1
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Vázquez Torres S, Leung PJY, Venkatesh P, Lutz ID, Hink F, Huynh HH, Becker J, Yeh AHW, Juergens D, Bennett NR, Hoofnagle AN, Huang E, MacCoss MJ, Expòsit M, Lee GR, Bera AK, Kang A, De La Cruz J, Levine PM, Li X, Lamb M, Gerben SR, Murray A, Heine P, Korkmaz EN, Nivala J, Stewart L, Watson JL, Rogers JM, Baker D. De novo design of high-affinity binders of bioactive helical peptides. Nature 2024; 626:435-442. [PMID: 38109936 PMCID: PMC10849960 DOI: 10.1038/s41586-023-06953-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 12/07/2023] [Indexed: 12/20/2023]
Abstract
Many peptide hormones form an α-helix on binding their receptors1-4, and sensitive methods for their detection could contribute to better clinical management of disease5. De novo protein design can now generate binders with high affinity and specificity to structured proteins6,7. However, the design of interactions between proteins and short peptides with helical propensity is an unmet challenge. Here we describe parametric generation and deep learning-based methods for designing proteins to address this challenge. We show that by extending RFdiffusion8 to enable binder design to flexible targets, and to refining input structure models by successive noising and denoising (partial diffusion), picomolar-affinity binders can be generated to helical peptide targets by either refining designs generated with other methods, or completely de novo starting from random noise distributions without any subsequent experimental optimization. The RFdiffusion designs enable the enrichment and subsequent detection of parathyroid hormone and glucagon by mass spectrometry, and the construction of bioluminescence-based protein biosensors. The ability to design binders to conformationally variable targets, and to optimize by partial diffusion both natural and designed proteins, should be broadly useful.
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Affiliation(s)
- Susana Vázquez Torres
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA
| | - Philip J Y Leung
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA
| | - Preetham Venkatesh
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA
| | - Isaac D Lutz
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Fabian Hink
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Huu-Hien Huynh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Jessica Becker
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Andy Hsien-Wei Yeh
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - David Juergens
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA
| | - Nathaniel R Bennett
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Eric Huang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Marc Expòsit
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA
| | - Gyu Rie Lee
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Joshmyn De La Cruz
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Paul M Levine
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Xinting Li
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Mila Lamb
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Stacey R Gerben
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Analisa Murray
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Piper Heine
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Elif Nihal Korkmaz
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jeff Nivala
- School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Joseph L Watson
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
| | - Joseph M Rogers
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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2
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Rochal S, Levshov D, Avramenko M, Arenal R, Cao TT, Nguyen VC, Sauvajol JL, Paillet M. Chirality manifestation in elastic coupling between the layers of double-walled carbon nanotubes. NANOSCALE 2019; 11:16092-16102. [PMID: 31432840 DOI: 10.1039/c9nr03853a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The search for new relatively easy physicochemical methods for the structural identification of carbon nanotubes represents a key challenge. Here, analyzing the experimental data on double-walled carbon nanotubes (DWCNTs) obtained by us and taken from the literature, we have expressed the magnitude of elastic coupling between two tubular walls forming a DWCNT as a simple function dependent not only on DWCNT diameters but also on the difference between the chirality angles of the constituent nanotubes. To get this quite unexpected result, which allows us to relate more precisely the structural parameters of a DWCNT with frequencies of its radial breathing-like modes (RBLM), we have developed a new model for the RBLM dynamics that takes into account a possible deposition of water molecules from ambient air onto the DWCNT surface. The model constructed allows us to predict the higher prevalence of DWCNTs comprising two walls with identical handedness. The application of the results obtained for the identification of DWCNTs is also considered.
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Affiliation(s)
- Sergei Rochal
- Department of Nanotechnology, Faculty of Physics, Southern Federal University, 5, Zorge Street, Rostov-on-Don, 344090, Russia.
