151
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am Ende CW, Meng HY, Ye M, Pandey AK, Zondlo NJ. Design of lanthanide fingers: compact lanthanide-binding metalloproteins. Chembiochem 2010; 11:1738-47. [PMID: 20623571 DOI: 10.1002/cbic.201000056] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Lanthanides have interesting chemical properties; these include luminescent, magnetic, and catalytic functions. Toward the development of proteins incorporating novel functions, we have designed a new lanthanide-binding motif, lanthanide fingers. These were designed based on the Zif268 zinc finger, which exhibits a beta beta alpha structural motif. Lanthanide fingers utilize an Asp(2)Glu(2) metal-coordination environment to bind lanthanides through a tetracarboxylate peptide ligand. The iterative design of a general lanthanide-binding peptide incorporated the following key elements: 1) residues with high alpha-helix and beta-sheet propensities in the respective secondary structures; 2) an optimized big box alpha-helix N-cap; 3) a Schellman alpha-helix C-cap motif; and 4) an optional D-Pro-Ser type II' beta-turn in the beta-hairpin. The peptides were characterized for lanthanide binding by circular dichroism (CD), NMR, and fluorescence spectroscopy. In all instances, stabilization of the peptide secondary structures resulted in an increase in metal affinity. The optimized protein design was a 25-residue peptide that was a general lanthanide-binding motif; this binds all lanthanides examined in a competitive aqueous environment, with a dissociation constant of 9.3 microM for binding Er(3+). CD spectra of the peptide-lanthanide complexes are similar to those of zinc fingers and other beta beta alpha proteins. Metal binding involves residues from the N-terminal beta-hairpin and the C terminal alpha-helical segments of the peptide. NMR data indicated that metal binding induced a global change in the peptide structure. The D-Pro-Ser type II' beta-turn motif could be replaced by Thr-Ile to generate genetically encodable lanthanide fingers. Replacement of the central Phe with Trp generated genetically encodable lanthanide fingers that exhibited terbium luminescence greater than that of an EF-hand peptide.
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Affiliation(s)
- Christopher W am Ende
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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152
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Patel K, Goyal B, Kumar A, Kishore N, Durani S. Cured of “Stickiness”, Poly-l β-Hairpin is Promoted with ll-to-dd Mutation as a Protein and a Hydrolase Mimic. J Phys Chem B 2010; 114:16887-93. [DOI: 10.1021/jp1062572] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Kirti Patel
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Bhupesh Goyal
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Anil Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
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153
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Krishnan V, Tronin A, Strzalka J, Fry HC, Therien MJ, Blasie JK. Control of the orientational order and nonlinear optical response of the "push-pull" chromophore RuPZn via specific incorporation into densely packed monolayer ensembles of an amphiphilic four-helix bundle peptide: characterization of the peptide-chromophore complexes. J Am Chem Soc 2010; 132:11083-92. [PMID: 20698674 DOI: 10.1021/ja1010702] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
"Push-pull" chromophores based on extended pi-electron systems have been designed to exhibit exceptionally large molecular hyperpolarizabilities. We have engineered an amphiphilic four-helix bundle peptide to vectorially incorporate such hyperpolarizable chromophores having a metalloporphyrin moiety, with high specificity into the interior core of the bundle. The amphiphilic exterior of the bundle facilitates the formation of densely packed monolayer ensembles of the vectorially oriented peptide-chromophore complexes at the liquid-gas interface. Chemical specificity designed into the ends of the bundle facilitates the subsequent covalent attachment of these monolayer ensembles onto the surface of an inorganic substrate. In this article, we describe the structural characterization of these monolayer ensembles at each stage of their fabrication for one such peptide-chromophore complex designated as AP0-RuPZn. In the accompanying article, we describe the characterization of their macroscopic nonlinear optical properties.
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Affiliation(s)
- Venkata Krishnan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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154
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Browne W, Geissler PL. The susceptibility of α-helical secondary structure to steric strain: Coarse-grained simulation of dendronized polypeptides. J Chem Phys 2010; 133:145102. [PMID: 20950049 DOI: 10.1063/1.3498780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The propensity of a peptide chain for adopting helical secondary structure can be modulated not only through the solvation properties of its side chains but also through their size and shape. Here we examine a coarse-grained model for dendronized polypeptides that focuses on the susceptibility of α-helical structure to the steric strain exerted by hydrophilic pendant groups. Undecorated molecules exhibit a pronounced transition from random coil to helix upon cooling [J. P. Kemp and J. Z. Y. Chen, Biomacromolecules 2, 389 (2001)]. As gauged by specific heat and by order parameters characterizing helicity at several length scales, this transition is quite robust to the introduction of first- and second-generation dendron side chains. More highly branched side chains, however, reduce the entropy of compact states so severely that helical ordering is undetectable over the entire temperature range accessible to our importance sampling methods. Consistent with experimental observations for side chains comparable to those of our model in volume-excluding size and shape, we find the backbone of these third-generation molecules to assume a distended rodlike state that is both stiff and achiral.
