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Naudin EA, Albanese KI, Smith AJ, Mylemans B, Baker EG, Weiner OD, Andrews DM, Tigue N, Savery NJ, Woolfson DN. From peptides to proteins: coiled-coil tetramers to single-chain 4-helix bundles. Chem Sci 2022; 13:11330-11340. [PMID: 36320580 PMCID: PMC9533478 DOI: 10.1039/d2sc04479j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/24/2022] [Indexed: 11/21/2022] Open
Abstract
The design of completely synthetic proteins from first principles-de novo protein design-is challenging. This is because, despite recent advances in computational protein-structure prediction and design, we do not understand fully the sequence-to-structure relationships for protein folding, assembly, and stabilization. Antiparallel 4-helix bundles are amongst the most studied scaffolds for de novo protein design. We set out to re-examine this target, and to determine clear sequence-to-structure relationships, or design rules, for the structure. Our aim was to determine a common and robust sequence background for designing multiple de novo 4-helix bundles. In turn, this could be used in chemical and synthetic biology to direct protein-protein interactions and as scaffolds for functional protein design. Our approach starts by analyzing known antiparallel 4-helix coiled-coil structures to deduce design rules. In terms of the heptad repeat, abcdefg -i.e., the sequence signature of many helical bundles-the key features that we identify are: a = Leu, d = Ile, e = Ala, g = Gln, and the use of complementary charged residues at b and c. Next, we implement these rules in the rational design of synthetic peptides to form antiparallel homo- and heterotetramers. Finally, we use the sequence of the homotetramer to derive in one step a single-chain 4-helix-bundle protein for recombinant production in E. coli. All of the assembled designs are confirmed in aqueous solution using biophysical methods, and ultimately by determining high-resolution X-ray crystal structures. Our route from peptides to proteins provides an understanding of the role of each residue in each design.
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Affiliation(s)
- Elise A Naudin
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Katherine I Albanese
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Abigail J Smith
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
| | - Bram Mylemans
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Max Planck-Bristol Centre for Minimal Biology, 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
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
| | - Orion D Weiner
- Cardiovascular Research Institute, Department of Biochemistry and Biophysics, University of California 555 Mission Bay Blvd. South San Francisco CA 94158 USA
| | - David M Andrews
- Oncology R&D, AstraZeneca Cambridge Science Park, Darwin Building Cambridge CB4 0WG UK
| | - Natalie Tigue
- BioPharmaceuticals R&D, AstraZeneca Granta Park Cambridge CB21 6GH UK
| | - Nigel J Savery
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisEngBio, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol Cantock's Close Bristol BS8 1TS UK
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisEngBio, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
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2
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Jorgensen MD, Chmielewski J. Recent advances in coiled-coil peptide materials and their biomedical applications. Chem Commun (Camb) 2022; 58:11625-11636. [PMID: 36172799 DOI: 10.1039/d2cc04434j] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extensive research has gone into deciphering the sequence requirements for peptides to fold into coiled-coils of varying oligomeric states. More recently, additional signals have been introduced within coiled-coils to promote higher order assembly into biomaterials with a rich distribution of morphologies. Herein we describe these strategies for association of coiled-coil building blocks and biomedical applications. With many of the systems described herein having proven use in protein storage, cargo binding and delivery, three dimensional cell culturing and vaccine development, the future potential of coiled-coil materials to have significant biomedical impact is highly promising.
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Affiliation(s)
- Michael D Jorgensen
- Purdue University, Department of Chemistry, 560 Oval Drive, West Lafayette, Indiana, USA.
| | - Jean Chmielewski
- Purdue University, Department of Chemistry, 560 Oval Drive, West Lafayette, Indiana, USA.
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3
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Gutte B, Klauser S. Design of catalytic polypeptides and proteins. Protein Eng Des Sel 2018; 31:457-470. [PMID: 31241746 DOI: 10.1093/protein/gzz009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Indexed: 11/13/2022] Open
Abstract
The first part of this review article lists examples of complete, empirical de novo design that made important contributions to the development of the field and initiated challenging projects. The second part of this article deals with computational design of novel enzymes in native protein scaffolds; active designs were refined through random and site-directed mutagenesis producing artificial enzymes with nearly native enzyme- like activities against a number of non-natural substrates. Combining aspects of de novo design and biological evolution of nature's enzymes has started and will accelerate the development of novel enzyme activities.