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3
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Lombardi A, Pirro F, Maglio O, Chino M, DeGrado WF. De Novo Design of Four-Helix Bundle Metalloproteins: One Scaffold, Diverse Reactivities. Acc Chem Res 2019; 52:1148-1159. [PMID: 30973707 DOI: 10.1021/acs.accounts.8b00674] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
De novo protein design represents an attractive approach for testing and extending our understanding of metalloprotein structure and function. Here, we describe our work on the design of DF (Due Ferri or two-iron in Italian), a minimalist model for the active sites of much larger and more complex natural diiron and dimanganese proteins. In nature, diiron and dimanganese proteins protypically bind their ions in 4-Glu, 2-His environments, and they catalyze diverse reactions, ranging from hydrolysis, to O2-dependent chemistry, to decarbonylation of aldehydes. In the design of DF, the position of each atom-including the backbone, the first-shell ligands, the second-shell hydrogen-bonded groups, and the well-packed hydrophobic core-was bespoke using precise mathematical equations and chemical principles. The first member of the DF family was designed to be of minimal size and complexity and yet to display the quintessential elements required for binding the dimetal cofactor. After thoroughly characterizing its structural, dynamic, spectroscopic, and functional properties, we added additional complexity in a rational stepwise manner to achieve increasingly sophisticated catalytic functions, ultimately demonstrating substrate-gated four-electron reduction of O2 to water. We also briefly describe the extension of these studies to the design of proteins that bind nonbiological metal cofactors (a synthetic porphyrin and a tetranuclear cluster), and a Zn2+/proton antiporting membrane protein. Together these studies demonstrate a successful and generally applicable strategy for de novo metalloprotein design, which might indeed mimic the process by which primordial metalloproteins evolved. We began the design process with a highly symmetrical backbone and binding site, by using point-group symmetry to assemble the secondary structures that position the amino acid side chains required for binding. The resulting models provided a rough starting point and initial parameters for the subsequent precise design of the final protein using modern methods of computational protein design. Unless the desired site is itself symmetrical, this process requires reduction of the symmetry or lifting it altogether. Nevertheless, the initial symmetrical structure can be helpful to restrain the search space during assembly of the backbone. Finally, the methods described here should be generally applicable to the design of highly stable and robust catalysts and sensors. There is considerable potential in combining the efficiency and knowledge base associated with homogeneous metal catalysis with the programmability, biocompatibility, and versatility of proteins. While the work reported here focuses on testing and learning the principles of natural metalloproteins by designing and studying proteins one at a time, there is also considerable potential for using designed proteins that incorporate both biological and nonbiological metal ion cofactors for the evolution of novel catalysts.
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Affiliation(s)
- Angela Lombardi
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 26, 80126 Napoli, Italy
| | - Fabio Pirro
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 26, 80126 Napoli, Italy
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158-9001, United States
| | - Ornella Maglio
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 26, 80126 Napoli, Italy
- IBB, National Research Council, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 26, 80126 Napoli, Italy
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158-9001, United States
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4
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Gaines JC, Acebes S, Virrueta A, Butler M, Regan L, O'Hern CS. Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins. Proteins 2018; 86:581-591. [PMID: 29427530 PMCID: PMC5912992 DOI: 10.1002/prot.25479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/23/2018] [Accepted: 02/06/2018] [Indexed: 12/26/2022]
Abstract
We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these 3 protein classes. We show that the solvent-inaccessible cores of the 3 classes of proteins are equally densely packed. As a result, the side chains of core residues at protein-protein interfaces and in the membrane-exposed regions of transmembrane proteins can be predicted by the hard-sphere plus stereochemical constraint model with the same high prediction accuracies (>90%) as core residues in soluble proteins. We also find that for all 3 classes of proteins, as one moves away from the solvent-inaccessible core, the packing fraction decreases as the solvent accessibility increases. However, the side chain predictability remains high (80% within 30°) up to a relative solvent accessibility, rSASA≲0.3, for all 3 protein classes. Our results show that ≈40% of the interface regions in protein complexes are "core", that is, densely packed with side chain conformations that can be accurately predicted using the hard-sphere model. We propose packing fraction as a metric that can be used to distinguish real protein-protein interactions from designed, non-binding, decoys. Our results also show that cores of membrane proteins are the same as cores of soluble proteins. Thus, the computational methods we are developing for the analysis of the effect of hydrophobic core mutations in soluble proteins will be equally applicable to analyses of mutations in membrane proteins.