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Affiliation(s)
- William Browne
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, USA
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155
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Dai Q, Dong M, Liu Z, Prorok M, Castellino FJ. Ca 2+-induced self-assembly in designed peptides with optimally spaced gamma-carboxyglutamic acid residues. J Inorg Biochem 2010; 105:52-7. [PMID: 21134602 DOI: 10.1016/j.jinorgbio.2010.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Revised: 08/08/2010] [Accepted: 10/01/2010] [Indexed: 11/18/2022]
Abstract
We have previously elucidated a new paradigm for the metal ion-induced helix-helix assembly in the natural γ-carboxyglutamic acid (Gla)-containing class of conantokin (con) peptides, typified by con-G and a variant of con-T, con-T[K7Gla], independent of the hydrophobic effect. In these "metallo-zipper" structures, Gla residues spaced at i, i+4, i+7, i+11 intervals, which is similar to the arrangement of a and d residues in typical heptads of coiled-coils, coordinate with Ca(2+) and form specific antiparallel helical dimers. In order to evaluate the common role of Gla residues in peptide self-assembly, we extend herein the same Gla arrangement to designed peptides: NH(2)-(γLSγEAK)(3)-CONH(2) (peptide 1) and NH(2)-γLSγEAKγLSγQANγLSγKAE-CONH(2) (peptide 2). Peptide 1 and peptide 2 exhibit no helicity alone, but undergo structural transitions to helical conformations in the presence of a variety of divalent cations. Sedimentation equilibrium ultracentrifugation analyses showed that peptide 1 and peptide 2 form helical dimers in the presence of Ca(2+), but not Mg(2+). Folding and thiol-disulfide rearrangement assays with Cys-containing peptide variants indicated that the helical dimers are mixtures of antiparallel and parallel dimers, which is different from the strict antiparallel strand orientations of con-G and con-T[K7γGla] dimers. These findings suggest that the Gla arrangement, i, i+4, i+7, i+11, i+14, plays a key role in helix formation, without a strict adherence to strand orientation of the helical dimer.
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Affiliation(s)
- Qiuyun Dai
- Institute of Biotechnology, Beijing 100071, China.
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156
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Yokoi N, Inaba H, Terauchi M, Stieg AZ, Sanghamitra NJM, Koshiyama T, Yutani K, Kanamaru S, Arisaka F, Hikage T, Suzuki A, Yamane T, Gimzewski JK, Watanabe Y, Kitagawa S, Ueno T. Construction of robust bio-nanotubes using the controlled self-assembly of component proteins of bacteriophage T4. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2010; 6:1873-1879. [PMID: 20661999 DOI: 10.1002/smll.201000772] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- Norihiko Yokoi
- Department of Chemistry, Graduate School of Science, Nagoya university, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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157
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Castro GR, Knubovets T. Homogeneous Biocatalysis in Organic Solvents and Water-Organic Mixtures. Crit Rev Biotechnol 2010. [DOI: 10.1080/bty.23.3.195] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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158
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Roy L, Case MA. Protein Core Packing by Dynamic Combinatorial Chemistry. J Am Chem Soc 2010; 132:8894-6. [DOI: 10.1021/ja1029717] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Liton Roy
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405
| | - Martin A. Case
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405
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159
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Helix Induction by Dirhodium: Access to Biocompatible Metallopeptides with Defined Secondary Structure. Chemistry 2010; 16:6651-9. [DOI: 10.1002/chem.200903092] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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160
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Yang D, Liu GJ, Hao Y, Li W, Dong ZM, Zhang DW, Zhu NY. Conformational Studies on Peptides of α-Aminoxy Acids with Functionalized Side Chains. Chem Asian J 2010; 5:1356-63. [DOI: 10.1002/asia.200900636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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161
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162
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163
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Smaldone RA, Lin EC, Moore JS. Intrastrand foldamer crosslinking by reductive amination. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/pola.23848] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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164
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Jabre ND, Respondek T, Ulku SA, Korostelova N, Kodanko JJ. A Divergent Strategy for Attaching Polypyridyl Ligands to Peptides. J Org Chem 2010; 75:650-9. [DOI: 10.1021/jo9021953] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nitinkumar D. Jabre
- Department of Chemistry, Wayne State Universty, 5101 Cass Ave, Detroit, Michigan 48202
| | - Tomasz Respondek
- Department of Chemistry, Wayne State Universty, 5101 Cass Ave, Detroit, Michigan 48202
| | - Selma A. Ulku
- Department of Chemistry, Wayne State Universty, 5101 Cass Ave, Detroit, Michigan 48202
| | - Nadiya Korostelova
- Department of Chemistry, Wayne State Universty, 5101 Cass Ave, Detroit, Michigan 48202
| | - Jeremy J. Kodanko
- Department of Chemistry, Wayne State Universty, 5101 Cass Ave, Detroit, Michigan 48202
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165
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Tian P. Computational protein design, from single domain soluble proteins to membrane proteins. Chem Soc Rev 2010; 39:2071-82. [DOI: 10.1039/b810924a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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166
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Faiella M, Andreozzi C, de Rosales RTM, Pavone V, Maglio O, Nastri F, DeGrado WF, Lombardi A. An artificial di-iron oxo-protein with phenol oxidase activity. Nat Chem Biol 2009; 5:882-4. [PMID: 19915535 PMCID: PMC3808167 DOI: 10.1038/nchembio.257] [Citation(s) in RCA: 157] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Accepted: 09/15/2009] [Indexed: 12/11/2022]
Abstract
Here we report the de novo design and NMR structure of a four-helical bundle di-iron protein with phenol oxidase activity. The introduction of the cofactor-binding and phenol-binding sites required the incorporation of residues that were detrimental to the free energy of folding of the protein. Sufficient stability was, however, obtained by optimizing the sequence of a loop distant from the active site.
