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Slope LN, Daubney OJ, Campbell H, White SA, Peacock AFA. Location-Dependent Lanthanide Selectivity Engineered into Structurally Characterized Designed Coiled Coils. Angew Chem Int Ed Engl 2021; 60:24473-24477. [PMID: 34495573 PMCID: PMC8597134 DOI: 10.1002/anie.202110500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Indexed: 11/08/2022]
Abstract
Herein we report unprecedented location-dependent, size-selective binding to designed lanthanide (Ln3+ ) sites within miniature protein coiled coil scaffolds. Not only do these engineered sites display unusual Ln3+ selectivity for moderately large Ln3+ ions (Nd to Tb), for the first time we demonstrate that selectivity can be location-dependent and can be programmed into the sequence. A 1 nm linear translation of the binding site towards the N-terminus can convert a selective site into a highly promiscuous one. An X-ray crystal structure, the first of a lanthanide binding site within a coiled coil to be reported, coupled with CD studies, reveal the existence of an optimal radius that likely stems from the structural constraints of the coiled coil scaffold. To the best of our knowledge this is the first report of location-dependent metal selectivity within a coiled coil scaffold, as well as the first report of location-dependent Ln3+ selectivity within a protein.
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Affiliation(s)
- Louise N. Slope
- School of ChemistryUniversity of BirminghamEdgbastonB15 2TTUK
| | | | - Hannah Campbell
- School of ChemistryUniversity of BirminghamEdgbastonB15 2TTUK
| | - Scott A. White
- School of BiosciencesUniversity of BirminghamEdgbastonB15 2TTUK
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2
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Slope LN, Daubney OJ, Campbell H, White SA, Peacock AFA. Location‐Dependent Lanthanide Selectivity Engineered into Structurally Characterized Designed Coiled Coils. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Louise N. Slope
- School of Chemistry University of Birmingham Edgbaston B15 2TT UK
| | | | - Hannah Campbell
- School of Chemistry University of Birmingham Edgbaston B15 2TT UK
| | - Scott A. White
- School of Biosciences University of Birmingham Edgbaston B15 2TT UK
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3
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Yokoyama K, D. Catalfamo C, Yuan M. Reversible peptide oligomerization over nanoscale gold surfaces. AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.4.649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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4
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Hagen S, Mattay D, Räuber C, Müller KM, Arndt KM. Characterization and inhibition of AF10-mediated interaction. J Pept Sci 2014; 20:385-97. [PMID: 24692230 DOI: 10.1002/psc.2626] [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: 10/14/2013] [Revised: 02/13/2014] [Accepted: 02/14/2014] [Indexed: 12/24/2022]
Abstract
The non-random chromosomal translocations t(10;11)(p13;q23) and t(10;11)(p13;q14-21) result in leukemogenic fusion proteins comprising the coiled coil domain of the transcription factor AF10 and the proteins MLL or CALM, respectively, and subsequently cause certain types of acute leukemia. The AF10 coiled-coil domain, which is crucial for the leukemogenic effect, has been shown to interact with GAS41, a protein previously identified as the product of an amplified gene in glioblastoma. Using sequential synthetic peptides, we mapped the potential AF10/GAS41 interaction site, which was subsequently be used as scaffold for a library targeting the AF10 coiled-coil domain. Using phage display, we selected a peptide that binds the AF10 coiled-coil domain with higher affinity than the respective coiled-coil region of wild-type GAS41, as demonstrated by phage ELISA, CD, and PCAs. Furthermore, we were able to successfully deploy the inhibitory peptide in a mammalian cell line to lower the expression of Hoxa genes that have been described to be overexpressed in these leukemias. This work dissects molecular determinants mediating AF10-directed interactions in leukemic fusions comprising the N-terminal parts of the proteins MLL or CALM and the C-terminal coiled-coil domain of AF10. Furthermore, it outlines the first steps in recognizing and blocking the leukemia-associated AF10 interaction in histiocytic lymphoma cells and therefore, may have significant implications in future diagnostics and therapeutics.