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Affiliation(s)
- B Gutte
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, Zürich, Switzerland
| | - S Klauser
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, Zürich, Switzerland
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4
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Szczepaniak K, Ludwiczak J, Winski A, Dunin-Horkawicz S. Variability of the core geometry in parallel coiled-coil bundles. J Struct Biol 2018; 204:117-124. [DOI: 10.1016/j.jsb.2018.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 06/15/2018] [Accepted: 07/01/2018] [Indexed: 10/28/2022]
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5
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Thomas F, Dawson WM, Lang EJM, Burton AJ, Bartlett GJ, Rhys GG, Mulholland AJ, Woolfson DN. De Novo-Designed α-Helical Barrels as Receptors for Small Molecules. ACS Synth Biol 2018; 7:1808-1816. [PMID: 29944338 DOI: 10.1021/acssynbio.8b00225] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We describe de novo-designed α-helical barrels (αHBs) that bind and discriminate between lipophilic biologically active molecules. αHBs have five or more α-helices arranged around central hydrophobic channels the diameters of which scale with oligomer state. We show that pentameric, hexameric, and heptameric αHBs bind the environmentally sensitive dye 1,6-diphenylhexatriene (DPH) in the micromolar range and fluoresce. Displacement of the dye is used to report the binding of nonfluorescent molecules: palmitic acid and retinol bind to all three αHBs with submicromolar inhibitor constants; farnesol binds the hexamer and heptamer; but β-carotene binds only the heptamer. A co-crystal structure of the hexamer with farnesol reveals oriented binding in the center of the hydrophobic channel. Charged side chains engineered into the lumen of the heptamer facilitate binding of polar ligands: a glutamate variant binds a cationic variant of DPH, and introducing lysine allows binding of the biosynthetically important farnesol diphosphate.
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Affiliation(s)
- Franziska Thomas
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany
| | - William M. Dawson
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Eric J. M. Lang
- 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
| | - Antony J. Burton
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- Frick Chemistry Laboratory, Princeton, New Jersey 084544, United States
| | - Gail J. Bartlett
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Guto G. Rhys
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Adrian J. Mulholland
- 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
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, 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, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, U.K
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6
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Kawaguchi K, Nakagawa S, Kurniawan I, Kodama K, Arwansyah MS, Nagao H. A coarse-grained model of the effective interaction for charged amino acid residues and its application to formation of GCN4-pLI tetramer. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1393574] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Kazutomo Kawaguchi
- Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | - Satoshi Nakagawa
- Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | - Isman Kurniawan
- Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | - Koichi Kodama
- Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | | | - Hidemi Nagao
- Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
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7
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Vavra KC, Xia Y, Rock RS. Competition between Coiled-Coil Structures and the Impact on Myosin-10 Bundle Selection. Biophys J 2017; 110:2517-2527. [PMID: 27276269 DOI: 10.1016/j.bpj.2016.04.048] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/28/2016] [Accepted: 04/29/2016] [Indexed: 12/27/2022] Open
Abstract
Coiled-coil fusions are a useful approach to enforce dimerization in protein engineering. However, the final structures of coiled-coil fusion proteins have received relatively little attention. Here, we determine the structural outcome of adjacent parallel and antiparallel coiled coils. The targets are coiled coils that stabilize myosin-10 in single-molecule biophysical studies. We reveal the solution structure of a short, antiparallel, myosin-10 coiled-coil fused to the parallel GCN4-p1 coiled coil. Surprisingly, this structure is a continuous, antiparallel coiled coil where GCN4-p1 pairs with myosin-10 rather than itself. We also show that longer myosin-10 segments in these parallel/antiparallel fusions are dynamic and do not fold cooperatively. Our data resolve conflicting results on myosin-10 selection of actin filament bundles, demonstrating the importance of understanding coiled-coil orientation and stability.
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Affiliation(s)
- Kevin C Vavra
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Youlin Xia
- Minnesota NMR Center, University of Minnesota, Minneapolis, Minnesota
| | - Ronald S Rock
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois.