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Affiliation(s)
- Marina Faiella
- Department of Chemistry, University Federico II of Napoli, Complesso Universitario Monte S. Angelo, Italy
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167
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Diss ML, Kennan AJ. Heterotrimeric coiled coils with core residue urea side chains. J Org Chem 2009; 73:9752-5. [PMID: 19032043 DOI: 10.1021/jo802379p] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report several coiled coil heterotrimers with varying core residue buried polar groups, all with T(m) values >43 degrees C. Introduction of new synthetic side chain structures, including some terminating in monosubstituted ureas, diversifies the pool of viable core residue candidates. A study of core charge pairings demonstrates that, unlike dimeric systems, trimeric coiled coils do not tolerate guanidine-guanidine contacts, even in the presence of a compensating carboxylate. Overall, the roster of feasible coiled coil designs is significantly expanded.
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Affiliation(s)
- Maria L Diss
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
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168
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Engineering responsive mechanisms to control the assembly of peptide-based nanostructures. Biochem Soc Trans 2009; 37:653-9. [PMID: 19614570 DOI: 10.1042/bst0370653] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Complex biological machines arise from self-assembly on the basis of structural features programmed into sequence-specific macromolecules (i.e. polypeptides and polynucleotides) at the molecular level. As a consequence of the near-absolute control of macromolecular architecture that results from such sequence specificity, biological structural platforms may have advantages for the creation of functional supramolecular assemblies in comparison with synthetic polymers. Thus biological structural motifs present an attractive target for the synthesis of artificial nanoscale systems on the basis of relationships between sequence and supramolecular structure that have been established for native biological assemblies. In the present review, we describe an approach to the creation of structurally defined supramolecular assemblies derived from synthetic alpha-helical coiled-coil structural motifs. Two distinct challenges are encountered in this approach to materials design: the ability to recode the canonical sequences of native coiled-coil structural motifs to accommodate the formation of structurally defined supramolecular assemblies (e.g. synthetic helical fibrils) and the development of methods to control supramolecular self-assembly of these peptide-based materials under defined conditions that would be amenable to conventional processing methods. In the present review, we focus on the development of mechanisms based on guest-host recognition to control fibril assembly/disassembly. This strategy utilizes the latent structural specificity encoded within sequence-defined peptides to couple a conformational transition within the coiled-coil motifs to incremental changes in environmental conditions. The example of a selective metal-ion-induced conformational switch will be employed to validate the design principles.
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169
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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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170
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Zaykov A, MacKenzie K, Ball Z. Controlling Peptide Structure with Coordination Chemistry: Robust and Reversible Peptide-Dirhodium Ligation. Chemistry 2009; 15:8961-5. [DOI: 10.1002/chem.200901266] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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171
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Abstract
Metalloproteins catalyse some of the most complex and important processes in nature, such as photosynthesis and water oxidation. An ultimate test of our knowledge of how metalloproteins work is to design new metalloproteins. Doing so not only can reveal hidden structural features that may be missing from studies of native metalloproteins and their variants, but also can result in new metalloenzymes for biotechnological and pharmaceutical applications. Although it is much more challenging to design metalloproteins than non-metalloproteins, much progress has been made in this area, particularly in functional design, owing to recent advances in areas such as computational and structural biology.
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Affiliation(s)
- Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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172
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Coquière D, Bos J, Beld J, Roelfes G. Enantioselective artificial metalloenzymes based on a bovine pancreatic polypeptide scaffold. Angew Chem Int Ed Engl 2009; 48:5159-62. [PMID: 19557756 DOI: 10.1002/anie.200901134] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Site creation: Enantioselective artificial metalloenzymes have been created by grafting a new active site onto bovine pancreatic polypeptide through the introduction of an amino acid capable of coordinating a copper(II) ion. This hybrid catalyst gave good enantioselectivities in the Diels-Alder and Michael addition reactions in water (see scheme) and displayed a very high substrate selectivity.