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Affiliation(s)
- Sven Hagen
- Molecular Biotechnology, University of Potsdam, Potsdam/Golm, Germany; Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany; Institute for Biology III, University of Freiburg, Freiburg, Germany
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5
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Doyle CM, Rumfeldt JA, Broom HR, Broom A, Stathopulos PB, Vassall KA, Almey JJ, Meiering EM. Energetics of oligomeric protein folding and association. Arch Biochem Biophys 2012; 531:44-64. [PMID: 23246784 DOI: 10.1016/j.abb.2012.12.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/29/2012] [Accepted: 12/05/2012] [Indexed: 12/11/2022]
Abstract
In nature, proteins most often exist as complexes, with many of these consisting of identical subunits. Understanding of the energetics governing the folding and misfolding of such homooligomeric proteins is central to understanding their function and misfunction, in disease or biotechnology. Much progress has been made in defining the mechanisms and thermodynamics of homooligomeric protein folding. In this review, we outline models as well as calorimetric and spectroscopic methods for characterizing oligomer folding, and describe extensive results obtained for diverse proteins, ranging from dimers to octamers and higher order aggregates. To our knowledge, this area has not been reviewed comprehensively in years, and the collective progress is impressive. The results provide evolutionary insights into the development of subunit interfaces, mechanisms of oligomer folding, and contributions of oligomerization to protein stability, function and regulation. Thermodynamic analyses have also proven valuable for understanding protein misfolding and aggregation mechanisms, suggesting new therapeutic avenues. Successful recent designs of novel, functional proteins demonstrate increased understanding of oligomer folding. Further rigorous analyses using multiple experimental and computational approaches are still required, however, to achieve consistent and accurate prediction of oligomer folding energetics. Modeling the energetics remains challenging but is a promising avenue for future advances.
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Affiliation(s)
- Colleen M Doyle
- Guelph-Waterloo Centre for Graduate Studies in Chemistry and Biochemistry, and Department of Chemistry, University of Waterloo, 200 University Ave. West, Waterloo, ON, Canada
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6
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Defining the nature of thermal intermediate in 3 state folding proteins: apoflavodoxin, a study case. PLoS Comput Biol 2012; 8:e1002647. [PMID: 22927805 PMCID: PMC3426563 DOI: 10.1371/journal.pcbi.1002647] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 06/18/2012] [Indexed: 11/29/2022] Open
Abstract
The early stages of the thermal unfolding of apoflavodoxin have been determined by using atomistic multi microsecond-scale molecular dynamics (MD) simulations complemented with a variety of experimental techniques. Results strongly suggest that the intermediate is reached very early in the thermal unfolding process and that it has the properties of an “activated” form of the native state, where thermal fluctuations in the loops break loop-loop contacts. The unrestrained loops gain then kinetic energy corrupting short secondary structure elements without corrupting the core of the protein. The MD-derived ensembles agree with experimental observables and draw a picture of the intermediate state inconsistent with a well-defined structure and characteristic of a typical partially disordered protein. Our results allow us to speculate that proteins with a well packed core connected by long loops might behave as partially disordered proteins under native conditions, or alternatively behave as three state folders. Small details in the sequence, easily tunable by evolution, can yield to one or the other type of proteins. A simplistic view of protein structure tends to emphasize the opposition between the native state and the denatured ensemble of unfolded conformations. In addition to these extreme conformations, proteins subjected to a variety of perturbations often populate alternative partly unfolded conformations, some of which are close in energy to the native state and, accordingly, can be populated under native or quasi-native conditions. There is increasing evidence that these “perturbed” conformations participate in protein function or, in some cases, are related to the outcome of folding diseases. We have used the “state of the art” molecular dynamics combined with a variety of experimental techniques to characterize for the first time, to our knowledge, the thermal intermediate of a three-state folding protein (apoflavodoxin). Based on our results we have been able to suggest a general mechanism of thermal unfolding in complex proteins and to determine interesting links between thermal intermediates and partially unfolded proteins.
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Chen Z, Vohidov F, Coughlin JM, Stagg LJ, Arold ST, Ladbury JE, Ball ZT. Catalytic Protein Modification with Dirhodium Metallopeptides: Specificity in Designed and Natural Systems. J Am Chem Soc 2012; 134:10138-45. [DOI: 10.1021/ja302284p] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Zhen Chen
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Farrukh Vohidov
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Jane M. Coughlin
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Loren J. Stagg
- The University of Texas, M.D. Anderson Cancer Center, Houston, Texas
77030, United States
| | - Stefan T. Arold
- The University of Texas, M.D. Anderson Cancer Center, Houston, Texas
77030, United States
| | - John E. Ladbury
- The University of Texas, M.D. Anderson Cancer Center, Houston, Texas
77030, United States
| | - Zachary T. Ball
