1
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Winski A, Ludwiczak J, Orlowska M, Madaj R, Kaminski K, Dunin‐Horkawicz S. AlphaFold2 captures the conformational landscape of the HAMP signaling domain. Protein Sci 2024; 33:e4846. [PMID: 38010737 PMCID: PMC10731501 DOI: 10.1002/pro.4846] [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: 05/23/2023] [Revised: 10/30/2023] [Accepted: 11/19/2023] [Indexed: 11/29/2023]
Abstract
In this study, we present a conformational landscape of 5000 AlphaFold2 models of the Histidine kinases, Adenyl cyclases, Methyl-accepting proteins and Phosphatases (HAMP) domain, a short helical bundle that transduces signals from sensors to effectors in two-component signaling proteins such as sensory histidine kinases and chemoreceptors. The landscape reveals the conformational variability of the HAMP domain, including rotations, shifts, displacements, and tilts of helices, many combinations of which have not been observed in experimental structures. HAMP domains belonging to a single family tend to occupy a defined region of the landscape, even when their sequence similarity is low, suggesting that individual HAMP families have evolved to operate in a specific conformational range. The functional importance of this structural conservation is illustrated by poly-HAMP arrays, in which HAMP domains from families with opposite conformational preferences alternate, consistent with the rotational model of signal transduction. The only poly-HAMP arrays that violate this rule are predicted to be of recent evolutionary origin and structurally unstable. Finally, we identify a family of HAMP domains that are likely to be dynamic due to the presence of a conserved pi-helical bulge. All code associated with this work, including a tool for rapid sequence-based prediction of the rotational state in HAMP domains, is deposited at https://github.com/labstructbioinf/HAMPpred.
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Affiliation(s)
- Aleksander Winski
- Laboratory of Structural Bioinformatics, Centre of New TechnologiesUniversity of WarsawWarsawPoland
| | - Jan Ludwiczak
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research CentreUniversity of WarsawWarsawPoland
- Present address:
Prescient Design, Genentech Research & Early DevelopmentRoche GroupBaselSwitzerland
| | - Malgorzata Orlowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research CentreUniversity of WarsawWarsawPoland
| | - Rafal Madaj
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research CentreUniversity of WarsawWarsawPoland
| | - Kamil Kaminski
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research CentreUniversity of WarsawWarsawPoland
| | - Stanislaw Dunin‐Horkawicz
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research CentreUniversity of WarsawWarsawPoland
- Department of Protein EvolutionMax Planck Institute for Biology TübingenTübingenGermany
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2
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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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3
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Pinter TBJ, Ruckthong L, Stuckey JA, Deb A, Penner-Hahn JE, Pecoraro VL. Open Reading Frame 1 Protein of the Human Long Interspersed Nuclear Element 1 Retrotransposon Binds Multiple Equivalents of Lead. J Am Chem Soc 2021; 143:15271-15278. [PMID: 34494819 PMCID: PMC11069406 DOI: 10.1021/jacs.1c06461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The human long interspersed nuclear element 1 (LINE1) has been implicated in numerous diseases and has been suggested to play a significant role in genetic evolution. Open reading frame 1 protein (ORF1p) is one of the two proteins encoded in this self-replicating mobile genetic element, both of which are essential for retrotransposition. The structure of the three-stranded coiled-coil domain of ORF1p was recently solved and showed the presence of tris-cysteine layers in the interior of the coiled-coil that could function as metal binding sites. Here, we demonstrate that ORF1p binds Pb(II). We designed a model peptide, GRCSL16CL23C, to mimic two of the ORF1p Cys3 layers and crystallized the peptide both as the apo-form and in the presence of Pb(II). Structural comparison of the ORF1p with apo-(GRCSL16CL23C)3 shows very similar Cys3 layers, preorganized for Pb(II) binding. We propose that exposure to heavy metals, such as lead, could influence directly the structural parameters of ORF1p and thus impact the overall LINE1 retrotransposition frequency, directly relating heavy metal exposure to genetic modification.