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Affiliation(s)
- David Coquière
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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173
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Narasimhan SK, Kerwood DJ, Wu L, Li J, Lombardi R, Freedman TB, Luk YY. Induced Folding by Chiral Nonplanar Aromatics. J Org Chem 2009; 74:7023-33. [DOI: 10.1021/jo9013047] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Lei Wu
- Department of Chemistry, Syracuse University, Syracuse, New York 13244
| | - Jun Li
- Department of Chemistry, Syracuse University, Syracuse, New York 13244
| | - Rosina Lombardi
- Department of Chemistry, Syracuse University, Syracuse, New York 13244
| | | | - Yan-Yeung Luk
- Department of Chemistry, Syracuse University, Syracuse, New York 13244
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174
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Rajapandian V, Raman SS, Hakkim V, Parthasarathi R, Subramanian V. Molecular mechanics and molecular dynamics study on azurin using extensible and systematic force field (ESFF). ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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175
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Dudev T, Lim C. Metal-Binding Affinity and Selectivity of Nonstandard Natural Amino Acid Residues from DFT/CDM Calculations. J Phys Chem B 2009; 113:11754-64. [DOI: 10.1021/jp904249s] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Todor Dudev
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, and the Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, and the Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
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176
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Marsh ENG, Buer BC, Ramamoorthy A. Fluorine--a new element in the design of membrane-active peptides. MOLECULAR BIOSYSTEMS 2009; 5:1143-7. [PMID: 19756303 DOI: 10.1039/b909864j] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Antimicrobial peptides (also known as genetically encoded peptide antibiotics) are a diverse class of short cationic amphipathic polypeptides that exhibit a broad-spectrum of antimicrobial activities by selectively disrupting the bacterial cell membrane. In this review article, we present the use of fluorinated amino acids in the design of antimicrobial peptides and other membrane-active peptides.
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Affiliation(s)
- E Neil G Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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177
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Lataifeh A, Beheshti S, Kraatz H. Designer Peptides: Attempt to Control Peptide Structure by Exploiting Ferrocene as a Scaffold. Eur J Inorg Chem 2009. [DOI: 10.1002/ejic.200900268] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anas Lataifeh
- Department of Chemistry, University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada, Fax: +1‐519‐661‐3022
| | - Samaneh Beheshti
- Department of Chemistry, University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada, Fax: +1‐519‐661‐3022
| | - Heinz‐Bernhard Kraatz
- Department of Chemistry, University of Western Ontario, 1151 Richmond Street, London, Ontario, N6A 5B7, Canada, Fax: +1‐519‐661‐3022
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178
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Kang H, Liu H, Phillips JA, Cao Z, Kim Y, Chen Y, Yang Z, Li J, Tan W. Single-DNA molecule nanomotor regulated by photons. NANO LETTERS 2009; 9:2690-6. [PMID: 19499899 PMCID: PMC2772652 DOI: 10.1021/nl9011694] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We report the design of a single-molecule nanomotor driven by photons. The nanomotor is a DNA hairpin-structured molecule incorporated with azobenzene moieties to facilitate reversible photocontrollable switching. Upon repeated UV-vis irradiation, this nanomotor displayed 40-50% open-close conversion efficiency. This type of nanomotor displays well-regulated responses and can be operated under mild conditions with no output of waste. In contrast to multiple-component DNA nanomachines, the intramolecular interaction in this single-molecule system offers unique concentration-independent motor functionality. Moreover, the hairpin structure of the motor backbone can significantly improve the efficiency of light-to-movement energy conversion. These results suggest that azobenzene-incorporated, hairpin-structured single-molecule DNA nanomotors have promising potential for applications which require highly efficient light-driven molecular motors.
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Affiliation(s)
- Huaizhi Kang
- Center for Research at the Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200
| | - Haipeng Liu
- Center for Research at the Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200
| | - Joseph A. Phillips
- Center for Research at the Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200
| | - Zehui Cao
- Center for Research at the Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200
| | - Youngmi Kim
- Center for Research at the Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200
| | - Yan Chen
- Center for Research at the Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution, 1115 NW Fourth Street, Gainesville, Florida 32601
| | - Jianwei Li
- Center for Research at the Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200
| | - Weihong Tan
- Center for Research at the Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200
- Corresponding author: ; phone and fax, 352 846 2410
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179
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Coquière D, Bos J, Beld J, Roelfes G. Enantioselective Artificial Metalloenzymes Based on a Bovine Pancreatic Polypeptide Scaffold. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200901134] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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180
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Tang J, Kang SG, Saven JG, Gai F. Characterization of the cofactor-induced folding mechanism of a zinc-binding peptide using computationally designed mutants. J Mol Biol 2009; 389:90-102. [PMID: 19361525 DOI: 10.1016/j.jmb.2009.03.074] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 03/26/2009] [Accepted: 03/31/2009] [Indexed: 10/20/2022]
Abstract
Metals are the most commonly encountered protein cofactors, and they play important structural and functional roles in biology. In many cases, metal binding provides a major driving force for a polypeptide chain to fold. While there are many studies on the structure, stability, and function of metal-binding proteins, there are few studies focusing on understanding the kinetic mechanism of metal-induced folding. Herein, the Zn(2+)-induced folding kinetics of a small zinc-binding protein are studied; the CH1(1) peptide is derived from the first cysteine/histidine-rich region (CH1 domain) of the protein interaction domains of the transcriptional coregulator CREB-binding protein. Computational design is used to introduce tryptophan and histidine mutations that are structurally consistent with CH1(1); these mutants are studied using stopped-flow tryptophan fluorescence experiments. The Zn(2+)-induced CH1(1) folding kinetics are consistent with two parallel pathways, where the initial binding of Zn(2+) occurs at two sites. However, the initially formed Zn(2+)-bound complexes can proceed either directly to the folded state where zinc adopts a tetrahedral coordination or to an off-pathway misligated intermediate. While elimination of those ligands responsible for misligation simplifies the folding kinetics, it also leads to a decrease in the zinc binding constant. Therefore, these results suggest why these nonnative zinc ligands in the CH1(1) motif are conserved in several distantly related organisms and why the requirement for function can lead to kinetic frustration in folding. In addition, the loop closure rate of the CH1(1) peptide is determined based on the proposed model and temperature-dependent kinetic measurements.