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
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8
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Tarafdar PK, Vedantam LV, Kondreddy A, Podile AR, Swamy MJ. Biophysical investigations on the aggregation and thermal unfolding of harpinPss and identification of leucine-zipper-like motifs in harpins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1684-92. [DOI: 10.1016/j.bbapap.2009.07.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 07/11/2009] [Accepted: 07/31/2009] [Indexed: 11/17/2022]
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9
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Selectional and mutational scope of peptides sequestering the Jun-Fos coiled-coil domain. J Mol Biol 2008; 381:73-88. [PMID: 18586270 DOI: 10.1016/j.jmb.2008.04.030] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Revised: 04/07/2008] [Accepted: 04/11/2008] [Indexed: 01/14/2023]
Abstract
The activator protein-1 (AP-1) complex plays a crucial role in numerous pathways, and its ability to induce tumorigenesis is well documented. Thus, AP-1 represents an interesting therapeutic target. We selected peptides from phage display and compared their ability to disrupt the cFos/cJun interaction to a previously described in vivo protein-fragment complementation assay (PCA). A cJun-based library was screened to enrich for peptides that disrupt the AP-1 complex by binding to the cFos coiled-coil domain. Interestingly, phage display identified one helix, JunW(Ph1) [phage-selected winning peptide (clone 1) targeting cFos], which differs in only 2 out of 10 randomized positions to JunW (PCA-selected winning peptide targeting cFos). Phage-selected peptides revealed higher affinity to cFos than wild-type cJun, harboring a T(m) of 53 degrees C compared to 16 degrees C for cFos/cJun or 44 degrees C for cFos/JunW. In PCA growth assays in the presence of cJun as competitor, phage-selected JunW(Ph1) conferred shorter generation times than JunW. Bacterial growth was barely detectable, using JunW(Ph1) as a competitor for the wild-type cJun/cFos interaction, indicating efficient cFos removal from the dimeric wild-type complex. Importantly, all inhibitory peptides were able to interfere with DNA binding as demonstrated in gel shift assays. The selected sequences have consequently improved our 'bZIP coiled-coil interaction prediction algorithm' in distinguishing interacting from noninteracting coiled-coil sequences. Predicting and manipulating protein interaction will accelerate the systems biology field, and generated peptides will be valuable tools for analytical and biomedical applications.
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López de la Osa J, Bateman DA, Ho S, González C, Chakrabartty A, Laurents DV. Getting specificity from simplicity in putative proteins from the prebiotic earth. Proc Natl Acad Sci U S A 2007; 104:14941-6. [PMID: 17855563 PMCID: PMC1986592 DOI: 10.1073/pnas.0706876104] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Indexed: 11/18/2022] Open
Abstract
Can unique protein structures arise from a limited set of amino acids present on the prebiotic earth? To address this question, we have determined the stability and structure of KIA7, a 20-residue polypeptide containing chiefly Lys, Ile, and Ala. NMR methods reveal that KIA7 tetramerizes and folds on the millisecond time scale to adopt a four-helix X-bundle structure with a tightly and specifically packed core. Denaturation studies and hydrogen exchange measurements of KIA7 and several variants demonstrate that ridges-into-grooves packing of Ala and Ile side chains and the packing of a C-terminal aromatic group into the hydrophobic core are sufficient to give rise to a rather stable, well folded protein structure, with no favorable electrostatic interactions or tertiary or quaternary hydrogen bonds. Both modern proteins and RNAs can adopt specific structures, but RNAs do so with a limited "alphabet" of residues and types of stabilizing interactions. The results reported here show that specific, well folded protein structures can also arise from a highly reduced set of stabilizing interactions and amino acids that are thought to have been present on the prebiotic earth.
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Affiliation(s)
- Jaime López de la Osa
- *Instituto de Química Física “Rocasolano,” Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain; and
| | - David A. Bateman
- Departments of Medical Biophysics and Biochemistry, University of Toronto, Toronto, ON, Canada M5G-2M9
| | - Sylvia Ho
- Departments of Medical Biophysics and Biochemistry, University of Toronto, Toronto, ON, Canada M5G-2M9
| | - Carlos González
- *Instituto de Química Física “Rocasolano,” Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain; and
| | - Avijit Chakrabartty
- Departments of Medical Biophysics and Biochemistry, University of Toronto, Toronto, ON, Canada M5G-2M9
| | - Douglas V. Laurents
- *Instituto de Química Física “Rocasolano,” Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain; and
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11
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Ali MH, Imperiali B. Protein oligomerization: how and why. Bioorg Med Chem 2005; 13:5013-20. [PMID: 15993087 DOI: 10.1016/j.bmc.2005.05.037] [Citation(s) in RCA: 257] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2005] [Accepted: 05/25/2005] [Indexed: 11/16/2022]
Abstract
A large fraction of cellular proteins are oligomeric. Protein oligomerization may often be an advantageous feature from the perspective of protein evolution and has probably evolved by a variety of mechanisms. The study of protein oligomerization may provide insights into the early protein environment and the evolution of modern proteins. Oligomeric mini-proteins, short peptides with discrete protein-like structures, may serve as valuable models for understanding features of protein oligomerization.