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Affiliation(s)
- J C Gaines
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, 06520
- Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut, 06520
| | - S Acebes
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut, 06520
| | - A Virrueta
- Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut, 06520
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut, 06520
| | - M Butler
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, 90007
| | - L Regan
- Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut, 06520
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, 06520
- Department of Chemistry, Yale University, New Haven, Connecticut, 06520
| | - C S O'Hern
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, 06520
- Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut, 06520
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut, 06520
- Department of Physics, Yale University, New Haven, Connecticut, 06520
- Department of Applied Physics, Yale University, New Haven, Connecticut, 06520
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5
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Empirical and computational design of iron-sulfur cluster proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1256-62. [PMID: 22342202 DOI: 10.1016/j.bbabio.2012.02.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 01/13/2012] [Accepted: 02/01/2012] [Indexed: 11/21/2022]
Abstract
Here, we compare two approaches of protein design. A computational approach was used in the design of the coiled-coil iron-sulfur protein, CCIS, as a four helix bundle binding an iron-sulfur cluster within its hydrophobic core. An empirical approach was used for designing the redox-chain maquette, RCM as a four-helix bundle assembling iron-sulfur clusters within loops and one heme in the middle of its hydrophobic core. We demonstrate that both ways of design yielded the desired proteins in terms of secondary structure and cofactors assembly. Both approaches, however, still have much to improve in predicting conformational changes in the presence of bound cofactors, controlling oligomerization tendency and stabilizing the bound iron-sulfur clusters in the reduced state. Lessons from both ways of design and future directions of development are discussed. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.
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6
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Grigoryan G, Kim YH, Acharya R, Axelrod K, Jain RM, Willis L, Drndic M, Kikkawa JM, DeGrado WF. Computational design of virus-like protein assemblies on carbon nanotube surfaces. Science 2011; 332:1071-6. [PMID: 21617073 PMCID: PMC3264056 DOI: 10.1126/science.1198841] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
There is a general need for the engineering of protein-like molecules that organize into geometrically specific superstructures on molecular surfaces, directing further functionalization to create richly textured, multilayered assemblies. Here we describe a computational approach whereby the surface properties and symmetry of a targeted surface define the sequence and superstructure of surface-organizing peptides. Computational design proceeds in a series of steps that encode both surface recognition and favorable intersubunit packing interactions. This procedure is exemplified in the design of peptides that assemble into a tubular structure surrounding single-walled carbon nanotubes (SWNTs). The geometrically defined, virus-like coating created by these peptides converts the smooth surfaces of SWNTs into highly textured assemblies with long-scale order, capable of directing the assembly of gold nanoparticles into helical arrays along the SWNT axis.
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Affiliation(s)
- Gevorg Grigoryan
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
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7
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Abstract
A long-standing goal of computational protein design is to create proteins similar to those found in Nature. One motivation is to harness the exquisite functional capabilities of proteins for our own purposes. The extent of similarity between designed and natural proteins also reports on how faithfully our models represent the selective pressures that determine protein sequences. As the field of protein design shifts emphasis from reproducing native-like protein structure to function, it has become important that these models treat the notion of specificity in molecular interactions. Although specificity may, in some cases, be achieved by optimization of a desired protein in isolation, methods have been developed to address directly the desire for proteins that exhibit specific functions and interactions.