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Affiliation(s)
- Tyler B. J. Pinter
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Leela Ruckthong
- Department of Chemistry, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Bang Mod, Thung Khru, Bangkok, 10140, Thailand
| | - Jeanne A. Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, 48109, United States
| | - Aniruddha Deb
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - James E. Penner-Hahn
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States
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4
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Szczepaniak K, Bukala A, da Silva Neto AM, Ludwiczak J, Dunin-Horkawicz S. A library of coiled-coil domains: from regular bundles to peculiar twists. Bioinformatics 2021; 36:5368-5376. [PMID: 33325494 PMCID: PMC8016460 DOI: 10.1093/bioinformatics/btaa1041] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/30/2020] [Accepted: 12/07/2020] [Indexed: 11/30/2022] Open
Abstract
MOTIVATION Coiled coils are widespread protein domains involved in diverse processes ranging from providing structural rigidity to the transduction of conformational changes. They comprise two or more α-helices that are wound around each other to form a regular supercoiled bundle. Owing to this regularity, coiled-coil structures can be described with parametric equations, thus enabling the numerical representation of their properties, such as the degree and handedness of supercoiling, rotational state of the helices, and the offset between them. These descriptors are invaluable in understanding the function of coiled coils and designing new structures of this type. The existing tools for such calculations require manual preparation of input and are therefore not suitable for the high-throughput analyses. RESULTS To address this problem, we developed SamCC-Turbo, a software for fully automated, per-residue measurement of coiled coils. By surveying Protein Data Bank with SamCC-Turbo, we generated a comprehensive atlas of ∼50 000 coiled-coil regions. This machine learning-ready dataset features precise measurements as well as decomposes coiled-coil structures into fragments characterized by various degrees of supercoiling. The potential applications of SamCC-Turbo are exemplified by analyses in which we reveal general structural features of coiled coils involved in functions requiring conformational plasticity. Finally, we discuss further directions in the prediction and modeling of coiled coils. AVAILABILITY AND IMPLEMENTATION SamCC-Turbo is available as a web server (https://lbs.cent.uw.edu.pl/samcc_turbo) and as a Python library (https://github.com/labstructbioinf/samcc_turbo), whereas the results of the Protein Data Bank scan can be browsed and downloaded at https://lbs.cent.uw.edu.pl/ccdb. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Krzysztof Szczepaniak
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Adriana Bukala
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Antonio Marinho da Silva Neto
- Molecular Prospecting and Bioinformatics Group, Laboratory of Immunopathology Keizo Asami, Federal University of Pernambuco, 50670-901 Recife, Brazil
| | - Jan Ludwiczak
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland
| | - Stanislaw Dunin-Horkawicz
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
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5
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Polizzi NF, DeGrado WF. A defined structural unit enables de novo design of small-molecule-binding proteins. Science 2020; 369:1227-1233. [PMID: 32883865 PMCID: PMC7526616 DOI: 10.1126/science.abb8330] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 06/29/2020] [Indexed: 12/21/2022]
Abstract
The de novo design of proteins that bind highly functionalized small molecules represents a great challenge. To enable computational design of binders, we developed a unit of protein structure-a van der Mer (vdM)-that maps the backbone of each amino acid to statistically preferred positions of interacting chemical groups. Using vdMs, we designed six de novo proteins to bind the drug apixaban; two bound with low and submicromolar affinity. X-ray crystallography and mutagenesis confirmed a structure with a precisely designed cavity that forms favorable interactions in the drug-protein complex. vdMs may enable design of functional proteins for applications in sensing, medicine, and catalysis.
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Affiliation(s)
- Nicholas F Polizzi
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
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6
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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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7
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Designed peptides that assemble into cross-α amyloid-like structures. Nat Chem Biol 2018; 14:870-875. [PMID: 30061717 DOI: 10.1038/s41589-018-0105-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/19/2018] [Indexed: 11/08/2022]
Abstract
Amyloids adopt 'cross-β' structures composed of long, twisted fibrils with β-strands running perpendicular to the fibril axis. Recently, a toxic peptide was proposed to form amyloid-like cross-α structures in solution, with a planar bilayer-like assembly observed in the crystal structure. Here we crystallographically characterize designed peptides that assemble into spiraling cross-α amyloid-like structures, which resemble twisted β-amyloid fibrils. The peptides form helical dimers, stabilized by packing of small and apolar residues, and the dimers further assemble into cross-α amyloid-like fibrils with superhelical pitches ranging from 170 Å to 200 Å. When a small residue that appeared critical for packing was converted to leucine, it resulted in structural rearrangement to a helical polymer. Fluorescently tagged versions of the designed peptides form puncta in mammalian cells, which recover from photobleaching with markedly different kinetics. These structural folds could be potentially useful for directing in vivo protein assemblies with predetermined spacing and stabilities.