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8
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Collie GW, Bailly R, Pulka-Ziach K, Lombardo CM, Mauran L, Taib-Maamar N, Dessolin J, Mackereth CD, Guichard G. Molecular Recognition within the Cavity of a Foldamer Helix Bundle: Encapsulation of Primary Alcohols in Aqueous Conditions. J Am Chem Soc 2017; 139:6128-6137. [DOI: 10.1021/jacs.7b00181] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gavin W. Collie
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert
Escarpit, 33607 Pessac, France
| | - Remy Bailly
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, All. Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Karolina Pulka-Ziach
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert
Escarpit, 33607 Pessac, France
| | - Caterina M. Lombardo
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert
Escarpit, 33607 Pessac, France
| | - Laura Mauran
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert
Escarpit, 33607 Pessac, France
- UREkA, Sarl, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Nada Taib-Maamar
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, All. Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Jean Dessolin
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, All. Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Cameron D. Mackereth
- Univ. Bordeaux, Inserm, CNRS, ARNA Laboratory, U1212, UMR 5320, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33076 Pessac, France
| | - Gilles Guichard
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert
Escarpit, 33607 Pessac, France
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9
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Kawaguchi K, Nakagawa S, Kinoshita S, Wada M, Saito H, Nagao H. A simple coarse-grained model for interacting protein complex. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1234652] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Kazutomo Kawaguchi
- Institute of Science and Engineering, Kanazawa University , Kanazawa, Japan
| | - Satoshi Nakagawa
- Institute of Science and Engineering, Kanazawa University , Kanazawa, Japan
| | - Shogo Kinoshita
- Institute of Science and Engineering, Kanazawa University , Kanazawa, Japan
| | - Makoto Wada
- Institute of Science and Engineering, Kanazawa University , Kanazawa, Japan
| | - Hiroaki Saito
- Institute of Science and Engineering, Kanazawa University , Kanazawa, Japan
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10
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Shaping quaternary assemblies of water-soluble non-peptide helical foldamers by sequence manipulation. Nat Chem 2015; 7:871-8. [DOI: 10.1038/nchem.2353] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 08/19/2015] [Indexed: 12/28/2022]
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11
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Cottee MA, Muschalik N, Johnson S, Leveson J, Raff JW, Lea SM. The homo-oligomerisation of both Sas-6 and Ana2 is required for efficient centriole assembly in flies. eLife 2015; 4:e07236. [PMID: 26002084 PMCID: PMC4471874 DOI: 10.7554/elife.07236] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/22/2015] [Indexed: 12/29/2022] Open
Abstract
Sas-6 and Ana2/STIL proteins are required for centriole duplication and the homo-oligomerisation properties of Sas-6 help establish the ninefold symmetry of the central cartwheel that initiates centriole assembly. Ana2/STIL proteins are poorly conserved, but they all contain a predicted Central Coiled-Coil Domain (CCCD). Here we show that the Drosophila Ana2 CCCD forms a tetramer, and we solve its structure to 0.8 Å, revealing that it adopts an unusual parallel-coil topology. We also solve the structure of the Drosophila Sas-6 N-terminal domain to 2.9 Å revealing that it forms higher-order oligomers through canonical interactions. Point mutations that perturb Sas-6 or Ana2 homo-oligomerisation in vitro strongly perturb centriole assembly in vivo. Thus, efficient centriole duplication in flies requires the homo-oligomerisation of both Sas-6 and Ana2, and the Ana2 CCCD tetramer structure provides important information on how these proteins might cooperate to form a cartwheel structure. DOI:http://dx.doi.org/10.7554/eLife.07236.001 Most animal cells contain structures known as centrioles. Typically, a cell that is not dividing contains a pair of centrioles. But when a cell prepares to divide, the centrioles are duplicated. The two pairs of centrioles then organize the scaffolding that shares the genetic material equally between the newly formed cells at cell division. Centriole assembly is tightly regulated and abnormalities in this process can lead to developmental defects and cancer. Centrioles likely contain several hundred proteins, but only a few of these are strictly needed for centriole assembly. New centrioles usually assemble from a cartwheel-like arrangement of proteins, which includes a protein called SAS-6. Previous work has suggested that in the fruit fly Drosophila melanogaster, Sas-6 can only form this cartwheel when another protein called Ana2 is also present, but the details of this process are unclear. Now, Cottee, Muschalik et al. have investigated potential features in the Ana2 protein that might be important for centriole assembly. These experiments revealed that a region in the Ana2 protein, called the ‘central coiled-coil domain’, is required to target Ana2 to centrioles. Furthermore, purified coiled-coil domains were found to bind together in groups of four (called tetramers). Cottee, Muschalik et al. then used a technique called X-ray crystallography to work out the three-dimensional structure of one of these tetramers and part of the Sas-6 protein with a high level of detail. These structures confirmed that Sas-6 proteins also associate with each other. When fruit flies were engineered to produce either Ana2 or Sas-6 proteins that cannot self-associate, the flies' cells were unable to efficiently make centrioles. Furthermore, an independent study by Rogala et al. found similar results for a protein that is related to Ana2: a protein called SAS-5 from the microscopic worm Caenorhabditis elegans. Further work is needed to understand how Sas-6 and Ana2 work with each other to form the cartwheel-like arrangement at the core of centrioles. DOI:http://dx.doi.org/10.7554/eLife.07236.002
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Affiliation(s)
- Matthew A Cottee
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Nadine Muschalik
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Joanna Leveson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Jordan W Raff
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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12
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Scholey JE, Nithianantham S, Scholey JM, Al-Bassam J. Structural basis for the assembly of the mitotic motor Kinesin-5 into bipolar tetramers. eLife 2014; 3:e02217. [PMID: 24714498 PMCID: PMC3978770 DOI: 10.7554/elife.02217] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Chromosome segregation during mitosis depends upon Kinesin-5 motors, which display a conserved, bipolar homotetrameric organization consisting of two motor dimers at opposite ends of a central rod. Kinesin-5 motors crosslink adjacent microtubules to drive or constrain their sliding apart, but the structural basis of their organization is unknown. In this study, we report the atomic structure of the bipolar assembly (BASS) domain that directs four Kinesin-5 subunits to form a bipolar minifilament. BASS is a novel 26-nm four-helix bundle, consisting of two anti-parallel coiled-coils at its center, stabilized by alternating hydrophobic and ionic four-helical interfaces, which based on mutagenesis experiments, are critical for tetramerization. Strikingly, N-terminal BASS helices bend as they emerge from the central bundle, swapping partner helices, to form dimeric parallel coiled-coils at both ends, which are offset by 90°. We propose that BASS is a mechanically stable, plectonemically-coiled junction, transmitting forces between Kinesin-5 motor dimers during microtubule sliding. DOI: http://dx.doi.org/10.7554/eLife.02217.001.