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Affiliation(s)
- Jia Tang
- Department of Chemistry, University of Pennsylvania, Philadelphia, 19104, USA
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181
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Łuczkowski M, Stachura M, Schirf V, Demeler B, Hemmingsen L, Pecoraro VL. Design of thiolate rich metal binding sites within a peptidic framework. Inorg Chem 2009; 47:10875-88. [PMID: 18959366 DOI: 10.1021/ic8009817] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A de novo protein design strategy provides a powerful tool to elucidate how heavy metals interact with proteins.Cysteine derivatives of the TRI peptide family (Ac-G(LKALEEK)4G-NH2) have been shown to bind heavy metals in an unusual trigonal geometry. Our present objective was to design binding sites in R-helical scaffolds that are able to form higher coordination number complexes with Cd(II) and Hg(II). Herein, we evaluate the binding of Cd(II) and Hg(II) to double cysteine substituted TRI peptides lacking intervening leucines between sulfurs in the heptads. We compare a -Cysd-X-X-X-Cysa- binding motif found in TRIL12CL16C to the more common -Cysa-X-X-Cysd- sequence of native proteins found in TRIL9CL12C. Compared to TRI, these substitutions destabilize the helical aggregates,leading to mixtures of two- and three-stranded bundles. The three-stranded coiled coils are stabilized by the addition of metals. TRIL9CL12C forms distorted tetrahedral complexes with both Cd(II) and Hg(II), as supported by UV-vis,CD, 113Cd NMR, 199Hg NMR and 111mCd PAC spectroscopy. Additionally, these signatures are very similar to those found for heavy metal substituted rubredoxin. These results suggest that in terms of Hg(II) binding, TRIL9CL12Ccan be considered as a good mimic of the metallochaperone HAH1, that has previously been shown to form protein dimers. TRIL12CL16C has limited ability to generate homoleptic tetrahedral complexes (Cd(SR)42-). These type of complexes were identified only for Hg(II). However, the spectroscopic signatures suggest a different geometry around the metal ion, demonstrating that effective metal sequestration into the hydrophobic interior of the bundle requires more than simply adding two sulfur residues in adjacent layers of the peptide core. Thus, proper design of metal binding sites must also consider the orientation of cysteine sidechains in a vs d positions of the heptads.
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Affiliation(s)
- Marek Łuczkowski
- Department of Chemistry, UniVersity of Michigan, Ann Arbor, Michigan 48109-1055, USA
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182
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Bode BE, Plackmeyer J, Bolte M, Prisner TF, Schiemann O. PELDOR on an exchange coupled nitroxide copper(II) spin pair. J Organomet Chem 2009. [DOI: 10.1016/j.jorganchem.2008.11.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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183
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Pires MM, Chmielewski J. Self-assembly of Collagen Peptides into Microflorettes via Metal Coordination. J Am Chem Soc 2009; 131:2706-12. [PMID: 19182901 DOI: 10.1021/ja8088845] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marcos M. Pires
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084
| | - Jean Chmielewski
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084
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184
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Engineering heme binding sites in monomeric rop. J Biol Inorg Chem 2009; 14:497-505. [PMID: 19152012 DOI: 10.1007/s00775-009-0465-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 12/26/2008] [Indexed: 10/21/2022]
Abstract
Heme ligands were introduced in the hydrophobic core of an engineered monomeric ColE1 repressor of primer (rop-S55) in two different layers of the heptad repeat. Mutants rop-L63M/F121H (layer 1) and rop-L56H/L113H (layer 3) were found to bind heme with a K (D) of 1.1 +/- 0.2 and 0.47 +/- 0.07 microM, respectively. The unfolding of heme-bound and heme-free mutants, in the presence of guanidinium hydrochloride, was monitored by both circular dichroism and fluorescence spectroscopy. For the heme-bound rop mutants, the total free energy change was 0.5 kcal/mol higher in the layer 3 mutant compared with that in the layer1 mutant. Heme binding also stabilized these mutants by increasing the [DGobsH2O] by 1.4 and 1.8 kcal/mol in rop-L63M/F121H and rop-L56H/L113H, respectively. The reduction potentials measured by spectroelectrochemical titrations were calculated to be -154 +/- 2 mV for rop-56H/113H and -87.5 +/- 1.2 mV for rop-L63M/F121H. The mutant designed to bind heme in a more buried environment (layer 3) showed tighter heme binding, a higher stability, and a different reduction potential compared with the mutant designed to bind heme in layer 1.