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Affiliation(s)
- James J Havranek
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110, USA.
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8
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Computational Design of Calmodulin Mutants with up to 900-Fold Increase in Binding Specificity. J Mol Biol 2009; 385:1470-80. [DOI: 10.1016/j.jmb.2008.09.053] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Revised: 09/14/2008] [Accepted: 09/17/2008] [Indexed: 11/15/2022]
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9
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Abstract
Computationally designed peptides against transmembrane helices point to new approaches to studying membrane protein function. A recent report describes the design of short peptides that bind specifically to transmembrane regions of integrins, providing an exciting tool for probing the biology of membrane proteins.
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Affiliation(s)
- Amy E Keating
- MIT Department of Biology, Massachusetts Avenue, Cambridge, MA 02139, USA.
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10
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Yin H, Slusky JS, Berger BW, Walters RS, Vilaire G, Litvinov RI, Lear JD, Caputo GA, Bennett JS, DeGrado WF. Computational design of peptides that target transmembrane helices. Science 2007; 315:1817-22. [PMID: 17395823 DOI: 10.1126/science.1136782] [Citation(s) in RCA: 234] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A variety of methods exist for the design or selection of antibodies and other proteins that recognize the water-soluble regions of proteins; however, companion methods for targeting transmembrane (TM) regions are not available. Here, we describe a method for the computational design of peptides that target TM helices in a sequence-specific manner. To illustrate the method, peptides were designed that specifically recognize the TM helices of two closely related integrins (alphaIIbbeta3 and alphavbeta3) in micelles, bacterial membranes, and mammalian cells. These data show that sequence-specific recognition of helices in TM proteins can be achieved through optimization of the geometric complementarity of the target-host complex.
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Affiliation(s)
- Hang Yin
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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11
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Floudas C, Fung H, McAllister S, Mönnigmann M, Rajgaria R. Advances in protein structure prediction and de novo protein design: A review. Chem Eng Sci 2006. [DOI: 10.1016/j.ces.2005.04.009] [Citation(s) in RCA: 175] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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12
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Tucker MJ, Oyola R, Gai F. A novel fluorescent probe for protein binding and folding studies:p-cyano-phenylalanine. Biopolymers 2006; 83:571-6. [PMID: 16917881 DOI: 10.1002/bip.20587] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Recently, it is has been shown that the C=N stretching vibration of a non-natural amino acid, p-cyano-phenylalanine (PheCN), could be used as an infrared reporter of local environment. Here, we further showed that the fluorescence emission of PheCN is also sensitive to solvent and, therefore, could be used as a novel optical probe for protein binding and folding studies. Moreover, we found that the fluorescence quantum yield of PheCN is nearly five times larger than that of phenylalanine and, more importantly, can be selectively excited even when other aromatic amino acids are present, thus making it a more versatile fluorophore. To test the feasibility of using PheCN as a practical fluorescent probe, we studied the binding of calmodulin (CaM) to a peptide derived from the CaM-binding domain of skeletal muscle myosin light chain kinase (MLCK). The peptide (MLCK3CN) contains a single PheCN residue and has been shown to bind to CaM with high affinity. As expected, addition of CaM into a MLCK3CN solution resulted in quenching of the PheCN fluorescence. A series of stochiometric titrations further allowed us to determine the binding affinity (Kd) of this peptide to CaM. Taken together, these results indicated that the PheCN fluorescence is sensitive to environment and could be applicable to a wide variety of biological problems.
