proteins. The chimeras stably fold but have a range of diminished thermal stabilities and catalytic activities. Evolutionary coupling analysis indicates that the residues of this α-helix are under selection pressure to maintain catalytic activity in DHFR. Reversion to phenylalanine at key position 31 was found to partially restore catalytic activity, which could be explained by evolutionary coupling values. We performed molecular dynamics simulations using replica exchange with solute tempering. Chimeras with low catalytic activity exhibit nonhelical conformations that block the binding site and disrupt the positioning of the catalytically essential residue D27. Simulation observables and in vitro measurements of thermal stability and substrate-binding affinity are strongly correlated. Several E. coli strains with chromosomally integrated chimeric DHFRs can grow, with growth rates that follow predictions from a kinetic flux model that depends on the intracellular abundance and catalytic activity of DHFR. Our findings show that although α-helices are not universally substitutable, the molecular and fitness effects of modular segments can be predicted by the biophysical compatibility of the replacement segment.
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Affiliation(s)
- Victor Y Zhao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - João V Rodrigues
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Elena R Lozovsky
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts.
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10
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Collu G, Bierig T, Krebs AS, Engilberge S, Varma N, Guixà-González R, Sharpe T, Deupi X, Olieric V, Poghosyan E, Benoit RM. Chimeric single α-helical domains as rigid fusion protein connections for protein nanotechnology and structural biology. Structure 2021; 30:95-106.e7. [PMID: 34587504 DOI: 10.1016/j.str.2021.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/17/2021] [Accepted: 09/08/2021] [Indexed: 12/19/2022]
Abstract
Chimeric fusion proteins are essential tools for protein nanotechnology. Non-optimized protein-protein connections are usually flexible and therefore unsuitable as structural building blocks. Here we show that the ER/K motif, a single α-helical domain (SAH), can be seamlessly fused to terminal helices of proteins, forming an extended, partially free-standing rigid helix. This enables the connection of two domains at a defined distance and orientation. We designed three constructs termed YFPnano, T4Lnano, and MoStoNano. Analysis of experimentally determined structures and molecular dynamics simulations reveals a certain degree of plasticity in the connections that allows the adaptation to crystal contact opportunities. Our data show that SAHs can be stably integrated into designed structural elements, enabling new possibilities for protein nanotechnology, for example, to improve the exposure of epitopes on nanoparticles (structural vaccinology), to engineer crystal contacts with minimal impact on construct flexibility (for the study of protein dynamics), and to design novel biomaterials.
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Affiliation(s)
- Gabriella Collu
- Laboratory of Nanoscale Biology, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Tobias Bierig
- Laboratory of Nanoscale Biology, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Anna-Sophia Krebs
- Laboratory of Nanoscale Biology, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Sylvain Engilberge
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Niveditha Varma
- Laboratory of Nanoscale Biology, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Ramon Guixà-González
- Condensed Matter Theory Group, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Timothy Sharpe
- Biophysics Core Facility, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Xavier Deupi
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland; Condensed Matter Theory Group, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Emiliya Poghosyan
- Laboratory of Nanoscale Biology, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Roger M Benoit
- Laboratory of Nanoscale Biology, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland.
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11
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High rates of calcium-free diffusion in the cytosol of living cells. Biophys J 2021; 120:3960-3972. [PMID: 34454909 DOI: 10.1016/j.bpj.2021.08.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/07/2021] [Accepted: 08/11/2021] [Indexed: 11/20/2022] Open
Abstract
Calcium (Ca2+) is a universal second messenger that participates in the regulation of innumerous physiological processes. The way in which local elevations of the cytosolic Ca2+ concentration spread in space and time is key for the versatility of the signals. Ca2+ diffusion in the cytosol is hindered by its interaction with proteins that act as buffers. Depending on the concentrations and the kinetics of the interactions, there is a large range of values at which Ca2+ diffusion can proceed. Having reliable estimates of this range, particularly of its highest end, which corresponds to the ions free diffusion, is key to understand how the signals propagate. In this work, we present the first experimental results with which the Ca2+-free diffusion coefficient is directly quantified in the cytosol of living cells. By means of fluorescence correlation spectroscopy experiments performed in Xenopus laevis oocytes and in cells of Saccharomyces cerevisiae, we show that the ions can freely diffuse in the cytosol at a higher rate than previously thought.
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12
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Petzoldt AG, Götz TWB, Driller JH, Lützkendorf J, Reddy-Alla S, Matkovic-Rachid T, Liu S, Knoche E, Mertel S, Ugorets V, Lehmann M, Ramesh N, Beuschel CB, Kuropka B, Freund C, Stelzl U, Loll B, Liu F, Wahl MC, Sigrist SJ. RIM-binding protein couples synaptic vesicle recruitment to release sites. J Cell Biol 2021; 219:151735. [PMID: 32369542 PMCID: PMC7337501 DOI: 10.1083/jcb.201902059] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 02/03/2020] [Accepted: 04/07/2020] [Indexed: 11/24/2022] Open
Abstract
At presynaptic active zones, arrays of large conserved scaffold proteins mediate fast and temporally precise release of synaptic vesicles (SVs). SV release sites could be identified by clusters of Munc13, which allow SVs to dock in defined nanoscale relation to Ca2+ channels. We here show in Drosophila that RIM-binding protein (RIM-BP) connects release sites physically and functionally to the ELKS family Bruchpilot (BRP)-based scaffold engaged in SV recruitment. The RIM-BP N-terminal domain, while dispensable for SV release site organization, was crucial for proper nanoscale patterning of the BRP scaffold and needed for SV recruitment of SVs under strong stimulation. Structural analysis further showed that the RIM-BP fibronectin domains form a “hinge” in the protein center, while the C-terminal SH3 domain tandem binds RIM, Munc13, and Ca2+ channels release machinery collectively. RIM-BPs’ conserved domain architecture seemingly provides a relay to guide SVs from membrane far scaffolds into membrane close release sites.
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Affiliation(s)
- Astrid G Petzoldt
- Freie Universität Berlin, Institute for Biology and Genetics, Berlin, Germany
| | - Torsten W B Götz
- Freie Universität Berlin, Institute for Biology and Genetics, Berlin, Germany
| | - Jan Heiner Driller
- Freie Universität Berlin, Institute of Chemistry and Biochemistry/Structural Biochemistry Berlin, Berlin, Germany
| | - Janine Lützkendorf
- Freie Universität Berlin, Institute for Biology and Genetics, Berlin, Germany
| | - Suneel Reddy-Alla
- Freie Universität Berlin, Institute for Biology and Genetics, Berlin, Germany
| | | | - Sunbin Liu
- Freie Universität Berlin, Institute of Chemistry and Biochemistry/Structural Biochemistry Berlin, Berlin, Germany
| | - Elena Knoche
- Freie Universität Berlin, Institute for Biology and Genetics, Berlin, Germany
| | - Sara Mertel
- Freie Universität Berlin, Institute for Biology and Genetics, Berlin, Germany
| | - Vladimir Ugorets
- Freie Universität Berlin, Institute for Biology and Genetics, Berlin, Germany
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V., Campus Berlin-Buch, Berlin, Germany
| | - Niraja Ramesh
- Freie Universität Berlin, Institute for Biology and Genetics, Berlin, Germany
| | | | - Benno Kuropka
- Universität Berlin, Institute for Chemistry and Biochemistry, Berlin, Germany
| | - Christian Freund
- Universität Berlin, Institute for Chemistry and Biochemistry, Berlin, Germany
| | - Ulrich Stelzl
- Institut für Pharmazeutische Wissenschaften, Graz, Austria
| | - Bernhard Loll
- Freie Universität Berlin, Institute of Chemistry and Biochemistry/Structural Biochemistry Berlin, Berlin, Germany
| | - Fan Liu
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V., Campus Berlin-Buch, Berlin, Germany
| | - Markus C Wahl
- Freie Universität Berlin, Institute of Chemistry and Biochemistry/Structural Biochemistry Berlin, Berlin, Germany.,Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Berlin, Germany
| | - Stephan J Sigrist
- Freie Universität Berlin, Institute for Biology and Genetics, Berlin, Germany.,NeuroCure, Charité, Berlin, Germany
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13
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β2-adrenoceptor ligand efficacy is tuned by a two-stage interaction with the Gαs C terminus. Proc Natl Acad Sci U S A 2021; 118:2017201118. [PMID: 33836582 DOI: 10.1073/pnas.2017201118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Classical pharmacological models have incorporated an "intrinsic efficacy" parameter to capture system-independent effects of G protein-coupled receptor (GPCR) ligands. However, the nonlinear serial amplification of downstream signaling limits quantitation of ligand intrinsic efficacy. A recent biophysical study has characterized a ligand "molecular efficacy" that quantifies the influence of ligand-dependent receptor conformation on G protein activation. Nonetheless, the structural translation of ligand molecular efficacy into G protein activation remains unclear and forms the focus of this study. We first establish a robust, accessible, and sensitive assay to probe GPCR interaction with G protein and the Gα C terminus (G-peptide), an established structural determinant of G protein selectivity. We circumvent the need for extensive purification protocols by the single-step incorporation of receptor and G protein elements into giant plasma membrane vesicles (GPMVs). We use previously established SPASM FRET sensors to control the stoichiometry and effective concentration of receptor-G protein interactions. We demonstrate that GPMV-incorporated sensors (v-SPASM sensors) provide enhanced dynamic range, expression-insensitive readout, and a reagent level assay that yields single point measurements of ligand molecular efficacy. Leveraging this technology, we establish the receptor-G-peptide interaction as a sufficient structural determinant of this receptor-level parameter. Combining v-SPASM measurements with molecular dynamics (MD) simulations, we elucidate a two-stage receptor activation mechanism, wherein receptor-G-peptide interactions in an intermediate orientation alter the receptor conformational landscape to facilitate engagement of a fully coupled orientation that tunes G protein activation.