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185
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Peacock AFA, Iranzo O, Pecoraro VL. Harnessing natures ability to control metal ion coordination geometry using de novo designed peptides. Dalton Trans 2009:2271-80. [PMID: 19290357 DOI: 10.1039/b818306f] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Advances in protein chemistry and molecular and structural biology have empowered modern chemists to build complex biological architectures using a "first principles" approach, which is known as de novo protein design. In this Perspective we demonstrate how simple three-stranded alpha-helical constructs can be prepared by the sole consideration of the primary amino acid sequence of a peptide. With these well defined systems, we then demonstrate that metal binding cavities can be carved out of the hydrophobic cores of these aggregates in order to bind metal ions such as cadmium with well defined coordination geometries. Examples will be given of homoleptic CdS(3) complexes, CdS(3)O sites and proteins which contain equilibrium mixtures of these two species. We will provide a description of a strategy that allows us to build heterochromic peptides (small proteins that complex two metals in nearly identical environments but which result in different physical properties and allow for metal site selectivity). We conclude with a new class of designed peptides, diastereopeptides, which can exploit changes in amino acid chirality to control metal ion coordination number and lead to an alternative path towards heterochromic systems. The constructs described herein represent the initial steps of preparing protein structures that may simultaneous contain structural and catalytic metal binding centers. These studies inform the community on a developing field, which promises new opportunities for the study of bioinorganic chemistry.
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Affiliation(s)
- Anna F A Peacock
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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186
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Sharma GV, Rao KS, Ravi R, Narsimulu K, Nagendar P, Chandramouli C, Kumar SK, Kunwar A. Synthesis ofβ-Peptides withβ-Helices from New C-Linked Carbo-β-Amino Acids: Study on the Impact of Carbohydrate Side Chains. Chem Asian J 2009; 4:181-93. [DOI: 10.1002/asia.200800249] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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187
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Schweiker KL, Makhatadze GI. Protein stabilization by the rational design of surface charge-charge interactions. Methods Mol Biol 2009; 490:261-83. [PMID: 19157087 DOI: 10.1007/978-1-59745-367-7_11] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The design of proteins with increased stability has many important applications in biotechnology. In recent years, strategies involving directed evolution, sequence-based design, or computational design have proven successful for generating stabilized proteins. A brief overview of the various methods that have been used to increase protein stability is presented, followed by a detailed example of how the rational design of surface charge-charge interactions has provided a robust method for protein stabilization.
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Affiliation(s)
- Katrina L Schweiker
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
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188
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Schweiker KL, Makhatadze GI. A computational approach for the rational design of stable proteins and enzymes: optimization of surface charge-charge interactions. Methods Enzymol 2009; 454:175-211. [PMID: 19216927 DOI: 10.1016/s0076-6879(08)03807-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The design of stable proteins and enzymes is not only of particular biotechnological importance, but also addresses some important fundamental questions. While there are a number of different options available for designing or engineering stable proteins, the field of computational design provides fast and universal methods for stabilizing proteins of interest. One of the successful computational design strategies focuses on stabilizing proteins through the optimization of charge-charge interactions on the protein surface. By optimizing surface interactions, it is possible to alleviate some of the challenges that accompany efforts to redesign the protein core. The rational design of surface charge-charge interactions also allows one to optimize only the interactions that are distant from binding sites or active sites, making it possible to increase stability without adversely affecting activity. The optimization of surface charge-charge interactions is discussed in detail along with the experimental evidence to demonstrate that this is a robust and universal approach to designing proteins with enhanced stability.
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Affiliation(s)
- Katrina L Schweiker
- Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
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189
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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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190
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Peacock AFA, Hemmingsen L, Pecoraro VL. Using diastereopeptides to control metal ion coordination in proteins. Proc Natl Acad Sci U S A 2008; 105:16566-71. [PMID: 18940928 PMCID: PMC2575460 DOI: 10.1073/pnas.0806792105] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Indexed: 11/18/2022] Open
Abstract
Here, we report a previously undescribed approach for controlling metal ion coordination geometry in biomolecules by reorientating amino acid side chains through substitution of L- to D-amino acids. These diastereopeptides allow us to manipulate the spatial orientation of amino acid side chains to alter the sterics of metal binding pockets. We have used this approach to design the de novo metallopeptide, Cd(TRIL12L(D)L16C)(3)(-), which is an example of Cd(II) bound to 3 L-Cys as exclusively trigonal CdS(3), as characterized by a combination of (113)Cd NMR and (111m)Cd PAC spectroscopy. We subsequently show that the physical properties of such a site, such as the high pK(a2) for Cd(II) binding of 15.1, is due to the nature of the coordination number and not the ligating group. Further more this approach allowed for the design of a construct, GRANDL12L(D)L16CL26AL30C, capable of independently binding 2 equivalents of Cd(II) to 2 very similar Cys sites as exclusively 3- and 4-, CdS(3) and CdS(3)O, respectively. Demonstrating that we are capable of controlling the Cd(II) coordination number in these 2 sites solely by varying the nature of a noncoordinating second coordination sphere amino acid, with D-leucine and L-alanine resulting in exclusively 3- and 4-coordinate structures, respectively. Cd(II) was found to selectively bind to the 4-coordinate CdS(3)O site, demonstrating that a protein can be designed that displays metal-binding selectivity based solely on coordination number control and not on the chemical identity of coordinating ligands.