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Affiliation(s)
- Jessica E Scholey
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
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13
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Rydberg J, Baltzer L, Sarojini V. Intrinsically unstructured proteins by design-electrostatic interactions can control binding, folding, and function of a helix-loop-helix heterodimer. J Pept Sci 2013; 19:461-9. [PMID: 23813758 DOI: 10.1002/psc.2520] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 04/16/2013] [Accepted: 04/19/2013] [Indexed: 11/10/2022]
Abstract
Intrinsically disordered proteins that exist as unordered monomeric structures in aqueous solution at pH 7 but fold into four-helix bundles upon binding to recognized polypeptide targets have been designed. NMR and CD spectra of the monomeric polypeptides show the hallmarks of unordered structures, whereas in the bound state they are highly helical. Analytical ultracentrifugation data shows that the polypeptides bind to their targets to form exclusively heterodimers at neutral pH. To demonstrate the relationship between binding, folding, and function, a catalytic site for ester hydrolysis was introduced into an unordered and largely inactive monomer, but that was structured and catalytically active in the presence of a specific polypeptide target. Electrostatic interactions between surface-exposed residues inhibited the binding and folding of the monomers at pH 7. Charge-charge repulsion between ionizable amino acids was thus found to be sufficient to disrupt binding between polypeptide chains despite their inherent propensities for structure formation and may be involved in the folding and function of inherently disordered proteins in biology.
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Affiliation(s)
- Johan Rydberg
- Department of Chemistry-IFM, Linköping University, 581 83, Linköping, Sweden
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14
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Buer BC, Meagher JL, Stuckey JA, Marsh ENG. Comparison of the structures and stabilities of coiled-coil proteins containing hexafluoroleucine and t-butylalanine provides insight into the stabilizing effects of highly fluorinated amino acid side-chains. Protein Sci 2012; 21:1705-15. [PMID: 22930450 PMCID: PMC3527707 DOI: 10.1002/pro.2150] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 08/17/2012] [Accepted: 08/20/2012] [Indexed: 11/08/2022]
Abstract
Highly fluorinated analogs of hydrophobic amino acids are well known to increase the stability of proteins toward thermal unfolding and chemical denaturation, but there is very little data on the structural consequences of fluorination. We have determined the structures and folding energies of three variants of a de novo designed 4-helix bundle protein whose hydrophobic cores contain either hexafluoroleucine (hFLeu) or t-butylalanine (tBAla). Although the buried hydrophobic surface area is the same for all three proteins, the incorporation of tBAla causes a rearrangement of the core packing, resulting in the formation of a destabilizing hydrophobic cavity at the center of the protein. In contrast, incorporation of hFLeu, causes no changes in core packing with respect to the structure of the nonfluorinated parent protein which contains only leucine in the core. These results support the idea that fluorinated residues are especially effective at stabilizing proteins because they closely mimic the shape of the natural residues they replace while increasing buried hydrophobic surface area.
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Affiliation(s)
- Benjamin C Buer
- Department of Chemistry, University of MichiganAnn Arbor, Michigan 48109
| | - Jennifer L Meagher
- Life Sciences Institute, University of MichiganAnn Arbor, Michigan 48109
| | - Jeanne A Stuckey
- Life Sciences Institute, University of MichiganAnn Arbor, Michigan 48109
- Department of Biological Chemistry, University of Michigan Medical SchoolAnn Arbor, Michigan 48109
| | - E Neil G Marsh
- Department of Chemistry, University of MichiganAnn Arbor, Michigan 48109
- Department of Biological Chemistry, University of Michigan Medical SchoolAnn Arbor, Michigan 48109
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15
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Rezaei Araghi R, Baldauf C, Gerling UIM, Cadicamo CD, Koksch B. A systematic study of fundamentals in α-helical coiled coil mimicry by alternating sequences of β- and γ-amino acids. Amino Acids 2011; 41:733-42. [DOI: 10.1007/s00726-011-0941-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 05/11/2011] [Indexed: 10/18/2022]
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16
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Hu W. A possible degree of motional freedom in bacterial chemoreceptor cytoplasmic domains and its potential role in signal transduction. INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2011; 2:99-110. [PMID: 21968904 PMCID: PMC3180096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 02/14/2011] [Indexed: 05/31/2023]
Abstract
We describe an array of gaps in an antiparallel four-helix bundle structure, the cytoplasmic domains of bacterial chemoreceptors. For a given helix, the side chain interactions that define a helix's position are analyzed in terms of residue interfaces, the most important of which are a-a, g-g, d-d, g-d, and a-d. It was found that the interdigitation of the side groups does not entirely fill the space along the long axis of the structure, which results in a rather regular array of gaps. A simulated piston motion of helix CD1 along the helical axis direction by 1.2Å shows that 85% of the side chain interactions still satisfy Van der Waals criteria, while the remaining clashes could be avoided by small rotations of side chains. Therefore, two states could exist in the structure, related by a piston motion. Analysis of the crystal structure of a small four-helix bundle, the P1(short) domain of CheA in Thermotoga Maritima, reveals that the two coexisting states related by a 1.3-1.7Å piston motion are defined by the same mechanism. This two-state model is a plausible candidate mechanism for the long distance signal transduction in bacterial chemoreceptors and is qualitatively consistent with literature chemoreceptor mutagenesis results. Such a mechanism could exist in many other structures with interdigitating α-helices.