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14
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Gräwe A, Stein V. Linker Engineering in the Context of Synthetic Protein Switches and Sensors. Trends Biotechnol 2020; 39:731-744. [PMID: 33293101 DOI: 10.1016/j.tibtech.2020.11.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 12/17/2022]
Abstract
Linkers play critical roles in the construction of synthetic protein switches and sensors as they functionally couple a receptor with an actuator. With an increasing number of molecular toolboxes and experimental strategies becoming available that can be applied to engineer protein switches and sensors with tailored response functions, optimising the connecting linkers remains an idiosyncratic and empiric process. This review aims to provide an in-depth analysis of linker motifs, the biophysical properties they confer, and how they impact the performance of synthetic protein switches and sensors while identifying trends, mechanisms, and strategies that underlie the most potent switches and sensors.
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Affiliation(s)
- Alexander Gräwe
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany; Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany
| | - Viktor Stein
- Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany; Centre for Synthetic Biology, TU Darmstadt, 64283 Darmstadt, Germany.
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15
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Touma AM, Malik RU, Gupte T, Sivaramakrishnan S. Allosteric modulation of adenosine A1 and cannabinoid 1 receptor signaling by G-peptides. Pharmacol Res Perspect 2020; 8:e00673. [PMID: 33124765 PMCID: PMC7596666 DOI: 10.1002/prp2.673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 01/18/2023] Open
Abstract
While allosteric modulation of GPCR signaling has gained prominence to address the need for receptor specificity, efforts have mainly focused on allosteric sites adjacent to the orthosteric ligand-binding pocket and lipophilic molecules that target transmembrane helices. In this study, we examined the allosteric influence of native peptides derived from the C-terminus of the Gα subunit (G-peptides) on signaling from two Gi-coupled receptors, adenosine A1 receptor (A1 R) and cannabinoid receptor 1 (CB1 ). We expressed A1 R and CB1 fusions with G-peptides derived from Gαs, Gαi, and Gαq in HEK 293 cells using systematic protein affinity strength modulation (SPASM) and monitored the impact on downstream signaling in the cell compared to a construct lacking G-peptides. We used agonists N6 -Cyclopentyladenosine (CPA) and 5'-N-Ethylcarboxamidoadenosine (NECA) for A1 R and 2-Arachidonoylglycerol (2-AG) and WIN 55,212-2 mesylate (WN) for CB1 . G-peptides derived from Gαi and Gαq enhance agonist-dependent cAMP inhibition, demonstrating their effect as positive allosteric modulators of Gi-coupled signaling. In contrast, both G-peptides suppress agonist-dependent IP1 levels suggesting that they differentially function as negative allosteric modulators of Gq-coupled signaling. Taken together with our previous studies on Gs-coupled receptors, this study provides an extended model for the allosteric effects of G-peptides on GPCR signaling, and highlights their potential as probe molecules to enhance receptor specificity.
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Affiliation(s)
- Anja M. Touma
- Department of Genetics, Cell Biology, and DevelopmentUniversity of MinnesotaMinneapolisMNUSA
| | - Rabia U. Malik
- Department of Genetics, Cell Biology, and DevelopmentUniversity of MinnesotaMinneapolisMNUSA
| | - Tejas Gupte
- Department of Genetics, Cell Biology, and DevelopmentUniversity of MinnesotaMinneapolisMNUSA
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16
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Gupte TM, Ritt M, Sivaramakrishnan S. ER/K-link-Leveraging a native protein linker to probe dynamic cellular interactions. Methods Enzymol 2020; 647:173-208. [PMID: 33482988 PMCID: PMC8009693 DOI: 10.1016/bs.mie.2020.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
ER/K α-helices are a subset of single alpha helical domains, which exhibit unusual stability as isolated protein secondary structures. They adopt an elongated structural conformation, while regulating the frequency of interactions between proteins or polypeptides fused to their ends. Here we review recent advances on the structure, stability and function of ER/K α-helices as linkers (ER/K linkers) in native proteins. We describe methodological considerations in the molecular cloning, protein expression and measurement of interaction strengths, using sensors incorporating ER/K linkers. We highlight biological insights obtained over the last decade by leveraging distinct biophysical features of ER/K-linked sensors. We conclude with the outlook for the use of ER/K linkers in the selective modulation of dynamic cellular interactions.
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Affiliation(s)
- Tejas M Gupte
- Department of Genetics, Cell Biology, and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States
| | - Michael Ritt
- Department of Genetics, Cell Biology, and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology, and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States.
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17
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Kumari T, Verma DP, Afshan T, Verma NK, Pant G, Ali M, Shukla PK, Mitra K, Ghosh JK. A Noncytotoxic Temporin L Analogue with In Vivo Antibacterial and Antiendotoxin Activities and a Nonmembrane-Lytic Mode of Action. ACS Infect Dis 2020; 6:2369-2385. [PMID: 32786286 DOI: 10.1021/acsinfecdis.0c00022] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Cytotoxic frog antimicrobial peptide Temporin L (TempL) is an attractive molecule for the design of lead antimicrobial agents due to its short size and versatile biological activities. However, noncytotoxic TempL variants with desirable biological activities have rarely been reported. TempL analogue Q3K,TempL is water-soluble and possesses a significant antiendotoxin property along with comparable cytotoxicity to TempL. A phenylalanine residue, located at the hydrophobic face of Q3K,TempL and the "d" position of its phenylalanine zipper sequence, was replaced with a cationic lysine residue. This analogue, Q3K,F8K,TempL, showed reduced hydrophobic moment and was noncytotoxic with lower antimicrobial activity. Interestingly, swapping between tryptophan at the fourth and serine at the sixth positions turned Q3K,F8K,TempL totally amphipathic as reflected by its helical wheel projection with clusters of hydrophobic and hydrophilic residues and the highest hydrophobic moment among these peptides. Surprisingly, this analogue, SW,Q3K,F8K,TempL, was as noncytotoxic as Q3K,F8K,TempL but showed augmented antimicrobial and antiendotoxin properties, comparable to that of TempL and Q3K,TempL. SW,Q3K,F8K,TempL exhibited appreciable survival of mice against P. aeruginosa infection and a lipopolysaccharide (LPS) challenge. Unlike TempL and Q3K,TempL, SW,Q3K,F8K,TempL adopted an unordered secondary structure in bacterial membrane mimetic lipid vesicles and did not permeabilize them or depolarize the bacterial membrane. Overall, the results demonstrate the design of a nontoxic TempL analogue that possesses clusters of hydrophobic and hydrophilic residues with impaired secondary structure and shows a nonmembrane-lytic mechanism and in vivo antiendotoxin and antimicrobial activities. This paradigm of design of antimicrobial peptide with clusters of hydrophobic and hydrophilic residues and high hydrophobic moment but low secondary structure could be attempted further.