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Affiliation(s)
- Matthew J Tucker
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
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13
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Ali MH, Taylor CM, Grigoryan G, Allen KN, Imperiali B, Keating AE. Design of a heterospecific, tetrameric, 21-residue miniprotein with mixed alpha/beta structure. Structure 2005; 13:225-34. [PMID: 15698566 DOI: 10.1016/j.str.2004.12.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2004] [Revised: 12/05/2004] [Accepted: 12/06/2004] [Indexed: 10/25/2022]
Abstract
The study of short, autonomously folding peptides, or "miniproteins," is important for advancing our understanding of protein stability and folding specificity. Although many examples of synthetic alpha-helical structures are known, relatively few mixed alpha/beta structures have been successfully designed. Only one mixed-secondary structure oligomer, an alpha/beta homotetramer, has been reported thus far. In this report, we use structural analysis and computational design to convert this homotetramer into the smallest known alpha/beta-heterotetramer. Computational screening of many possible sequence/structure combinations led efficiently to the design of short, 21-residue peptides that fold cooperatively and autonomously into a specific complex in solution. A 1.95 A crystal structure reveals how steric complementarity and charge patterning encode heterospecificity. The first- and second-generation heterotetrameric miniproteins described here will be useful as simple models for the analysis of protein-protein interaction specificity and as structural platforms for the further elaboration of folding and function.
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Affiliation(s)
- Mayssam H Ali
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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14
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Rajagopal S, Meza-Romero R, Ghosh I. Dual surface selection methodology for the identification of thrombin binding epitopes from hotspot biased phage-display libraries. Bioorg Med Chem Lett 2004; 14:1389-93. [PMID: 15006368 DOI: 10.1016/j.bmcl.2003.09.098] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2003] [Accepted: 09/08/2003] [Indexed: 11/28/2022]
Abstract
Protein libraries biased towards amino-acid residues found at so-called 'hotspots' were incorporated into the beta-sheet region of the thermostable variant (HTB1) of the B1 domain of the immunoglobulin (IgG) binding protein G and expressed as gene 3 fusions on M13 bacteriophage. The HTB1 library (2.2 x 10(9)) variants with a minimal 12 amino acid basis set were selected for binding IgG, to ensure structural conservation, and subsequently to thrombin to evolve a thrombin-binding function. We believe that this dual surface selection strategy will have great utility in evolving new bi-functional proteins without compromising structure. Furthermore the discrete beta-sheet epitopes identified by our methodology will lend itself to small-molecule mimicry of beta-sheets.
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Affiliation(s)
- Srivats Rajagopal
- Department of Chemistry, University of Arizona, Tucson, AZ 85721-0041, USA
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15
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Abstract
Computational protein design strategies have been developed to reengineer protein-protein interfaces in an automated, generalizable fashion. In the past two years, these methods have been successfully applied to generate chimeric proteins and protein pairs with specificities different from naturally occurring protein-protein interactions. Although there are shortcomings in current approaches, both in the way conformational space is sampled and in the energy functions used to evaluate designed conformations, the successes suggest we are now entering an era in which computational methods can be used to modulate, reengineer and design protein-protein interaction networks in living cells.
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Affiliation(s)
- Tanja Kortemme
- Howard Hughes Medical Institute and Department of Biochemistry, University of Washington, Box 357350, Seattle, WA 98195, USA
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16
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Hutschenreiter S, Neumann L, Rädler U, Schmitt L, Tampé R. Metal-Chelating Amino Acids As Building Blocks For Synthetic Receptors Sensing Metal Ions And Histidine-Tagged Proteins. Chembiochem 2003; 4:1340-4. [PMID: 14661277 DOI: 10.1002/cbic.200200455] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Protein structure and function rely on a still not fully understood interplay of energetic and entropic constraints defined by the permutation of the twenty genetically encoded amino acids. Many attempts have been undertaken to design peptide-peptide interaction pairs and synthetic receptors de novo by using this limited number of building blocks. We describe a rational approach to creating a building block based on a tailored metal-chelating amino acid. Nepsilon,Nepsilon-bis(carboxymethyl)-L-lysine can be flexibly introduced into peptides by 9-fluorenylmethoxycarbonyl solid-phase chemistry. The corresponding metal-chelating peptides act as metal sensors and synthetic receptors for histidine-tagged proteins. These biochemical tweezers will open new ways to control protein-protein interactions, to design peptide-based interaction pairs, or to generate switchable protein function.