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Affiliation(s)
- Weiguo Hu
- Department of Polymer Science and Engineering, 120 Governor's Drive University of Massachusetts Amherst, MA 01003 USA
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17
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18
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Nomura W, Mino T, Narumi T, Ohashi N, Masuda A, Hashimoto C, Tsutsumi H, Tamamura H. Development of crosslink-type tag-probe pairs for fluorescent imaging of proteins. Biopolymers 2010; 94:843-52. [DOI: 10.1002/bip.21444] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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19
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Tsutsumi H, Nomura W, Abe S, Mino T, Masuda A, Ohashi N, Tanaka T, Ohba K, Yamamoto N, Akiyoshi K, Tamamura H. Fluorogenically active leucine zipper peptides as tag-probe pairs for protein imaging in living cells. Angew Chem Int Ed Engl 2010; 48:9164-6. [PMID: 19876989 DOI: 10.1002/anie.200903183] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Hiroshi Tsutsumi
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo 101-0062, Japan
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20
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Tsutsumi H, Nomura W, Abe S, Mino T, Masuda A, Ohashi N, Tanaka T, Ohba K, Yamamoto N, Akiyoshi K, Tamamura H. Fluorogenically Active Leucine Zipper Peptides as Tag-Probe Pairs for Protein Imaging in Living Cells. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903183] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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21
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Peacock A, Stuckey J, Pecoraro V. Switching the Chirality of the Metal Environment Alters the Coordination Mode in Designed Peptides. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902166] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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22
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Olia AS, Casjens S, Cingolani G. Structural plasticity of the phage P22 tail needle gp26 probed with xenon gas. Protein Sci 2009; 18:537-48. [PMID: 19241380 PMCID: PMC2760360 DOI: 10.1002/pro.53] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The tail needle, gp26, is a highly stable homo-trimeric fiber found in the tail apparatus of bacteriophage P22. In the mature virion, gp26 is responsible for plugging the DNA exit channel, and likely plays an important role in penetrating the host cell envelope. In this article, we have determined the 1.98 A resolution crystal structure of gp26 bound to xenon gas. The structure led us to identify a calcium and a chloride ion intimately bound at the interior of alpha-helical core, as well as seven small cavities occupied by xenon atoms. The two ions engage in buried polar interactions with gp26 side chains that provide specificity and register to gp26 helical core, thus enhancing its stability. Conversely, the distribution of xenon accessible cavities correlates well with the flexibility of the fiber observed in solution and in the crystal structure. We suggest that small internal cavities in gp26 between the helical core and the C-terminal tip allow for flexible swinging of the latter, without affecting the overall stability of the protein. The C-terminal tip may be important in scanning the bacterial surface in search of a cell-envelope penetration site, or for recognition of a yet unidentified receptor on the surface of the host.