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Affiliation(s)
- Tripti Kumari
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226 031, India
| | - Devesh Pratap Verma
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226 031, India
| | - Tayyaba Afshan
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226 031, India
| | - Neeraj Kumar Verma
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226 031, India
| | - Garima Pant
- Electron Microscopy Unit, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226 031, India
| | - Mehmood Ali
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226 031, India
| | - P. K. Shukla
- Microbiology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226 031, India
| | - Kalyan Mitra
- Electron Microscopy Unit, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226 031, India
| | - Jimut Kanti Ghosh
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226 031, India
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18
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Chen T, Pham H, Mohamadi A, Miller LW. Single-Chain Lanthanide Luminescence Biosensors for Cell-Based Imaging and Screening of Protein-Protein Interactions. iScience 2020; 23:101533. [PMID: 33083762 PMCID: PMC7509216 DOI: 10.1016/j.isci.2020.101533] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/23/2020] [Accepted: 09/02/2020] [Indexed: 11/27/2022] Open
Abstract
Lanthanide-based, Förster resonance energy transfer (LRET) biosensors enabled sensitive, time-gated luminescence (TGL) imaging or multiwell plate analysis of protein-protein interactions (PPIs) in living cells. We prepared stable cell lines that expressed polypeptides composed of an alpha helical linker flanked by a Tb(III) complex-binding domain, GFP, and two interacting domains at each terminus. The PPIs examined included those between FKBP12 and the rapamycin-binding domain of m-Tor (FRB) and between p53 (1–92) and HDM2 (1–128). TGL microscopy revealed dramatic differences (>500%) in donor- or acceptor-denominated, Tb(III)-to-GFP LRET ratios between open (unbound) and closed (bound) states of the biosensors. We observed much larger signal changes (>2,500%) and Z′-factors of 0.5 or more when we grew cells in 96- or 384-well plates and analyzed PPI changes using a TGL plate reader. The modular design and exceptional dynamic range of lanthanide-based LRET biosensors will facilitate versatile imaging and cell-based screening of PPIs. Non-invasive, microscopic imaging or screening of protein-protein interactions Intracellular assembly of sensor polypeptides with luminescent Tb(III) complexes High dynamic range with time-gated detection of Tb(III)-to-GFP sensitized emission
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Affiliation(s)
- Ting Chen
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Ha Pham
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Ali Mohamadi
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Lawrence W. Miller
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
- Corresponding author
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19
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Maziarz M, Park JC, Leyme A, Marivin A, Garcia-Lopez A, Patel PP, Garcia-Marcos M. Revealing the Activity of Trimeric G-proteins in Live Cells with a Versatile Biosensor Design. Cell 2020; 182:770-785.e16. [PMID: 32634377 DOI: 10.1016/j.cell.2020.06.020] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/21/2020] [Accepted: 06/08/2020] [Indexed: 12/28/2022]
Abstract
Heterotrimeric G-proteins (Gαβγ) are the main transducers of signals from GPCRs, mediating the action of countless natural stimuli and therapeutic agents. However, there are currently no robust approaches to directly measure the activity of endogenous G-proteins in cells. Here, we describe a suite of optical biosensors that detect endogenous active G-proteins with sub-second resolution in live cells. Using a modular design principle, we developed genetically encoded, unimolecular biosensors for endogenous Gα-GTP and free Gβγ: the two active species of heterotrimeric G-proteins. This design was leveraged to generate biosensors with specificity for different heterotrimeric G-proteins or for other G-proteins, such as Rho GTPases. Versatility was further validated by implementing the biosensors in multiple contexts, from characterizing cancer-associated G-protein mutants to neurotransmitter signaling in primary neurons. Overall, the versatile biosensor design introduced here enables studying the activity of endogenous G-proteins in live cells with high fidelity, temporal resolution, and convenience.
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Affiliation(s)
- Marcin Maziarz
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jong-Chan Park
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Anthony Leyme
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Arthur Marivin
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Alberto Garcia-Lopez
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Prachi P Patel
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Mikel Garcia-Marcos
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA.
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20
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Barnes CA, Shen Y, Ying J, Bax A. Modulating the Stiffness of the Myosin VI Single α-Helical Domain. Biophys J 2020; 118:1119-1128. [PMID: 32049057 DOI: 10.1016/j.bpj.2020.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/20/2019] [Accepted: 01/02/2020] [Indexed: 11/28/2022] Open
Abstract
Highly charged, single α-helical (SAH) domains contain a high percentage of Arg, Lys, and Glu residues. Their dynamic salt bridge pairing creates the exceptional stiffness of these helical rods, with a persistence length of more than 200 Å for the myosin VI SAH domain. With the aim of modulating the stiffness of the helical structure, we investigated the effect, using NMR spectroscopy, of substituting key charged Arg, Lys, Glu, and Asp residues by Gly or His. Results indicate that such mutations result in the transient breaking of the helix at the site of mutation but with noticeable impact on amide hydrogen exchange rates extending as far as ±2 helical turns, pointing to a substantial degree of cooperativity in SAH stability. Whereas a single Gly substitution caused transient breaks ∼20% of the time, two consecutive Gly substitutions break the helix ∼65% of the time. NMR relaxation measurements indicate that the exchange rate between an intact and a broken helix is fast (>300,000 s-1) and that for the wild-type sequence, the finite persistence length is dominated by thermal fluctuations of backbone torsion angles and H-bond lengths, not by transient helix breaking. The double mutation D27H/E28H causes a pH-dependent fraction of helix disruption, in which the helix breakage increases from 26% at pH 7.5 to 53% at pH 5.5. The ability to modulate helical integrity by pH may enable incorporation of externally tunable dynamic components in the design of molecular machines.
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Affiliation(s)
- C Ashley Barnes
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland
| | - Yang Shen
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland
| | - Jinfa Ying
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland
| | - Ad Bax
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland.
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21
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Abstract
Proteasomes are large, multicatalytic protein complexes that cleave cellular proteins into peptides. There are many distinct forms of proteasomes that differ in catalytically active subunits, regulatory subunits, and associated proteins. Proteasome inhibitors are an important class of drugs for the treatment of multiple myeloma and mantle cell lymphoma, and they are being investigated for other diseases. Bortezomib (Velcade) was the first proteasome inhibitor to be approved by the US Food and Drug Administration. Carfilzomib (Kyprolis) and ixazomib (Ninlaro) have recently been approved, and more drugs are in development. While the primary mechanism of action is inhibition of the proteasome, the downstream events that lead to selective cell death are not entirely clear. Proteasome inhibitors have been found to affect protein turnover but at concentrations that are much higher than those achieved clinically, raising the possibility that some of the effects of proteasome inhibitors are mediated by other mechanisms.
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Affiliation(s)
- Lloyd D. Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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22
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Nishimoto T, Takahashi Y, Miyama S, Furuta T, Sakurai M. Replica exchange molecular dynamics simulation study on the mechanism of desiccation-induced structuralization of an intrinsically disordered peptide as a model of LEA proteins. Biophys Physicobiol 2019; 16:196-204. [PMID: 31984172 PMCID: PMC6975979 DOI: 10.2142/biophysico.16.0_196] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/03/2019] [Indexed: 02/04/2023] Open
Abstract
Group 3 late embryogenesis abundant (G3LEA) proteins, which act as a well-characterized desiccation protectant in anhydrobiotic organisms, are structurally disordered in solution, but they acquire a predominantly α-helical structure during drying. Thus, G3LEA proteins are now accepted as intrinsically disordered proteins (IDPs). Their functional regions involve characteristic 11-mer repeating motifs. In the present study, to elucidate the origin of the IDP property of G3LEA proteins, we applied replica exchange molecular dynamics (REMD) simulation to a model peptide composed of two tandem repeats of an 11-mer motif and its counterpart peptide whose amino acid sequence was randomized with the same amino acid composition as that of the 11-mer motif. REMD simulations were performed for a single α-helical chain of each peptide and its double-bundled strand in a wide water content ranging from 5 to 78.3 wt%. In the latter case, we tested different types of arrangement: 1) the dipole moments of the two helices were parallel or anti-parallel and 2) due to the amphiphilic nature of the α-helix of the 11-mer motif, two types of the side-to-side contact were tested: hydrophilic-hydrophilic facing or hydrophobic-hydrophobic facing. Here, we revealed that the single chain alone exhibits no IDP-like properties, even if it involves the 11-mer motif, and the hydrophilic interaction of the two chains leads to the formation of a left-handed α-helical coiled coil in the dry state. These results support the cytoskeleton hypothesis that has been proposed as a mechanism by which G3LEA proteins work as a desiccation protectant.