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Affiliation(s)
- Silke Hutschenreiter
- Institute of Biochemistry, Biocenter, Johann-Wolfgang-Goethe University Frankfurt, Marie-Curie Strasse 9, 60439 Frankfurt am Main, Germany
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17
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Abstract
Protein grafting, the transfer of a binding epitope of one ligand onto the surface of another protein, is a potentially powerful technique for presenting peptides in preformed and active three-dimensional conformations. Its utility, however, has been limited by low biological activity of the designed ligands and low tolerance of the protein scaffolds to surface substitutions. Here, we graft the complete binding epitope (19 nonconsecutive amino acids with a solvent-accessible surface area of >2,000 A2) of an HIV-1 C-peptide, which is derived from the C-terminal region of HIV-1 gp41 and potently inhibits HIV-1 entry into cells, onto the surface of a GCN4 leucine zipper. The designed peptide, named C34coil, displays a potent antiviral activity approaching that of the native ligand. Moreover, whereas the linear C-peptide is unstructured and sensitive to degradation by proteases, C34coil is well structured, conformationally stable, and exhibits increased resistance to proteolytic degradation compared with the linear peptide. In addition to being a structured antiviral inhibitor, C34coil may also serve as the basis for the development of an alternative class of immunogens. This study demonstrates that "one-shot" protein grafting, without subsequent rounds of optimization, can be used to create ligands with structural conformations and improved biomedical properties.
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Affiliation(s)
- Samuel K Sia
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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19
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Maglio O, Nastri F, Pavone V, Lombardi A, DeGrado WF. Preorganization of molecular binding sites in designed diiron proteins. Proc Natl Acad Sci U S A 2003; 100:3772-7. [PMID: 12655072 PMCID: PMC152997 DOI: 10.1073/pnas.0730771100] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2003] [Indexed: 11/18/2022] Open
Abstract
De novo protein design provides an attractive approach to critically test the features that are required for metalloprotein structure and function. Previously we designed and crystallographically characterized an idealized dimeric model for the four-helix bundle class of diiron and dimanganese proteins [Dueferri 1 (DF1)]. Although the protein bound metal ions in the expected manner, access to its active site was blocked by large bulky hydrophobic residues. Subsequently, a substrate-access channel was introduced proximal to the metal-binding center, resulting in a protein with properties more closely resembling those of natural enzymes. Here we delineate the energetic and structural consequences associated with the introduction of these binding sites. To determine the extent to which the binding site was preorganized in the absence of metal ions, the apo structure of DF1 in solution was solved by NMR and compared with the crystal structure of the di-Zn(II) derivative. The overall fold of the apo protein was highly similar to that of the di-Zn(II) derivative, although there was a rotation of one of the helices. We also examined the thermodynamic consequences associated with building a small molecule-binding site within the protein. The protein exists in an equilibrium between folded dimers and unfolded monomers. DF1 is a highly stable protein (K(diss) = 0.001 fM), but the dissociation constant increases to 0.6 nM (deltadeltaG = 5.4 kcalmol monomer) as the active-site cavity is increased to accommodate small molecules.