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Affiliation(s)
- Adam S Olia
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical UniversitySyracuse, New York 13210
| | - Sherwood Casjens
- Department of Pathology, University of Utah School of MedicineSalt Lake City, Utah 84112
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical UniversitySyracuse, New York 13210,*Correspondence to: Gino Cingolani, Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210. E-mail:
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23
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Pendley SS, Yu YB, Cheatham TE. Molecular dynamics guided study of salt bridge length dependence in both fluorinated and non-fluorinated parallel dimeric coiled-coils. Proteins 2009; 74:612-29. [PMID: 18704948 PMCID: PMC2692595 DOI: 10.1002/prot.22177] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The alpha-helical coiled-coil is one of the most common oligomerization motifs found in both native and engineered proteins. To better understand the stability and dynamics of the coiled-coil motifs, including those modified by fluorination, several fluorinated and nonfluorinated parallel dimeric coiled-coil protein structures were designed and modeled. We also attempt to investigate how changing the length and geometry of the important stabilizing salt bridges influences the coiled-coil protein structure. Molecular dynamics (MD) and free energy simulations with AMBER used a particle mesh Ewald treatment of the electrostatics in explicit TIP3P solvent with balanced force field treatments. Preliminary studies with legacy force fields (ff94, ff96, and ff99) show a profound instability of the coiled-coil structures in short MD simulation. Significantly, better behavior is evident with the more balanced ff99SB and ff03 protein force fields. Overall, the results suggest that the coiled-coil structures can readily accommodate the larger acidic arginine or S-2,7-diaminoheptanedoic acid mutants in the salt bridge, whereas substitution of the smaller L-ornithine residue leads to rapid disruption of the coiled-coil structure on the MD simulation time scale. This structural distortion of the secondary structure allows both the formation of large hydration pockets proximal to the charged groups and within the hydrophobic core. Moreover, the increased structural fluctuations and movement lead to a decrease in the water occupancy lifetimes in the hydration pockets. In contrast, analysis of the hydration in the stable dimeric coiled-coils shows high occupancy water sites along the backbone residues with no water occupancy in the hydrophobic core, although transitory water interactions with the salt bridge residues are evident. The simulations of the fluorinated coiled-coils suggest that in some cases fluorination electrostatically stabilizes the intermolecular coiled-coil salt bridges. Structural analyses also reveal different side chain rotamer preferences for leucine when compared with 5,5,5,5',5',5'-hexafluoroleucine mutants. These observed differences in the side chain rotamer populations suggest differential changes in the side chain conformational entropy upon coiled-coil formation when the protein is fluorinated. The free energy of hydration of the isolated 5,5,5,5',5',5'-hexafluoroleucine amino acid is calculated to be 1.1 kcal/mol less stable than leucine; this hydrophobic penalty in the monomer may provide a driving force for coiled-coil dimer formation. Estimation of the ellipticity at 222 nm from a series of snapshots from the MD simulations with DicroCalc shows distinct increases in the ellipticity when the coiled-coil is fluorinated, which suggests that the helicity in the folded coiled-coils is greater when fluorinated.
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Affiliation(s)
- Scott S. Pendley
- Departments of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
| | - Yihua B. Yu
- Departments of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
- Departments of Pharmaceutical Sciences and Bioengineering, University of Maryland, University of Maryland, 20 Penn Street, Rm. 635, Baltimore, MD 21201
| | - Thomas E. Cheatham
- Departments of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
- Department of Medicinal Chemistry, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
- Department of Bioengineering, University of Utah, 2000 South 30 East, Skaggs Hall 201, Salt Lake City, UT 84112
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24
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Peacock AFA, Stuckey JA, Pecoraro VL. Switching the chirality of the metal environment alters the coordination mode in designed peptides. Angew Chem Int Ed Engl 2009; 48:7371-4. [PMID: 19579245 PMCID: PMC3014729 DOI: 10.1002/anie.200902166] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The effects of switching the chirality of a single layer of amino acids in a three stranded coiled coil has been investigated. X-ray crystallography reveals that this modification is well tolerated and does not alter the designed structure. In contrast, spectroscopic studies of cadmium binding to both the L- and D- enantiomers of the penicillamine, provide evidence that this switch dramatically alters the metal binding capability, the resulting coordination environment and the position of binding.
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Affiliation(s)
- Anna F. A. Peacock
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109 (USA)
| | - Jeanne A. Stuckey
- Life Sciences Institute, University and Michigan, Ann Arbor, MI 48109 (USA)
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25
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Mizuno T, Hasegawa C, Tanabe Y, Hamajima K, Muto T, Nishi Y, Oda M, Kobayashi Y, Tanaka T. Organic ligand binding by a hydrophobic cavity in a designed tetrameric coiled-coil protein. Chemistry 2008; 15:1491-8. [PMID: 19115294 DOI: 10.1002/chem.200800855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The design and characterization of a hydrophobic cavity in de novo designed proteins provides a wide range of information about the functions of de novo proteins. We designed a de novo tetrameric coiled-coil protein with a hydrophobic pocketlike cavity. Tetrameric coiled coils with hydrophobic cavities have previously been reported. By replacing one Leu residue at the a position with Ala, hydrophobic cavities that did not flatten out due to loose peptide chains were reliably created. To perform a detailed examination of the ligand-binding characteristics of the cavities, we originally designed two other coiled-coil proteins: AM2, with eight Ala substitutions at the adjacent a and d positions at the center of a bundled structure, and AM2W, with one Trp and seven Ala substitutions at the same positions. To increase the association of the helical peptides, each helical peptide was connected with flexible linkers, which resulted in a single peptide chain. These proteins exhibited CD spectra corresponding to superhelical structures, despite weakened hydrophobic packing. AM2W exhibited binding affinity for size-complementary organic compounds. The dissociation constants, K(d), of AM2W were 220 nM for adamantane, 81 microM for 1-adamantanol, and 294 microM for 1-adamantaneacetic acid, as measured by fluorescence titration analyses. Although it was contrary to expectations, AM2 did not exhibit any binding affinity, probably due to structural defects around the designed hydrophobic cavity. Interestingly, AM2W exhibited incremental structure stability through ligand binding. Plugging of structural defects with organic ligands would be expected to facilitate protein folding.