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Affiliation(s)
- Tatsushi Nishimoto
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Yuta Takahashi
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Shohei Miyama
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Tadaomi Furuta
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
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23
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Gupte TM, Ritt M, Dysthe M, Malik RU, Sivaramakrishnan S. Minute-scale persistence of a GPCR conformation state triggered by non-cognate G protein interactions primes signaling. Nat Commun 2019; 10:4836. [PMID: 31645561 PMCID: PMC6811539 DOI: 10.1038/s41467-019-12755-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 09/17/2019] [Indexed: 02/01/2023] Open
Abstract
Despite the crowded nature of the cellular milieu, ligand-GPCR-G protein interactions are traditionally viewed as spatially and temporally isolated events. In contrast, recent reports suggest the spatial and temporal coupling of receptor-effector interactions, with the potential to diversify downstream responses. In this study, we combine protein engineering of GPCR-G protein interactions with affinity sequestration and photo-manipulation of the crucial Gα C terminus, to demonstrate the temporal coupling of cognate and non-cognate G protein interactions through priming of the GPCR conformation. We find that interactions of the Gαs and Gαq C termini with the β2-adrenergic receptor (β2-AR), targeted at the G-protein-binding site, enhance Gs activation and cyclic AMP levels. β2-AR-Gα C termini interactions alter receptor conformation, which persists for ~90 s following Gα C terminus dissociation. Non-cognate G-protein expression levels impact cognate signaling in cells. Our study demonstrates temporal allostery in GPCRs, with implications for the modulation of downstream responses through the canonical G-protein-binding interface.
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Affiliation(s)
- Tejas M Gupte
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin-Cities, Minneapolis, Minnesota, 55455, USA
| | - Michael Ritt
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin-Cities, Minneapolis, Minnesota, 55455, USA
| | - Matthew Dysthe
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin-Cities, Minneapolis, Minnesota, 55455, USA
| | - Rabia U Malik
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin-Cities, Minneapolis, Minnesota, 55455, USA
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin-Cities, Minneapolis, Minnesota, 55455, USA.
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24
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Adhikari S, Leissa JA, Karlsson AJ. Beyond function: Engineering improved peptides for therapeutic applications. AIChE J 2019. [DOI: 10.1002/aic.16776] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Sayanee Adhikari
- Department of Chemical and Biomolecular Engineering University of Maryland College Park Maryland
| | - Jesse A. Leissa
- Department of Chemical and Biomolecular Engineering University of Maryland College Park Maryland
| | - Amy J. Karlsson
- Department of Chemical and Biomolecular Engineering University of Maryland College Park Maryland
- Fischell Department of Bioengineering University of Maryland College Park Maryland
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Barnes CA, Shen Y, Ying J, Takagi Y, Torchia DA, Sellers JR, Bax A. Remarkable Rigidity of the Single α-Helical Domain of Myosin-VI As Revealed by NMR Spectroscopy. J Am Chem Soc 2019; 141:9004-9017. [PMID: 31117653 PMCID: PMC6556874 DOI: 10.1021/jacs.9b03116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Indexed: 11/29/2022]
Abstract
Although the α-helix has long been recognized as an all-important element of secondary structure, it generally requires stabilization by tertiary interactions with other parts of a protein's structure. Highly charged single α-helical (SAH) domains, consisting of a high percentage (>75%) of Arg, Lys, and Glu residues, are exceptions to this rule but have been difficult to characterize structurally. Our study focuses on the 68-residue medial tail domain of myosin-VI, which is found to contain a highly ordered α-helical structure extending from Glu-6 to Lys-63. High hydrogen exchange protection factors (15-150), small (ca. 4 Hz) 3 JHNHα couplings, and a near-perfect fit to an ideal model α-helix for its residual dipolar couplings (RDCs), measured in a filamentous phage medium, support the high regularity of this helix. Remarkably, the hydrogen exchange rates are far more homogeneous than the protection factors derived from them, suggesting that for these transiently broken helices the intrinsic exchange rates derived from the amino acid sequence are not appropriate reference values. 15N relaxation data indicate a very high degree of rotational diffusion anisotropy ( D∥/ D⊥ ≈ 7.6), consistent with the hydrodynamic behavior predicted for such a long, nearly straight α-helix. Alignment of the helix by a paramagnetic lanthanide ion attached to its N-terminal region shows a decrease in alignment as the distance from the tagging site increases. This decrease yields a precise measure for the persistence length of 224 ± 10 Å at 20 °C, supporting the idea that the role of the SAH helix is to act as an extension of the myosin-VI lever arm.
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Abstract
Kinesin motor proteins that drive intracellular transport share an overall architecture of two motor domain-containing subunits that dimerize through a coiled-coil stalk. Dimerization allows kinesins to be processive motors, taking many steps along the microtubule track before detaching. However, whether dimerization is required for intracellular transport remains unknown. Here, we address this issue using a combination of in vitro and cellular assays to directly compare dimeric motors across the kinesin-1, -2, and -3 families to their minimal monomeric forms. Surprisingly, we find that monomeric motors are able to work in teams to drive peroxisome dispersion in cells. However, peroxisome transport requires minimal force output, and we find that most monomeric motors are unable to disperse the Golgi complex, a high-load cargo. Strikingly, monomeric versions of the kinesin-2 family motors KIF3A and KIF3B are able to drive Golgi dispersion in cells, and teams of monomeric KIF3B motors can generate over 8 pN of force in an optical trap. We find that intracellular transport and force output by monomeric motors, but not dimeric motors, are significantly decreased by the addition of longer and more flexible motor-to-cargo linkers. Together, these results suggest that dimerization of kinesin motors is not required for intracellular transport; however, it enables motor-to-motor coordination and high force generation regardless of motor-to-cargo distance. Dimerization of kinesin motors is thus critical for cellular events that require an ability to generate or withstand high forces.
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27
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Batchelor M, Wolny M, Baker EG, Paci E, Kalverda AP, Peckham M. Dynamic ion pair behavior stabilizes single α-helices in proteins. J Biol Chem 2019; 294:3219-3234. [PMID: 30593502 PMCID: PMC6398138 DOI: 10.1074/jbc.ra118.006752] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/17/2018] [Indexed: 11/06/2022] Open
Abstract
Ion pairs are key stabilizing interactions between oppositely charged amino acid side chains in proteins. They are often depicted as single conformer salt bridges (hydrogen-bonded ion pairs) in crystal structures, but it is unclear how dynamic they are in solution. Ion pairs are thought to be particularly important in stabilizing single α-helix (SAH) domains in solution. These highly stable domains are rich in charged residues (such as Arg, Lys, and Glu) with potential ion pairs across adjacent turns of the helix. They provide a good model system to investigate how ion pairs can contribute to protein stability. Using NMR spectroscopy, small-angle X-ray light scattering (SAXS), and molecular dynamics simulations, we provide here experimental evidence that ion pairs exist in a SAH in murine myosin 7a (residues 858-935), but that they are not fixed or long lasting. In silico modeling revealed that the ion pairs within this α-helix exhibit dynamic behavior, rapidly forming and breaking and alternating between different partner residues. The low-energy helical state was compatible with a great variety of ion pair combinations. Flexible ion pair formation utilizing a subset of those available at any one time avoided the entropic penalty of fixing side chain conformations, which likely contributed to helix stability overall. These results indicate the dynamic nature of ion pairs in SAHs. More broadly, thermodynamic stability in other proteins is likely to benefit from the dynamic behavior of multi-option solvent-exposed ion pairs.
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Affiliation(s)
- Matthew Batchelor
- From the School of Molecular and Cellular Biology and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom and
| | - Marcin Wolny
- From the School of Molecular and Cellular Biology and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom and
| | - Emily G Baker
- the School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Emanuele Paci
- From the School of Molecular and Cellular Biology and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom and
| | - Arnout P Kalverda
- From the School of Molecular and Cellular Biology and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom and
| | - Michelle Peckham
- From the School of Molecular and Cellular Biology and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom and
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28
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Development of a rapid and sensitive electrochemical biosensor for detection of human norovirus via novel specific binding peptides. Biosens Bioelectron 2019; 123:223-229. [DOI: 10.1016/j.bios.2018.08.064] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/01/2018] [Accepted: 08/27/2018] [Indexed: 12/19/2022]
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Greenwald EC, Mehta S, Zhang J. Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks. Chem Rev 2018; 118:11707-11794. [PMID: 30550275 PMCID: PMC7462118 DOI: 10.1021/acs.chemrev.8b00333] [Citation(s) in RCA: 302] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular signaling networks are the foundation which determines the fate and function of cells as they respond to various cues and stimuli. The discovery of fluorescent proteins over 25 years ago enabled the development of a diverse array of genetically encodable fluorescent biosensors that are capable of measuring the spatiotemporal dynamics of signal transduction pathways in live cells. In an effort to encapsulate the breadth over which fluorescent biosensors have expanded, we endeavored to assemble a comprehensive list of published engineered biosensors, and we discuss many of the molecular designs utilized in their development. Then, we review how the high temporal and spatial resolution afforded by fluorescent biosensors has aided our understanding of the spatiotemporal regulation of signaling networks at the cellular and subcellular level. Finally, we highlight some emerging areas of research in both biosensor design and applications that are on the forefront of biosensor development.