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8
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Ludwiczak J, Jarmula A, Dunin-Horkawicz S. Combining Rosetta with molecular dynamics (MD): A benchmark of the MD-based ensemble protein design. J Struct Biol 2018; 203:54-61. [PMID: 29454111 DOI: 10.1016/j.jsb.2018.02.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 01/25/2018] [Accepted: 02/13/2018] [Indexed: 01/15/2023]
Abstract
Computational protein design is a set of procedures for computing amino acid sequences that will fold into a specified structure. Rosetta Design, a commonly used software for protein design, allows for the effective identification of sequences compatible with a given backbone structure, while molecular dynamics (MD) simulations can thoroughly sample near-native conformations. We benchmarked a procedure in which Rosetta design is started on MD-derived structural ensembles and showed that such a combined approach generates 20-30% more diverse sequences than currently available methods with only a slight increase in computation time. Importantly, the increase in diversity is achieved without a loss in the quality of the designed sequences assessed by their resemblance to natural sequences. We demonstrate that the MD-based procedure is also applicable to de novo design tasks started from backbone structures without any sequence information. In addition, we implemented a protocol that can be used to assess the stability of designed models and to select the best candidates for experimental validation. In sum our results demonstrate that the MD ensemble-based flexible backbone design can be a viable method for protein design, especially for tasks that require a large pool of diverse sequences.
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Affiliation(s)
- Jan Ludwiczak
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; Laboratory of Bioinformatics, Nencki Institute of Experimental Biology, Pasteura 3, 02-093 Warsaw, Poland
| | - Adam Jarmula
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology, Pasteura 3, 02-093 Warsaw, Poland
| | - Stanislaw Dunin-Horkawicz
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.
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9
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Zhang SQ, Chino M, Liu L, Tang Y, Hu X, DeGrado WF, Lombardi A. De Novo Design of Tetranuclear Transition Metal Clusters Stabilized by Hydrogen-Bonded Networks in Helical Bundles. J Am Chem Soc 2018; 140:1294-1304. [PMID: 29249157 PMCID: PMC5860638 DOI: 10.1021/jacs.7b08261] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
De novo design provides an attractive approach to test the mechanism by which metalloproteins define the geometry and reactivity of their metal ion cofactors. While there has been considerable progress in designing proteins that bind transition metal ions including iron-sulfur clusters, the design of tetranuclear clusters with oxygen-rich environments has not been accomplished. Here, we describe the design of tetranuclear clusters, consisting of four Zn2+ and four carboxylate oxygens situated at the vertices of a distorted cube-like structure. The tetra-Zn2+ clusters are bound at a buried site within a four-helix bundle, with each helix donating a single carboxylate (Glu or Asp) and imidazole (His) ligand, as well as second- and third-shell ligands. Overall, the designed site consists of four Zn2+ and 16 polar side chains in a fully connected hydrogen-bonded network. The designed proteins have apolar cores at the top and bottom of the bundle, which drive the assembly of the liganding residues near the center of the bundle. The steric bulk of the apolar residues surrounding the binding site was varied to determine how subtle changes in helix-helix packing affect the binding site. The crystal structures of two of four proteins synthesized were in good agreement with the overall design; both formed a distorted cuboidal site stabilized by flanking second- and third-shell interactions that stabilize the primary ligands. A third structure bound a single Zn2+ in an unanticipated geometry, and the fourth bound multiple Zn2+ at multiple sites at partial occupancy. The metal-binding and conformational properties of the helical bundles in solution, probed by circular dichroism spectroscopy, analytical ultracentrifugation, and NMR, were consistent with the crystal structures.
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Affiliation(s)
- Shao-Qing Zhang
- Department of Chemistry, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA 19104-6396, United States
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
| | - Marco Chino
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, I-80126 Napoli, Italy
| | - Lijun Liu
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
- DLX Scientific, Lawrence, KS 66049, United States
| | - Youzhi Tang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
- College of Veterinary Medicine, South China Agricultural University, Guangdong 510642, China
| | - Xiaozhen Hu
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
| | - Angela Lombardi
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, I-80126 Napoli, Italy
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10
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Abstract
α-Helical coiled coils constitute one of the most diverse folds yet described. They range in length over two orders of magnitude; they form rods, segmented ropes, barrels, funnels, sheets, spirals, and rings, which encompass anywhere from two to more than 20 helices in parallel or antiparallel orientation; they assume different helix crossing angles, degrees of supercoiling, and packing geometries. This structural diversity supports a wide range of biological functions, allowing them to form mechanically rigid structures, provide levers for molecular motors, project domains across large distances, mediate oligomerization, transduce conformational changes and facilitate the transport of other molecules. Unlike almost any other protein fold known to us, their structure can be computed from parametric equations, making them an ideal model system for rational protein design. Here we outline the principles by which coiled coils are structured, review the determinants of their folding and stability, and present an overview of their diverse architectures.