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Affiliation(s)
- Toshihisa Mizuno
- Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Nagoya, Aichi, 466-8555, Japan.
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26
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Huang ZZ, Leman L, Ghadiri M. Biomimetic Catalysis of Diketopiperazine and Dipeptide Syntheses. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200704266] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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27
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Huang ZZ, Leman LJ, Ghadiri MR. Biomimetic catalysis of diketopiperazine and dipeptide syntheses. Angew Chem Int Ed Engl 2008; 47:1758-61. [PMID: 18213666 PMCID: PMC2585744 DOI: 10.1002/anie.200704266] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Entry for the Table of Contents Modular, supramolecular catalysts based on the coiled coil peptide scaffold and designed to mimic nonribosomal peptide synthetases are demonstrated to catalyze the formation of diketopiperazine and linear dipeptides for several aminoacyl substrates. We further demonstrate that the nature of the active site residues in the peptide catalysts can be used to effect directed intermodular aminoacyl transfer processes and govern the relative yields of diketopiperazine, linear dipeptide, and hydrolyzed substrate.
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Affiliation(s)
- Zheng-Zheng Huang
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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28
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Wilcoxen KM, Leman LJ, Weinberger DA, Huang ZZ, Ghadiri MR. Biomimetic catalysis of intermodular aminoacyl transfer. J Am Chem Soc 2007; 129:748-9. [PMID: 17243796 PMCID: PMC2453065 DOI: 10.1021/ja067124h] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Keith M Wilcoxen
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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29
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Leman LJ, Weinberger DA, Huang ZZ, Wilcoxen KM, Ghadiri MR. Functional and mechanistic analyses of biomimetic aminoacyl transfer reactions in de novo designed coiled coil peptides via rational active site engineering. J Am Chem Soc 2007; 129:2959-66. [PMID: 17302417 PMCID: PMC2453064 DOI: 10.1021/ja068052x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ribosomes and nonribosomal peptide synthetases (NRPSs) carry out instructed peptide synthesis through a series of directed intermodular aminoacyl transfer reactions. We recently reported the design of coiled-coil assemblies that could functionally mimic the elementary aminoacyl loading and intermodular aminoacyl transfer steps of NRPSs. These peptides were designed initially to accelerate aminoacyl transfer mainly through catalysis by approximation by closely juxtaposing four active site moieties, two each from adjacent noncovalently associated helical modules. In our designs peptide self-assembly positions a cysteine residue that is used to covalently capture substrates from solution via transthiolesterification (substrate loading step to generate the aminoacyl donor site) adjacent to an aminoacyl acceptor site provided by a covalently tethered amino acid or modeled by the epsilon-amine of an active site lysine. However, through systematic functional analyses of 48 rationally designed peptide sequences, we have now determined that the substrate loading and intermodular aminoacyl transfer steps can be significantly influenced (up to approximately 103-fold) by engineering changes in the active site microenvironment through amino acid substitutions and variations in the inter-residue distances and geometry. Mechanistic studies based on 15N NMR and kinetic analysis further indicate that certain active site constellations furnish an unexpectedly large pK(a) depression (1.5 pH units) of the aminoacyl-acceptor moiety, helping to explain the observed high rates of aminoacyl transfer in those constructs. Taken together, our studies demonstrate the feasibility of engineering efficient de novo peptide sequences possessing active sites and functions reminiscent of those in natural enzymes.
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Affiliation(s)
- Luke J Leman
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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30
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Hulko M, Berndt F, Gruber M, Linder JU, Truffault V, Schultz A, Martin J, Schultz JE, Lupas AN, Coles M. The HAMP domain structure implies helix rotation in transmembrane signaling. Cell 2006; 126:929-40. [PMID: 16959572 DOI: 10.1016/j.cell.2006.06.058] [Citation(s) in RCA: 307] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2006] [Revised: 04/21/2006] [Accepted: 06/16/2006] [Indexed: 10/24/2022]
Abstract
HAMP domains connect extracellular sensory with intracellular signaling domains in over 7500 proteins, including histidine kinases, adenylyl cyclases, chemotaxis receptors, and phosphatases. The solution structure of an archaeal HAMP domain shows a homodimeric, four-helical, parallel coiled coil with unusual interhelical packing, related to the canonical packing by rotation of the helices. This suggests a model for the mechanism of signal transduction, in which HAMP alternates between the observed conformation and a canonical coiled coil. We explored this mechanism in vitro and in vivo using HAMP domain fusions with a mycobacterial adenylyl cyclase and an E. coli chemotaxis receptor. Structural and functional studies show that the equilibrium between the two forms is dependent on the side-chain size of residue 291, which is alanine in the wild-type protein.