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Affiliation(s)
- Eric C Greenwald
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Sohum Mehta
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Jin Zhang
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
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30
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Ma N, Lippert LG, Devamani T, Levy B, Lee S, Sandhu M, Vaidehi N, Sivaramakrishnan S. Bitopic Inhibition of ATP and Substrate Binding in Ser/Thr Kinases through a Conserved Allosteric Mechanism. Biochemistry 2018; 57:6387-6390. [PMID: 30339352 DOI: 10.1021/acs.biochem.8b00729] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein kinases achieve substrate selective phosphorylation through their conformational flexibility and dynamic interaction with the substrate. Designing substrate selective or kinase selective small molecule inhibitors remains a challenge because of a lack of understanding of the dynamic mechanism by which substrates are selected by the kinase. Using a combination of all-atom molecular dynamics simulations and FRET sensors, we have delineated an allosteric mechanism that results in interaction among the DFG motif, G-loop, and activation loop and structurally links the nucleotide and substrate binding interfaces in protein kinase Cα and three other Ser/Thr kinases. ATP-competitive staurosporine analogues engage this allosteric switch region located just outside the ATP binding site to displace substrate binding to varying degrees. These inhibitors function as bitopic ligands by occupying the ATP binding site and interacting with the allosteric switch region. The conserved mechanism identified in this study can be exploited to select and design bitopic inhibitors for kinases.
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Affiliation(s)
- Ning Ma
- Department of Computational and Quantitative Medicine , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Lisa G Lippert
- Department of Genetics, Cell Biology, and Development , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Titu Devamani
- Department of Genetics, Cell Biology, and Development , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Benjamin Levy
- Department of Computational and Quantitative Medicine , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Sangbae Lee
- Department of Computational and Quantitative Medicine , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Manbir Sandhu
- Department of Computational and Quantitative Medicine , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology, and Development , University of Minnesota , Minneapolis , Minnesota 55455 , United States
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Structural Characterisation of Predicted Helical Regions in the Chironex fleckeri CfTX-1 Toxin. Mar Drugs 2018; 16:md16060201. [PMID: 29880743 PMCID: PMC6024933 DOI: 10.3390/md16060201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 05/30/2018] [Accepted: 06/05/2018] [Indexed: 11/21/2022] Open
Abstract
The Australian jellyfish Chironex fleckeri, belongs to a family of cubozoan jellyfish known for their potent venoms. CfTX-1 and -2 are two highly abundant toxins in the venom, but there is no structural data available for these proteins. Structural information on toxins is integral to the understanding of the mechanism of these toxins and the development of an effective treatment. Two regions of CfTX-1 have been predicted to have helical structures that are involved with the mechanism of action. Here we have synthesized peptides corresponding to these regions and analyzed their structures using NMR spectroscopy. The peptide corresponding to the predicted N-terminal amphiphilic helix appears unstructured in aqueous solution. This lack of structure concurs with structural disorder predicted for this region of the protein using the Protein DisOrder prediction System PrDOS. Conversely, a peptide corresponding to a predicted transmembrane region is very hydrophobic, insoluble in aqueous solution and predicted to be structured by PrDOS. In the presence of SDS-micelles both peptides have well-defined helical structures showing that a membrane mimicking environment stabilizes the structures of both peptides and supports the prediction of the transmembrane region in CfTX-1. This is the first study to experimentally analyze the structure of regions of a C. fleckeri protein.
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32
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Zhou T, Yao X, Wang J, Feng Y. Solution structure of an archaeal DUF61 family protein SSO0941 encoded by a gene in the operon of box C/D RNA protein complexes. J Struct Biol 2018. [PMID: 29526782 DOI: 10.1016/j.jsb.2018.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Domain of unknown function 61 (DUF61) family proteins widely exist in archaea and the genes of DUF61 proteins in crenarchaea are in an operon containing two genes of box C/D RNA protein complexes. Here we report the solution NMR structure of DUF61 family member protein SSO0941, from the hyperthermophilic archaeon Sulfolobus solfataricus. SSO0941 has a rigid core structure and flexible N- and C-terminal regions as well as a negatively-charged independent C-terminal helix. The core structure consists of N- and C-terminal subdomains, in which the C-terminal subdomain shows significant structural similarity with several nucleic acid binding proteins. The structure of SSO0941 is the first representative structure of DUF61 family proteins.
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Affiliation(s)
- Tao Zhou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xingzhe Yao
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Jinfeng Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
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33
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Simm D, Kollmar M. Waggawagga-CLI: A command-line tool for predicting stable single α-helices (SAH-domains), and the SAH-domain distribution across eukaryotes. PLoS One 2018; 13:e0191924. [PMID: 29444145 PMCID: PMC5812594 DOI: 10.1371/journal.pone.0191924] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/12/2018] [Indexed: 12/15/2022] Open
Abstract
Stable single-alpha helices (SAH-domains) function as rigid connectors and constant force springs between structural domains, and can provide contact surfaces for protein-protein and protein-RNA interactions. SAH-domains mainly consist of charged amino acids and are monomeric and stable in polar solutions, characteristics which distinguish them from coiled-coil domains and intrinsically disordered regions. Although the number of reported SAH-domains is steadily increasing, genome-wide analyses of SAH-domains in eukaryotic genomes are still missing. Here, we present Waggawagga-CLI, a command-line tool for predicting and analysing SAH-domains in protein sequence datasets. Using Waggawagga-CLI we predicted SAH-domains in 24 datasets from eukaryotes across the tree of life. SAH-domains were predicted in 0.5 to 3.5% of the protein-coding content per species. SAH-domains are particularly present in longer proteins supporting their function as structural building block in multi-domain proteins. In human, SAH-domains are mainly used as alternative building blocks not being present in all transcripts of a gene. Gene ontology analysis showed that yeast proteins with SAH-domains are particular enriched in macromolecular complex subunit organization, cellular component biogenesis and RNA metabolic processes, and that they have a strong nuclear and ribonucleoprotein complex localization and function in ribosome and nucleic acid binding. Human proteins with SAH-domains have roles in all types of RNA processing and cytoskeleton organization, and are predicted to function in RNA binding, protein binding involved in cell and cell-cell adhesion, and cytoskeletal protein binding. Waggawagga-CLI allows the user to adjust the stabilizing and destabilizing contribution of amino acid interactions in i,i+3 and i,i+4 spacings, and provides extensive flexibility for user-designed analyses.
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Affiliation(s)
- Dominic Simm
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
- Theoretical Computer Science and Algorithmic Methods, Institute of Computer Science, Georg-August-University Göttingen, Göttingen, Germany
| | - Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
- * E-mail:
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34
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Malik RU, Dysthe M, Ritt M, Sunahara RK, Sivaramakrishnan S. ER/K linked GPCR-G protein fusions systematically modulate second messenger response in cells. Sci Rep 2017; 7:7749. [PMID: 28798477 PMCID: PMC5552854 DOI: 10.1038/s41598-017-08029-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 07/05/2017] [Indexed: 12/20/2022] Open
Abstract
FRET and BRET approaches are well established for detecting ligand induced GPCR-G protein interactions in cells. Currently, FRET/BRET assays rely on co-expression of GPCR and G protein, and hence depend on the stoichiometry and expression levels of the donor and acceptor probes. On the other hand, GPCR-G protein fusions have been used extensively to understand the selectivity of GPCR signaling pathways. However, the signaling properties of fusion proteins are not consistent across GPCRs. In this study, we describe and characterize novel sensors based on the Systematic Protein Affinity Strength Modulation (SPASM) technique. Sensors consist of a GPCR and G protein tethered by an ER/K linker flanked by FRET probes. SPASM sensors are tested for the β2-, α1-, and α2- adrenergic receptors, and adenosine type 1 receptor (A1R), tethered to Gαs-XL, Gαi2, or Gαq subunits. Agonist stimulation of β2-AR and α2-AR increases FRET signal comparable to co-expressed FRET/BRET sensors. SPASM sensors also retain signaling through the endogenous G protein milieu. Importantly, ER/K linker length systematically tunes the GPCR-G protein interaction, with consequent modulation of second messenger signaling for cognate interactions. SPASM GPCR sensors serve the dual purpose of detecting agonist-induced changes in GPCR-G protein interactions, and linking these changes to downstream signaling.