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Affiliation(s)
- Anna F. A. Peacock
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055; and
| | - Lars Hemmingsen
- Department of Natural Sciences, Faculty of Life Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055; and
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191
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Razeghifard R. Artificial photoactive proteins. PHOTOSYNTHESIS RESEARCH 2008; 98:677-685. [PMID: 18830805 DOI: 10.1007/s11120-008-9367-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2008] [Accepted: 09/09/2008] [Indexed: 05/26/2023]
Abstract
Solar power is the most abundant source of renewable energy. In this respect, the goal of making photoactive proteins is to utilize this energy to generate an electron flow. Photosystems have provided the blueprint for making such systems, since they are capable of converting the energy of light into an electron flow using a series of redox cofactors. Protein tunes the redox potential of the cofactors and arranges them such that their distance and orientation are optimal for the creation of a stable charge separation. The aim of this review is to present an overview of the literature with regard to some elegant functional structures that protein designers have created by introducing cofactors and photoactivity into synthetic proteins.
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Affiliation(s)
- Reza Razeghifard
- Division of Math, Science, and Technology, Farquhar College of Arts & Science, Nova Southeastern University, Fort Lauderdale, FL 33314, USA.
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192
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Kožíšek M, Svatoš A, Buděšínský M, Muck A, Bauer M, Kotrba P, Ruml T, Havlas Z, Linse S, Rulíšek L. Molecular Design of Specific Metal-Binding Peptide Sequences from Protein Fragments: Theory and Experiment. Chemistry 2008; 14:7836-46. [DOI: 10.1002/chem.200800178] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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193
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Crystal structure of a self-assembling lipopeptide detergent at 1.20 A. Proc Natl Acad Sci U S A 2008; 105:12861-6. [PMID: 18753631 DOI: 10.1073/pnas.0801941105] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lipopeptide detergents (LPDs) are a new class of amphiphile designed specifically for the structural study of integral membrane proteins. The LPD monomer consists of a 25-residue peptide with fatty acyl chains linked to side chains located at positions 2 and 24 of the peptide. LPDs are designed to form alpha-helices that self-assemble into cylindrical micelles, providing a more natural interior acyl chain packing environment relative to traditional detergents. We have determined the crystal structure of LPD-12, an LPD coupled to two dodecanoic acids, to a resolution of 1.20 A. The LPD-12 monomers adopt the target conformation and associate into cylindrical octamers as expected. Pairs of helices are strongly associated as Alacoil-type antiparallel dimers, and four of these dimers interact through much looser contacts into assemblies with approximate D(2) symmetry. The aligned helices form a cylindrical shell with a hydrophilic exterior that protects an interior hydrophobic cavity containing the 16 LPD acyl chains. Over 90% of the methylene/methyl groups from the acylated side chains are visible in the micelle interiors, and approximately 90% of these adopt trans dihedral angle conformations. Dodecylmaltoside (DDM) was required for the crystallization of LPD-12, and we find 10-24 ordered DDM molecules associated with each LPD assembly, resulting in an overall micelle molecular weight of approximately 30 kDa. The structures confirm the major design objectives of the LPD framework, and reveal unexpected features that will be helpful in the engineering additional versions of lipopeptide amphiphiles.
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194
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McAllister KA, Zou H, Cochran FV, Bender GM, Senes A, Fry HC, Nanda V, Keenan PA, Lear JD, Saven JG, Therien MJ, Blasie JK, DeGrado WF. Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays. J Am Chem Soc 2008; 130:11921-7. [PMID: 18710226 DOI: 10.1021/ja800697g] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed a computational design strategy based on the alpha-helical coiled-coil to generate modular peptide motifs capable of assembling into metalloporphyrin arrays of varying lengths. The current study highlights the extension of a two-metalloporphyrin array to a four-metalloporphyrin array through the incorporation of a coiled-coil repeat unit. Molecular dynamics simulations demonstrate that the initial design evolves rapidly to a stable structure with a small rmsd compared to the original model. Biophysical characterization reveals elongated proteins of the desired length, correct cofactor stoichiometry, and cofactor specificity. The successful extension of the two-porphyrin array demonstrates how this methodology serves as a foundation to create linear assemblies of organized electrically and optically responsive cofactors.