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Affiliation(s)
- Michael Hulko
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany
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31
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Liu J, Zheng Q, Deng Y, Kallenbach NR, Lu M. Conformational Transition between Four and Five-stranded Phenylalanine Zippers Determined by a Local Packing Interaction. J Mol Biol 2006; 361:168-79. [PMID: 16828114 DOI: 10.1016/j.jmb.2006.05.063] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2006] [Revised: 05/19/2006] [Accepted: 05/24/2006] [Indexed: 11/21/2022]
Abstract
Alpha-helical coiled coils play a crucial role in mediating specific protein-protein interactions. However, the rules and mechanisms that govern helix-helix association in coiled coils remain incompletely understood. Here we have engineered a seven heptad "Phe-zipper" protein (Phe-14) with phenylalanine residues at all 14 hydrophobic a and d positions, and generated a further variant (Phe-14(M)) in which a single core Phe residue is substituted with Met. Phe-14 forms a discrete alpha-helical pentamer in aqueous solution, while Phe-14(M) folds into a tetrameric helical structure. X-ray crystal structures reveal that in both the tetramer and the pentamer the a and d side-chains interlock in a classical knobs-into-holes packing to produce parallel coiled-coil structures enclosing large tubular cavities. However, the presence of the Met residue in the apolar interface of the tetramer markedly alters its local coiled-coil conformation and superhelical geometry. Thus, short-range interactions involving the Met side-chain serve to preferentially select for tetramer formation, either by inhibiting a nucleation step essential for pentamer folding or by abrogating an intermediate required to form the pentamer. Although specific trigger sequences have not been clearly identified in dimeric coiled coils, higher-order coiled coils, as well as other oligomeric multi-protein complexes, may require such sequences to nucleate and direct their assembly.
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Affiliation(s)
- Jie Liu
- Department of Biochemistry, Weill Medical College of Cornell University, New York, NY 10021, USA
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32
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Yadav MK, Leman LJ, Price DJ, Brooks CL, Stout CD, Ghadiri MR. Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution. Biochemistry 2006; 45:4463-73. [PMID: 16584182 PMCID: PMC1780269 DOI: 10.1021/bi060092q] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A detailed understanding of the mechanisms by which particular amino acid sequences can give rise to more than one folded structure, such as for proteins that undergo large conformational changes or misfolding, is a long-standing objective of protein chemistry. Here, we describe the crystal structures of a single coiled-coil peptide in distinct parallel and antiparallel tetrameric configurations and further describe the parallel or antiparallel crystal structures of several related peptide sequences; the antiparallel tetrameric assemblies represent the first crystal structures of GCN4-derived peptides exhibiting such a configuration. Intriguingly, substitution of a single solvent-exposed residue enabled the parallel coiled-coil tetramer GCN4-pLI to populate the antiparallel configuration, suggesting that the two configurations are close enough in energy for subtle sequence changes to have important structural consequences. We present a structural analysis of the small changes to the helix register and side-chain conformations that accommodate the two configurations and have supplemented these results using solution studies and a molecular dynamics energetic analysis using a replica exchange methodology. Considering the previous examples of structural nonspecificity in coiled-coil peptides, the findings reported here not only emphasize the predisposition of the coiled-coil motif to adopt multiple configurations but also call attention to the associated risk that observed crytstal structures may not represent the only (or even the major) species present in solution.
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Affiliation(s)
| | | | | | | | | | - M. Reza Ghadiri
- * Address correspondence to this author. (858) 784-2700 (phone); (858) 784-2798 (fax); (e-mail)
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33
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Cooper WJ, Waters ML. Molecular recognition with designed peptides and proteins. Curr Opin Chem Biol 2005; 9:627-31. [PMID: 16257571 DOI: 10.1016/j.cbpa.2005.10.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2005] [Accepted: 10/12/2005] [Indexed: 12/01/2022]
Abstract
The design of proteins and peptides as molecular receptors is a rapidly growing area of research. Two primary approaches have been utilized, involving the minimization of known protein binding motifs or the de novo design of binding pockets within well-folded protein structures. These approaches are complementary and help define the minimum requirements necessary for biomolecular recognition. Recent advances in this area include the design of cavities within helix bundles for the binding of anesthetics, the design of beta-hairpins for the recognition of nucleotides and oligonucleotides, the redesign of protein binding sites for unique ligands, and the design of mini-proteins via protein grafting for the recognition of proteins and DNA. These advances provide exciting new opportunities to develop novel biosensors, de novo designed catalysts, exogenously triggered synthetic signal transduction cascades, and novel approaches to therapeutic treatments.
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Affiliation(s)
- W John Cooper
- Department of Chemistry, CB 3290, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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