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Affiliation(s)
- Rabia U Malik
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Matthew Dysthe
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Michael Ritt
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Roger K Sunahara
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, 55455, USA.
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35
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Cho JH, Swanson CJ, Chen J, Li A, Lippert LG, Boye SE, Rose K, Sivaramakrishnan S, Chuong CM, Chow RH. The GCaMP-R Family of Genetically Encoded Ratiometric Calcium Indicators. ACS Chem Biol 2017; 12:1066-1074. [PMID: 28195691 PMCID: PMC5572679 DOI: 10.1021/acschembio.6b00883] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report on GCaMP-Rs, a new family of genetically encoded ratiometric calcium indicators that extend the virtues of the GCaMP proteins to ratiometric measurements. We have engineered a tandem construct of calcium-dependent GCaMP and calcium-independent mCherry fluorescent proteins. The tandem design assures that the two proteins localize in the same cellular compartment(s) and facilitates pixelwise ratiometric measurements; however, Förster resonance energy transfer (FRET) between the fluorophores reduces brightness of the sensor by up to half (depending on the GCaMP variant). To eliminate FRET, we introduced a rigid α-helix, the ER/K helix, between GCaMP and mCherry. Avoiding FRET significantly increases the brightness (notably, even at low calcium concentrations), the signal-to-noise ratio, and the dynamic range.
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Affiliation(s)
- Jung-Hwa Cho
- Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, United States
| | - Carter J. Swanson
- Biophysics Program, University of Michigan, 930 N. University, Room 4028, Ann Arbor, Michigan 48109, United States
| | - Jeannie Chen
- Department of Cell & Neurobiology, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, United States
| | - Ang Li
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, United States
| | - Lisa G. Lippert
- Department of Genetics, Cell Biology & Development, University of Minnesota Twin Cities, 4-130 MCB, 420 Washington Avenue SE, Minneapolis, Minnesota 55455, United States
| | - Shannon E. Boye
- Department of Ophthalmology, University of Florida, 2000 SW Archer Rd, Rm R3-128, Gainesville, Florida 32611, United States
| | - Kasey Rose
- Department of Cell & Neurobiology, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, United States
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology & Development, University of Minnesota Twin Cities, 4-130 MCB, 420 Washington Avenue SE, Minneapolis, Minnesota 55455, United States
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, United States
| | - Robert H. Chow
- Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, United States
- Department of Biomedical Engineering, Zilkha Neurogenetic Institute, University of Southern California, Room 323, Keck School of Medicine, Los Angeles, California 90089, United States
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36
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Simm D, Hatje K, Kollmar M. Distribution and evolution of stable single α-helices (SAH domains) in myosin motor proteins. PLoS One 2017; 12:e0174639. [PMID: 28369123 PMCID: PMC5378345 DOI: 10.1371/journal.pone.0174639] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 03/13/2017] [Indexed: 11/19/2022] Open
Abstract
Stable single-alpha helices (SAHs) are versatile structural elements in many prokaryotic and eukaryotic proteins acting as semi-flexible linkers and constant force springs. This way SAH-domains function as part of the lever of many different myosins. Canonical myosin levers consist of one or several IQ-motifs to which light chains such as calmodulin bind. SAH-domains provide flexibility in length and stiffness to the myosin levers, and may be particularly suited for myosins working in crowded cellular environments. Although the function of the SAH-domains in human class-6 and class-10 myosins has well been characterised, the distribution of the SAH-domain in all myosin subfamilies and across the eukaryotic tree of life remained elusive. Here, we analysed the largest available myosin sequence dataset consisting of 7919 manually annotated myosin sequences from 938 species representing all major eukaryotic branches using the SAH-prediction algorithm of Waggawagga, a recently developed tool for the identification of SAH-domains. With this approach we identified SAH-domains in more than one third of the supposed 79 myosin subfamilies. Depending on the myosin class, the presence of SAH-domains can range from a few to almost all class members indicating complex patterns of independent and taxon-specific SAH-domain gain and loss.
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Affiliation(s)
- Dominic Simm
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
- Theoretical Computer Science and Algorithmic Methods, Institute of Computer Science, Georg-August-University Göttingen, Göttingen, Germany
| | - Klas Hatje
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
- * E-mail:
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37
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Priming GPCR signaling through the synergistic effect of two G proteins. Proc Natl Acad Sci U S A 2017; 114:3756-3761. [PMID: 28325873 DOI: 10.1073/pnas.1617232114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Although individual G-protein-coupled receptors (GPCRs) are known to activate one or more G proteins, the GPCR-G-protein interaction is viewed as a bimolecular event involving the formation of a ternary ligand-GPCR-G-protein complex. Here, we present evidence that individual GPCR-G-protein interactions can reinforce each other to enhance signaling through canonical downstream second messengers, a phenomenon we term "GPCR priming." Specifically, we find that the presence of noncognate Gq protein enhances cAMP stimulated by two Gs-coupled receptors, β2-adrenergic receptor (β2-AR) and D1 dopamine receptor (D1-R). Reciprocally, Gs enhances IP1 through vasopressin receptor (V1A-R) but not α1 adrenergic receptor (α1-AR), suggesting that GPCR priming is a receptor-specific phenomenon. The C terminus of either the Gαs or Gαq subunit is sufficient to enhance Gα subunit activation and cAMP levels. Interaction of Gαs or Gαq C termini with the GPCR increases signaling potency, suggesting an altered GPCR conformation as the underlying basis for GPCR priming. We propose three parallel mechanisms involving (i) sequential G-protein interactions at the cognate site, (ii) G-protein interactions at distinct allosteric and cognate sites on the GPCR, and (iii) asymmetric GPCR dimers. GPCR priming suggests another layer of regulation in the classic GPCR ternary-complex model, with broad implications for the multiplicity inherent in signaling networks.
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38
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Wolny M, Batchelor M, Bartlett GJ, Baker EG, Kurzawa M, Knight PJ, Dougan L, Woolfson DN, Paci E, Peckham M. Characterization of long and stable de novo single alpha-helix domains provides novel insight into their stability. Sci Rep 2017; 7:44341. [PMID: 28287151 PMCID: PMC5347031 DOI: 10.1038/srep44341] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 02/07/2017] [Indexed: 12/22/2022] Open
Abstract
Naturally-occurring single α-helices (SAHs), are rich in Arg (R), Glu (E) and Lys (K) residues, and stabilized by multiple salt bridges. Understanding how salt bridges promote their stability is challenging as SAHs are long and their sequences highly variable. Thus, we designed and tested simple de novo 98-residue polypeptides containing 7-residue repeats (AEEEXXX, where X is K or R) expected to promote salt-bridge formation between Glu and Lys/Arg. Lys-rich sequences (EK3 (AEEEKKK) and EK2R1 (AEEEKRK)) both form SAHs, of which EK2R1 is more helical and thermo-stable suggesting Arg increases stability. Substituting Lys with Arg (or vice versa) in the naturally-occurring myosin-6 SAH similarly increased (or decreased) its stability. However, Arg-rich de novo sequences (ER3 (AEEERRR) and EK1R2 (AEEEKRR)) aggregated. Combining a PDB analysis with molecular modelling provides a rational explanation, demonstrating that Glu and Arg form salt bridges more commonly, utilize a wider range of rotamer conformations, and are more dynamic than Glu-Lys. This promiscuous nature of Arg helps explain the increased propensity of de novo Arg-rich SAHs to aggregate. Importantly, the specific K:R ratio is likely to be important in determining helical stability in de novo and naturally-occurring polypeptides, giving new insight into how single α-helices are stabilized.
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Affiliation(s)
- Marcin Wolny
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Matthew Batchelor
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Gail J. Bartlett
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, UK
| | - Emily G. Baker
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, UK
| | - Marta Kurzawa
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Peter J. Knight
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Lorna Dougan
- Astbury Centre for Structural Molecular Biology and School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK
| | - Derek N. Woolfson
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, UK
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol, BS8 1TD, UK
- BrisSynBio, University of Bristol, Life Sciences Building, Bristol, BS8 1TQ, UK
| | - Emanuele Paci
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Michelle Peckham
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
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39
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Li J, Chen Y, Deng Y, Unarta IC, Lu Q, Huang X, Zhang M. Ca 2+-Induced Rigidity Change of the Myosin VIIa IQ Motif-Single α Helix Lever Arm Extension. Structure 2017; 25:579-591.e4. [PMID: 28262393 DOI: 10.1016/j.str.2017.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 12/08/2016] [Accepted: 02/09/2017] [Indexed: 11/17/2022]
Abstract
Several unconventional myosins contain a highly charged single α helix (SAH) immediately following the calmodulin (CaM) binding IQ motifs, functioning to extend lever arms of these myosins. How such SAH is connected to the IQ motifs and whether the conformation of the IQ motifs-SAH segments are regulated by Ca2+ fluctuations are not known. Here, we demonstrate by solving its crystal structure that the predicted SAH of myosin VIIa (Myo7a) forms a stable SAH. The structure of Myo7a IQ5-SAH segment in complex with apo-CaM reveals that the SAH sequence can extend the length of the Myo7a lever arm. Although Ca2+-CaM remains bound to IQ5-SAH, the Ca2+-induced CaM binding mode change softens the conformation of the IQ5-SAH junction, revealing a Ca2+-induced lever arm flexibility change for Myo7a. We further demonstrate that the last IQ motif of several other myosins also binds to both apo- and Ca2+-CaM, suggesting a common Ca2+-induced conformational regulation mechanism.