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Affiliation(s)
- Karen A McAllister
- Department of Biochemistry and Molecular Biophysics, Johnson Foundation, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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195
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Laungani AC, Slattery JM, Krossing I, Breit B. Supramolecular bidentate ligands by metal-directed in situ formation of antiparallel beta-sheet structures and application in asymmetric catalysis. Chemistry 2008; 14:4488-502. [PMID: 18449870 DOI: 10.1002/chem.200800359] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The principles of protein structure design, molecular recognition, and supramolecular and combinatorial chemistry have been applied to develop a convergent metal-ion-assisted self-assembly approach that is a very simple and effective method for the de novo design and the construction of topologically predetermined antiparallel beta-sheet structures and self-assembled catalysts. A new concept of in situ generation of bidentate P-ligands for transition-metal catalysis, in which two complementary, monodentate, peptide-based ligands are brought together by employing peptide secondary structure motif as constructing tool to direct the self-assembly process, is achieved through formation of stable beta-sheet motifs and subsequent control of selectivity. The supramolecular structures were studied by (1)H, (31)P, and (13)C NMR spectroscopy, ESI mass spectrometry, X-ray structure analysis, and theoretical calculations. Our initial catalysis results confirm the close relationship between the self-assembled sheet conformations and the catalytic activity of these metallopeptides in the asymmetric rhodium-catalyzed hydroformylation. Good catalyst activity and moderate enantioselectivity were observed for the selected combination of catalyst and substrate, but most importantly the concept of this new methodology was successfully proven. This work presents a perspective interface between protein design and supramolecular catalysis for the design of beta-sheet mimetics and screening of libraries of self-organizing supramolecular catalysts.
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Affiliation(s)
- Andy C Laungani
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
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196
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Abstract
We present a new design of peptide-polymer conjugates where a polymer chain is covalently linked to the side chain of a helix bundle-forming peptide. The effect of conjugated polymer chains on the peptide structure was examined using a de novo designed three-helix bundle and a photoactive four-helix bundle. Upon attachment of poly(ethylene glycol) to the exterior of the coiled-coil helix bundle, the peptide secondary structure was stabilized and the tertiary structure, that is, the coiled-coil helix bundle, was retained. When a heme-binding peptide as an example is used, the new peptide-polymer conjugate architecture also preserves the built-in functionalities within the interior of the helix bundle. It is expected that the conjugated polymer chains act to mediate the interactions between the helix bundle and its external environment. Thus, this new peptide-polymer conjugate design strategy may open new avenues to macroscopically assemble the helix bundles and may enable them to function in nonbiological environments.
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Affiliation(s)
- Jessica Y. Shu
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720
| | - Cen Tan
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720
| | - William F. DeGrado
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Ting Xu
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720
- Department of Chemistry, University of California, Berkeley, California 94720
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
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197
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Raman SS, Vijayaraj R, Parthasarathi R, Subramanian V. Helix forming tendency of valine substituted poly-alanine: a molecular dynamics investigation. J Phys Chem B 2008; 112:9100-4. [PMID: 18597521 DOI: 10.1021/jp7119813] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In this study, classical molecular dynamics simulations have been carried out on the valine (guest) substituted poly alanine (host) using the host-guest peptide approach to understand the role of valine in the formation and stabilization of helix. Valine has been substituted in the host peptide starting from N terminal to C terminal. Various structural parameters have been obtained from the molecular dynamics simulation to understand the tolerance of helical motif to valine. Depending on the position of valine in the host peptide, it stabilizes (or destabilizes) the formation of the helical structure. The substitution of valine in the poly alanine at some positions has no effect on the helix formation (deformation). It is interesting to observe the coexistence of 3 10 and alpha-helix in the peptides due to the dynamical nature of the hydrogen bonding interaction and sterical interactions.
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Affiliation(s)
- S Sundar Raman
- Chemical Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020 India
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198
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Zhang J, Kuznetsov AM, Medvedev IG, Chi Q, Albrecht T, Jensen PS, Ulstrup J. Single-Molecule Electron Transfer in Electrochemical Environments. Chem Rev 2008; 108:2737-91. [PMID: 18620372 DOI: 10.1021/cr068073+] [Citation(s) in RCA: 252] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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199
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Pantoja-Uceda D, Pastor MT, Salgado J, Pineda-Lucena A, Pérez-Payá E. Design of a bivalent peptide with two independent elements of secondary structure able to fold autonomously. J Pept Sci 2008; 14:845-54. [DOI: 10.1002/psc.1015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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200
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Matsubara T, Iida M, Tsumuraya T, Fujii I, Sato T. Selection of a carbohydrate-binding domain with a helix-loop-helix structure. Biochemistry 2008; 47:6745-51. [PMID: 18540680 DOI: 10.1021/bi8000837] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We obtained a novel carbohydrate-binding peptide having a helix-loop-helix scaffold from a random peptide library. The helix-loop-helix peptide library randomized at five amino acid residues was displayed on the major coat protein of a filamentous phage. Affinity selection with a ganglioside, Galbeta1-3GalNAcbeta1-4(Neu5Acalpha2-3)Galbeta1-4Glcbeta1-1'Cer (GM1), gave positive phage clones. Surface plasmon resonance spectroscopy showed that a corresponding 35-mer synthetic peptide had high affinity for GM1 with a dissociation constant of 0.24 microM. This peptide preferentially binds to GM1 rather than asialo GM1 and GM2, suggesting that a terminal galactose and sialic acid are required for the binding as for cholera toxin. Circular dichroism spectroscopic studies indicated that a helical structure is important for the affinity and specificity. Furthermore, alanine scanning at randomized positions showed that arginine and phenylalanine play an especially important role in the recognition of carbohydrates. Such a de novo helix-loop-helix peptide would be available for the design of carbohydrate-binding proteins.
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