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Affiliation(s)
- Mayssam H Ali
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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12
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Piñeiro A, Villa A, Vagt T, Koksch B, Mark AE. A molecular dynamics study of the formation, stability, and oligomerization state of two designed coiled coils: possibilities and limitations. Biophys J 2005; 89:3701-13. [PMID: 16150975 PMCID: PMC1366940 DOI: 10.1529/biophysj.104.055590] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The formation, relative stability, and possible stoichiometries of two (self-)complementary peptide sequences (B and E) designed to form either a parallel homodimeric (B + B) or an antiparallel heterodimeric (B + E) coiled coil have been investigated. Peptide B shows a characteristic coiled coil pattern in circular dichroism spectra at pH 7.4, whereas peptide E is apparently random coiled under these conditions. The peptides are complementary to each other, with peptide E forming a coiled coil when mixed with peptide B. Molecular dynamics simulations show that combinations of B + B and B + E readily form a dimeric coiled coil, whereas E + E does not fall in line with the experimental data. However, the simulations strongly suggest the preferred orientation of the helices in the homodimeric coiled coil is antiparallel, with interactions at the interface quite different to that of the idealized model. In addition, molecular dynamics simulations suggest equilibrium between dimers, trimers, and tetramers of alpha-helices for peptide B.
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Affiliation(s)
- Angel Piñeiro
- Department of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
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13
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Campos LA, Bueno M, Lopez-Llano J, Jiménez MA, Sancho J. Structure of stable protein folding intermediates by equilibrium phi-analysis: the apoflavodoxin thermal intermediate. J Mol Biol 2004; 344:239-55. [PMID: 15504414 DOI: 10.1016/j.jmb.2004.08.081] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2004] [Revised: 08/19/2004] [Accepted: 08/26/2004] [Indexed: 11/17/2022]
Abstract
Protein intermediates in equilibrium with native states may play important roles in protein dynamics but, in cases, can initiate harmful aggregation events. Investigating equilibrium protein intermediates is thus important for understanding protein behaviour (useful or pernicious) but it is hampered by difficulties in gathering structural information. We show here that the phi-analysis techniques developed to investigate transition states of protein folding can be extended to determine low-resolution three-dimensional structures of protein equilibrium intermediates. The analysis proposed is based solely on equilibrium data and is illustrated by determination of the structure of the apoflavodoxin thermal unfolding intermediate. In this conformation, a large part of the protein remains close to natively folded, but a 40 residue region is clearly unfolded. This structure is fully consistent with the NMR data gathered on an apoflavodoxin mutant designed specifically to stabilise the intermediate. The structure shows that the folded region of the intermediate is much larger than the proton slow-exchange core at 25 degrees C. It also reveals that the unfolded region is made of elements whose packing surface is more polar than average. In addition, it constitutes a useful guide to rationally stabilise the native state relative to the intermediate state, a far from trivial task.
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Affiliation(s)
- Luis A Campos
- Biocomputation and Complex Systems Physics Institute and Department Bioquímica y Biología Molecular y Celular, Fac. Ciencias, University Zaragoza, 50009 Zaragoza, Spain
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14
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Affiliation(s)
- Jody M Mason
- Institut für Biologie III, Albert-Ludwigs-Universität Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
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Boon CL, Frost D, Chakrabartty A. Identification of stable helical bundles from a combinatorial library of amphipathic peptides. Biopolymers 2004; 76:244-57. [PMID: 15148684 DOI: 10.1002/bip.20074] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A set of combinatorial amphipathic helical peptides referred to as the KIA series has been screened to identify native-like helical bundles. The series contains the following consensus sequence: AKAxAAxxKAxAAxxKAGGY, where "x" positions are occupied by either Ala or Ile. The peptide sequences in the series comprise all possible combinations of four Ile residues occupying the six x positions. In each case, Ala occupied the two x positions not occupied by Ile. There are a total of 15 peptides in the KIA series; all of the peptides differ in the number of ridges and grooves formed by the Ile side chains, and two of the KIA peptides possess a canonical knobs-into-holes heptad repeat. The structure and stability of these 15 peptides and their pairwise mixtures were evaluated. One peptide in the series formed a stable four-helix bundle that folded with cooperativity similar to native proteins. Ten peptides assembled into molten globular helical assemblies, two peptides were unstructured, and two peptides assembled into helical filaments that were several micrometers long. One of the helical filament forming peptides could be diverted from forming filaments by the addition of another KIA peptide, and resulted in the formation of a heteromeric six-helix bundle. This study demonstrates that combinatorial peptides composed of only three types of amino acids can form a diverse array of structures, some of which are native-like.
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Affiliation(s)
- Chandra L Boon
- Division of Molecular and Structural Biology, Ontario Cancer Institute and Departments of Medical Biophysics and Biochemistry, University of Toronto, 610 University Avenue, Toronto, Ontario, Canada, M5G 2M9
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