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Affiliation(s)
- Jianchao Li
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
| | - Yiyun Chen
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yisong Deng
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Ilona Christy Unarta
- Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Qing Lu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Xuhui Huang
- Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Mingjie Zhang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
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40
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Sommese RF, Ritt M, Swanson CJ, Sivaramakrishnan S. The Role of Regulatory Domains in Maintaining Autoinhibition in the Multidomain Kinase PKCα. J Biol Chem 2017; 292:2873-2880. [PMID: 28049730 DOI: 10.1074/jbc.m116.768457] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/30/2016] [Indexed: 11/06/2022] Open
Abstract
Resolving the conformational dynamics of large multidomain proteins has proven to be a significant challenge. Here we use a variety of techniques to dissect the roles of individual protein kinase Cα (PKCα) regulatory domains in maintaining catalytic autoinhibition. We find that whereas the pseudosubstrate domain is necessary for autoinhibition it is not sufficient. Instead, each regulatory domain (C1a, C1b, and C2) appears to strengthen the pseudosubstrate-catalytic domain interaction in a nucleotide-dependent manner. The pseudosubstrate and C1a domains, however, are minimally essential for maintaining the inactivated state. Furthermore, disrupting known interactions between the C1a and other regulatory domains releases the autoinhibited interaction and increases basal activity. Modulating this interaction between the catalytic and regulatory domains reveals a direct correlation between autoinhibition and membrane translocation following PKC activation.
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Affiliation(s)
- Ruth F Sommese
- From the Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455 and
| | - Michael Ritt
- From the Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455 and
| | - Carter J Swanson
- the Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109
| | - Sivaraj Sivaramakrishnan
- From the Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455 and
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41
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Dudola D, Tóth G, Nyitray L, Gáspári Z. Consensus Prediction of Charged Single Alpha-Helices with CSAHserver. Methods Mol Biol 2017; 1484:25-34. [PMID: 27787817 DOI: 10.1007/978-1-4939-6406-2_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Charged single alpha-helices (CSAHs) constitute a rare structural motif. CSAH is characterized by a high density of regularly alternating residues with positively and negatively charged side chains. Such segments exhibit unique structural properties; however, there are only a handful of proteins where its existence is experimentally verified. Therefore, establishing a pipeline that is capable of predicting the presence of CSAH segments with a low false positive rate is of considerable importance. Here we describe a consensus-based approach that relies on two conceptually different CSAH detection methods and a final filter based on the estimated helix-forming capabilities of the segments. This pipeline was shown to be capable of identifying previously uncharacterized CSAH segments that could be verified experimentally. The method is available as a web server at http://csahserver.itk.ppke.hu and also a downloadable standalone program suitable to scan larger sequence collections.
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Affiliation(s)
- Dániel Dudola
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, Budapest, 1083, Hungary
| | - Gábor Tóth
- Department of Medical and Biological Sciences, National Research, Development and Innovation Office, Budapest, Hungary
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Zoltán Gáspári
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, Budapest, 1083, Hungary.
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42
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Ulrich AKC, Seeger M, Schütze T, Bartlick N, Wahl MC. Scaffolding in the Spliceosome via Single α Helices. Structure 2016; 24:1972-1983. [PMID: 27773687 DOI: 10.1016/j.str.2016.09.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/08/2016] [Accepted: 09/28/2016] [Indexed: 12/16/2022]
Abstract
The spliceosomal B complex-specific protein Prp38 forms a complex with the intrinsically unstructured proteins MFAP1 and Snu23. Our binding and crystal structure analyses show that MFAP1 and Snu23 contact Prp38 via ER/K motif-stabilized single α helices, which have previously been recognized only as rigid connectors or force springs between protein domains. A variant of the Prp38-binding single α helix of MFAP1, in which ER/K motifs not involved in Prp38 binding were mutated, was less α-helical in isolation and showed a reduced Prp38 affinity, with opposing tendencies in interaction enthalpy and entropy. Our results indicate that the strengths of single α helix-based interactions can be tuned by the degree of helix stabilization in the unbound state. MFAP1, Snu23, and several other spliceosomal proteins contain multiple regions that likely form single α helices via which they might tether several binding partners and act as intermittent scaffolds that facilitate remodeling steps during assembly of an active spliceosome.
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Affiliation(s)
- Alexander K C Ulrich
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany
| | - Martin Seeger
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany
| | - Tonio Schütze
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany
| | - Natascha Bartlick
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany
| | - Markus C Wahl
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany; Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, 12489 Berlin, Germany.
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43
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Dasgupta S, Yang C, Castro LM, Tashima AK, Ferro ES, Moir RD, Willis IM, Fricker LD. Analysis of the Yeast Peptidome and Comparison with the Human Peptidome. PLoS One 2016; 11:e0163312. [PMID: 27685651 PMCID: PMC5042401 DOI: 10.1371/journal.pone.0163312] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/07/2016] [Indexed: 12/22/2022] Open
Abstract
Peptides function as signaling molecules in species as diverse as humans and yeast. Mass spectrometry-based peptidomics techniques provide a relatively unbiased method to assess the peptidome of biological samples. In the present study, we used a quantitative peptidomic technique to characterize the peptidome of the yeast Saccharomyces cerevisiae and compare it to the peptidomes of mammalian cell lines and tissues. Altogether, 297 yeast peptides derived from 75 proteins were identified. The yeast peptides are similar to those of the human peptidome in average size and amino acid composition. Inhibition of proteasome activity with either bortezomib or epoxomicin led to decreased levels of some yeast peptides, suggesting that these peptides are generated by the proteasome. Approximately 30% of the yeast peptides correspond to the N- or C-terminus of the protein; the human peptidome is also highly represented in N- or C-terminal protein fragments. Most yeast and humans peptides are derived from a subset of abundant proteins, many with functions involving cellular metabolism or protein synthesis and folding. Of the 75 yeast proteins that give rise to peptides, 24 have orthologs that give rise to human and/or mouse peptides and for some, the same region of the proteins are found in the human, mouse, and yeast peptidomes. Taken together, these results support the hypothesis that intracellular peptides may have specific and conserved biological functions.
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Affiliation(s)
- Sayani Dasgupta
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, 10461, United States of America
| | - Ciyu Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, United States of America
| | - Leandro M. Castro
- Biomedical Science Institute, Campus on the São Paulo Coast, São Paulo State University, São Vicente, 11330–900, SP, Brazil
| | - Alexandre K. Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of Sao Paulo, Sao Paulo, SP, 04023–901, SP, Brazil
| | - Emer S. Ferro
- Department of Pharmacology, Biomedical Science Institute, University of São Paulo, São Paulo, 05508–000, SP, Brazil
| | - Robyn D. Moir
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, 10461, United States of America
| | - Ian M. Willis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, 10461, United States of America
- Department of Systems & Computational Biology, Albert Einstein College of Medicine, Bronx, New York, 10461, United States of America
| | - Lloyd D. Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, 10461, United States of America
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, 10461, United States of America
- * E-mail:
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44
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Doležal M, Hadravová R, Kožíšek M, Bednárová L, Langerová H, Ruml T, Rumlová M. Functional and Structural Characterization of Novel Type of Linker Connecting Capsid and Nucleocapsid Protein Domains in Murine Leukemia Virus. J Biol Chem 2016; 291:20630-42. [PMID: 27514744 DOI: 10.1074/jbc.m116.746461] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Indexed: 12/24/2022] Open
Abstract
The assembly of immature retroviral particles is initiated in the cytoplasm by the binding of the structural polyprotein precursor Gag with viral genomic RNA. The protein interactions necessary for assembly are mediated predominantly by the capsid (CA) and nucleocapsid (NC) domains, which have conserved structures. In contrast, the structural arrangement of the CA-NC connecting region differs between retroviral species. In HIV-1 and Rous sarcoma virus, this region forms a rod-like structure that separates the CA and NC domains, whereas in Mason-Pfizer monkey virus, this region is densely packed, thus holding the CA and NC domains in close proximity. Interestingly, the sequence connecting the CA and NC domains in gammaretroviruses, such as murine leukemia virus (MLV), is unique. The sequence is called a charged assembly helix (CAH) due to a high number of positively and negatively charged residues. Although both computational and deletion analyses suggested that the MLV CAH forms a helical conformation, no structural or biochemical data supporting this hypothesis have been published. Using an in vitro assembly assay, alanine scanning mutagenesis, and biophysical techniques (circular dichroism, NMR, microcalorimetry, and electrophoretic mobility shift assay), we have characterized the structure and function of the MLV CAH. We provide experimental evidence that the MLV CAH belongs to a group of charged, E(R/K)-rich, single α-helices. This is the first single α-helix motif identified in viral proteins.