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Affiliation(s)
- Ornella Maglio
- Department of Chemistry, University of Napoli Federico II, Complesso Universitario Monte S. Angelo, I-80126 Napoli, Italy
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20
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Abstract
We report the computational redesign of the protein-binding interface of calmodulin (CaM), a small, ubiquitous Ca(2+)-binding protein that is known to bind to and regulate a variety of functionally and structurally diverse proteins. The CaM binding interface was optimized to improve binding specificity towards one of its natural targets, smooth muscle myosin light chain kinase (smMLCK). The optimization was performed using optimization of rotamers by iterative techniques (ORBIT), a protein design program that utilizes a physically based force-field and the Dead-End Elimination theorem to compute sequences that are optimal for a given protein scaffold. Starting from the structure of the CaM-smMLCK complex, the program considered 10(22) amino acid residue sequences to obtain the lowest-energy CaM sequence. The resulting eightfold mutant, CaM_8, was constructed and tested for binding to a set of seven CaM target peptides. CaM_8 displayed high binding affinity to the smMLCK peptide (1.3nM), similar to that of the wild-type protein (1.8nM). The affinity of CaM_8 to six other target peptides was reduced, as intended, by 1.5-fold to 86-fold. Hence, CaM_8 exhibited increased binding specificity, preferring the smMLCK peptide to the other targets. Studies of this type may increase our understanding of the origins of binding specificity in protein-ligand complexes and may provide valuable information that can be used in the design of novel protein receptors and/or ligands.
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Affiliation(s)
- Julia M Shifman
- Howard Hughes Medical Institute and Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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21
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Summa CM, Rosenblatt MM, Hong JK, Lear JD, DeGrado WF. Computational de novo design, and characterization of an A(2)B(2) diiron protein. J Mol Biol 2002; 321:923-38. [PMID: 12206771 DOI: 10.1016/s0022-2836(02)00589-2] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Diiron proteins are found throughout nature and have a diverse range of functions; proteins in this class include methane monooxygenase, ribonucleotide reductase, Delta(9)-acyl carrier protein desaturase, rubrerythrin, hemerythrin, and the ferritins. Although each of these proteins has a very different overall fold, in every case the diiron active site is situated within a four-helix bundle. Additionally, nearly all of these proteins have a conserved Glu-Xxx-Xxx-His motif on two of the four helices with the Glu and His residues ligating the iron atoms. Intriguingly, subtle differences in the active site can result in a wide variety of functions. To probe the structural basis for this diversity, we designed an A(2)B(2) heterotetrameric four-helix bundle with an active site similar to those found in the naturally occurring diiron proteins. A novel computational approach was developed for the design, which considers the energy of not only the desired fold but also alternatively folded structures. Circular dichroism spectroscopy, analytical ultracentrifugation, and thermal unfolding studies indicate that the A and B peptides specifically associate to form an A(2)B(2) heterotetramer. Further, the protein binds Zn(II) and Co(II) in the expected manner and shows ferroxidase activity under single turnover conditions.
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Affiliation(s)
- Christopher M Summa
- Department of Biochemistry and Biophysics, School of Medicine, The University of Pennsylvania, 1010 Stellar-Chance Bldg, 421 Curie Blvd, Philadelphia 19104-6059, USA
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Ghirlanda G, Lear JD, Ogihara NL, Eisenberg D, DeGrado WF. A hierarchic approach to the design of hexameric helical barrels. J Mol Biol 2002; 319:243-53. [PMID: 12051949 DOI: 10.1016/s0022-2836(02)00233-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The design of large macromolecular assemblies is an endeavor with implications for protein engineering as well as nanotechnology. A hierarchic approach was used to design an antiparallel hexameric, tubular assembly of helices. In previous studies, a domain-swapped, dimeric three-helix bundle was designed from first principles. In the crystal lattice, three dimers associate around a 3-fold rotational axis to form a hexameric assembly. Although this hexameric assembly was not observed in solution, it was possible to stabilize its formation by changing three polar residues per monomer to hydrophobic (two Phe and one Trp) residues. Molecular models based on the crystallographic coordinates of DSD (PDB accession code 1G6U) show that these side-chains pack in the central cavity (the "supercore") of the hexameric bundle. Analytical ultracentrifugation, fluorescence spectroscopy, CD spectroscopy, and guanidine-HCl denaturation were used to determine the assembly of the hexamer. To probe the requirements for stabilizing the hexamer, we systematically varied the polarity and steric bulk of one of the Phe residues in the supercore of the hexamer. Depending on the nature of this side-chain, it is possible to modulate the stability of the hexamer in a predictable manner. This family of hexameric proteins may provide a useful framework for the construction of proteins that change their oligomeric states in response to binding of small molecules.