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11
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Nayak AR, Karade SS, Srivastava VK, Rana AK, Gupta CM, Sahasrabuddhe AA, Pratap JV. Structure of Leishmania donovani coronin coiled coil domain reveals an antiparallel 4 helix bundle with inherent asymmetry. J Struct Biol 2016; 195:129-38. [PMID: 26940672 DOI: 10.1016/j.jsb.2016.02.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 02/26/2016] [Accepted: 02/27/2016] [Indexed: 11/26/2022]
Abstract
Coiled coils are ubiquitous structural motifs that serve as a platform for protein-protein interactions and play a central role in myriad physiological processes. Though the formation of a coiled coil requires only the presence of suitably spaced hydrophobic residues, sequence specificities have also been associated with specific oligomeric states. RhXXhE is one such sequence motif, associated with parallel trimers, found in coronins and other proteins. Coronin, present in all eukaryotes, is an actin-associated protein involved in regulating actin turnover. Most eukaryotic coronins possess the RhXXhE trimerization motif. However, a unique feature of parasitic kinetoplastid coronin is that the positions of R and E are swapped within their coiled coil domain, but were still expected to form trimers. To understand the role of swapped motif in oligomeric specificity, we determined the X-ray crystal structure of Leishmania donovani coronin coiled coil domain (LdCoroCC) at 2.2Å, which surprisingly, reveals an anti-parallel tetramer assembly. Small angle X-ray scattering studies and chemical crosslinking confirm the tetramer in solution and is consistent with the oligomerization observed in the full length protein. Structural analyses reveal that LdCoroCC possesses an inherent asymmetry, in that one of the helices of the bundle is axially shifted with respect to the other three. The analysis also identifies steric reasons that cause this asymmetry. The bundle adapts an extended a-d-e core packing, the e residue being polar (with an exception) which results in a thermostable bundle with polar and apolar interfaces, unlike the existing a-d-e core antiparallel homotetramers with apolar core. Functional implications of the anti-parallel association in kinetoplastids are discussed.
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Affiliation(s)
- Ashok Ranjan Nayak
- Division of Molecular and Structural Biology, CSIR - Central Drug Research Institute, Jankipuram Extension, Sitapur Road, Lucknow 226031, India
| | - Sharanbasappa Shrimant Karade
- Division of Molecular and Structural Biology, CSIR - Central Drug Research Institute, Jankipuram Extension, Sitapur Road, Lucknow 226031, India
| | - Vijay Kumar Srivastava
- Division of Molecular and Structural Biology, CSIR - Central Drug Research Institute, Jankipuram Extension, Sitapur Road, Lucknow 226031, India
| | - Ajay Kumar Rana
- Division of Molecular and Structural Biology, CSIR - Central Drug Research Institute, Jankipuram Extension, Sitapur Road, Lucknow 226031, India
| | - C M Gupta
- Division of Molecular and Structural Biology, CSIR - Central Drug Research Institute, Jankipuram Extension, Sitapur Road, Lucknow 226031, India
| | - Amogh A Sahasrabuddhe
- Division of Molecular and Structural Biology, CSIR - Central Drug Research Institute, Jankipuram Extension, Sitapur Road, Lucknow 226031, India
| | - J Venkatesh Pratap
- Division of Molecular and Structural Biology, CSIR - Central Drug Research Institute, Jankipuram Extension, Sitapur Road, Lucknow 226031, India.
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12
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Malashkevich VN, Higgins CD, Almo SC, Lai JR. A switch from parallel to antiparallel strand orientation in a coiled-coil X-ray structure via two core hydrophobic mutations. Biopolymers 2015; 104:178-85. [PMID: 25753192 PMCID: PMC4768791 DOI: 10.1002/bip.22631] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 02/23/2015] [Indexed: 01/20/2023]
Abstract
The coiled-coil is one of the most ubiquitous and well studied protein structural motifs. Significant effort has been devoted to dissecting subtle variations of the typical heptad repeat sequence pattern that can designate larger topological features such as relative α-helical orientation and oligomer size. Here we report the X-ray structure of a model coiled-coil peptide, HA2-Del-L2seM, which forms an unanticipated core antiparallel dimer with potential sites for discrete higher-order multimerization (trimer or tetramer). In the X-ray structure, a third, partially-ordered α-helix is weakly associated with the antiparallel dimer and analytical ultracentrifugation experiments indicate the peptide forms a well-defined tetramer in solution. The HA2-Del-L2seM sequence is closely related to a parent model peptide, HA2-Del, which we previously reported adopts a parallel trimer; HA2-Del-L2seM differs by only hydrophobic leucine to selenomethione mutations and thus this subtle difference is sufficient to switch both relative α-helical topology and number of α-helices participating in the coiled-coil. Comparison of the X-ray structures of HA2-Del-L2seM (reported here) with the HA2-Del parent (reported previously) reveals novel interactions involving the selenomethionine residues that promote antiparallel coiled-coil configuration and preclude parallel trimer formation. These novel atomic insights are instructive for understanding subtle features that can affect coiled-coil topology and provide additional information for design of antiparallel coiled-coils.
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Affiliation(s)
| | | | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
| | - Jonathan R. Lai
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
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