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Affiliation(s)
- Michal Doležal
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6
| | - Romana Hadravová
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6
| | - Milan Kožíšek
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6
| | - Lucie Bednárová
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6
| | - Hana Langerová
- the Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague 6, Technická 3, 166 28 Prague, and
| | - Tomáš Ruml
- the Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague 6, Technická 3, 166 28 Prague, and
| | - Michaela Rumlová
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6, the Department of Biotechnology, University of Chemistry and Technology, Technická 5, 166 28 Prague, Czech Republic
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45
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Ritt M, Sivaramakrishnan S. Correlation between Activity and Domain Complementation in Adenylyl Cyclase Demonstrated with a Novel Fluorescence Resonance Energy Transfer Sensor. Mol Pharmacol 2016; 89:407-12. [PMID: 26801393 DOI: 10.1124/mol.115.101626] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/20/2016] [Indexed: 11/22/2022] Open
Abstract
Adenylyl cyclase (AC) activity relies on multiple effectors acting through distinct binding sites. Crystal structures have revealed the location of these sites, and biochemical studies have explored the kinetics of ACs, but the interplay between conformation and activity remains incompletely understood. Here, we describe a novel fluorescence resonance energy transfer (FRET) sensor that functions both as a soluble cyclase and a reporter of complementation within the catalytic domain. We report a strong linear correlation between catalytic domain complementation and cyclase activity upon stimulation with forskolin and Gαs. Exploiting this, we dissect the mechanism of action of a series of forskolin analogs and a P-site inhibitor, 2'-d3'-AMP. Finally, we demonstrate that this sensor is functional in live cells, wherein it reports forskolin-stimulated activity of AC.
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Affiliation(s)
- Michael Ritt
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota
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46
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Dasgupta S, Fishman MA, Mahallati H, Castro LM, Tashima AK, Ferro ES, Fricker LD. Reduced Levels of Proteasome Products in a Mouse Striatal Cell Model of Huntington's Disease. PLoS One 2015; 10:e0145333. [PMID: 26691307 PMCID: PMC4686214 DOI: 10.1371/journal.pone.0145333] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 12/02/2015] [Indexed: 12/25/2022] Open
Abstract
Huntington's disease is the result of a long polyglutamine tract in the gene encoding huntingtin protein, which in turn causes a large number of cellular changes and ultimately results in neurodegeneration of striatal neurons. Although many theories have been proposed, the precise mechanism by which the polyglutamine expansion causes cellular changes is not certain. Some evidence supports the hypothesis that the long polyglutamine tract inhibits the proteasome, a multiprotein complex involved in protein degradation. However, other studies report normal proteasome function in cells expressing long polyglutamine tracts. The controversy may be due to the methods used to examine proteasome activity in each of the previous studies. In the present study, we measured proteasome function by examining levels of endogenous peptides that are products of proteasome cleavage. Peptide levels were compared among mouse striatal cell lines expressing either 7 glutamines (STHdhQ7/Q7) or 111 glutamines in the huntingtin protein, either heterozygous (STHdhQ7/Q111) or homozygous (STHdhQ111/Q111). Both of the cell lines expressing huntingtin with 111 glutamines showed a large reduction in nearly all of the peptides detected in the cells, relative to levels of these peptides in cells homozygous for 7 glutamines. Treatment of STHdhQ7/Q7 cells with proteasome inhibitors epoxomicin or bortezomib also caused a large reduction in most of these peptides, suggesting that they are products of proteasome-mediated cleavage of cellular proteins. Taken together, these results support the hypothesis that proteasome function is impaired by the expression of huntingtin protein containing long polyglutamine tracts.
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Affiliation(s)
- Sayani Dasgupta
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York, 10461, United States of America
| | - Michael A. Fishman
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York, 10461, United States of America
| | - Hana Mahallati
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York, 10461, United States of America
| | - Leandro M. Castro
- São Paulo State University (UNESP), Experimental Campus on the São Paulo Coast, São Vicente, 11330–900, SP, Brazil
| | - Alexandre K. Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of Sao Paulo, Sao Paulo, SP, 04023–901, SP, Brazil
| | - Emer S. Ferro
- Department of Pharmacology, Biomedical Science Institute, University of São Paulo, São Paulo, 05508–000, SP, Brazil
| | - Lloyd D. Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York, 10461, United States of America
- Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York, 10461, United States of America
- * E-mail:
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47
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Dobson L, Nyitray L, Gáspári Z. A conserved charged single α-helix with a putative steric role in paraspeckle formation. RNA (NEW YORK, N.Y.) 2015; 21:2023-2029. [PMID: 26428695 PMCID: PMC4647456 DOI: 10.1261/rna.053058.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/27/2015] [Indexed: 06/05/2023]
Abstract
Paraspeckles are subnuclear particles involved in the regulation of mRNA expression. They are formed by the association of DBHS family proteins and the NEAT1 long noncoding RNA. Here, we show that a recently identified structural motif, the charged single α-helix, is largely conserved in the DBHS family. Based on the available structural data and a previously suggested multimerization scheme of DBHS proteins, we built a structural model of a (PSPC1/NONO)(n) multimer that might have relevance in paraspeckle formation. Our model contains an extended coiled-coil region that is followed by and partially overlaps with the predicted charged single α-helix. We suggest that the charged single α-helix can act as an elastic ruler governing the exact positioning of the dimeric core structures relative to each other during paraspeckle assembly along the NEAT1 noncoding RNA.
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Affiliation(s)
- László Dobson
- Pázmány Péter Catholic University, Faculty of Information Technology and Bionics, H-1083 Budapest, Hungary
| | - László Nyitray
- Eötvös Loránd University, Department of Biochemistry, H-1117 Budapest, Hungary
| | - Zoltán Gáspári
- Pázmány Péter Catholic University, Faculty of Information Technology and Bionics, H-1083 Budapest, Hungary
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48
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An unprecedented alteration in mode of action of IsCT resulting its translocation into bacterial cytoplasm and inhibition of macromolecular syntheses. Sci Rep 2015; 5:9127. [PMID: 25773522 PMCID: PMC4360471 DOI: 10.1038/srep09127] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/30/2015] [Indexed: 01/12/2023] Open
Abstract
IsCT, a 13-residue, non-cell-selective antimicrobial peptide is comprised of mostly hydrophobic residues and lesser cationic residues. Assuming that placement of an additional positive charge in the non-polar face of IsCT could reduce its hydrophobic interaction, resulting in its reduction of cytotoxicity, an analog, I9K-IsCT was designed. Two more analogs, namely, E7K-IsCT and E7K,I9K-IsCT, were designed to investigate the impact of positive charges in the polar face as well as polar and non-polar faces at a time. These amino acid substitutions resulted in a significant enhancement of therapeutic potential of IsCT. IsCT and E7K-IsCT seem to target bacterial membrane for their anti-bacterial activity. However, I9K-IsCT and E7K,I9K-IsCT inhibited nucleic acid and protein syntheses in tested E. coli without perturbing its membrane. This was further supported by the observation that NBD-IsCT localized onto bacterial membrane while NBD-labeled I9K-IsCT and E7K,I9K-IsCT translocated into bacterial cytoplasm. Interestingly, IsCT and E7K-IsCT were significantly helical while I9K-IsCT and E7K,I9K-IsCT were mostly unstructured with no helix content in presence of mammalian and bacterial membrane-mimetic lipid vesicles. Altogether, the results identify two novel cell-selective analogs of IsCT with new prototype amino acid sequences that can translocate into bacterial cytoplasm without any helical structure and inhibit macromolecular syntheses.
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