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Affiliation(s)
- Giovanna Ghirlanda
- Department of Biochemistry and Biophysics, The Johnson Research Foundation, University of Pennsylvania School of Medicine, Stellar Chance Building, Room 1010, 421 Curie Boulevard, Philadelphia, PA 19104-6059, USA
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23
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Sia SK, Kim PS. A designed protein with packing between left-handed and right-handed helices. Biochemistry 2001; 40:8981-9. [PMID: 11467960 DOI: 10.1021/bi010725v] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A common motif in protein structures is the assembly of alpha-helices. Natural alpha-helical assemblies, such as helical bundles and coiled coils, consist of multiple right-handed alpha-helices. Here we design a protein complex containing both left-handed and right-handed helices, with peptides of D- and L-amino acids, respectively. The two peptides, D-Acid and L-Base, feature hydrophobic heptad repeats and are designed to pack against each other in a "knobs-into-holes" manner. In solution, the peptides form a stable, helical heterotetramer with tight packing in the most solvent-protected core. This motif may be useful for designing protease-resistant, helical D-peptide ligands against biological protein targets.
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Affiliation(s)
- S K Sia
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
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24
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Taylor P, Dornan J, Carrello A, Minchin RF, Ratajczak T, Walkinshaw MD. Two structures of cyclophilin 40: folding and fidelity in the TPR domains. Structure 2001; 9:431-8. [PMID: 11377203 DOI: 10.1016/s0969-2126(01)00603-7] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
BACKGROUND The "large immunophilin" family consists of domains of cyclophilin or FK506 binding protein linked to a tetratricopeptide (TPR) domain. They are intimately associated with steroid receptor complexes and bind to the C-terminal domain of Hsp90 via the TPR domain. The competitive binding of specific large immunophilins and other TPR-Hsp90 proteins provides a regulatory mechanism for Hsp90 chaperone activity. RESULTS We have solved the X-ray structures of monoclinic and tetragonal forms of Cyp40. In the monoclinic form, the TPR domain consists of seven helices of variable length incorporating three TPR motifs, which provide a convincing binding surface for the Hsp90 C-terminal MEEVD sequence. The C-terminal residues of Cyp40 protrude out beyond the body of the TPR domain to form a charged helix-the putative calmodulin binding site. However, in the tetragonal form, two of the TPR helices have straightened out to form one extended helix, providing a dramatically different conformation of the molecule. CONCLUSIONS The X-ray structures are consistent with the role of Cyclophilin 40 as a multifunctional signaling protein involved in a variety of protein-protein interactions. The intermolecular helix-helix interactions in the tetragonal form mimic the intramolecular interactions found in the fully folded monoclinic form. These conserved intra- and intermolecular TPR-TPR interactions are illustrative of a high-fidelity recognition mechanism. The two structures also open up the possibility that partially folded forms of TPR may be important in domain swapping and protein recognition.
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Affiliation(s)
- P Taylor
- Structural Biochemistry Group, Institute of Cell and Molecular Biology, The University of Edinburgh, Michael Swann Building, King's Buildings, Mayfield Road, EH9 3JR, Edinburgh, United Kingdom
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25
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Abstract
Protein design has become a powerful approach for understanding the relationship between amino acid sequence and 3-dimensional structure. In the past 5 years, there have been many breakthroughs in the development of computational methods that allow the selection of novel sequences given the structure of a protein backbone. Successful design of protein scaffolds has now paved the way for new endeavors to design function. The ability to design sequences compatible with a fold may also be useful in structural and functional genomics by expanding the range of proteins used for fold recognition and for the identification of functionally important domains from multiple sequence alignments.
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Affiliation(s)
- N Pokala
- Department of Molecular and Cell Biology, University of California, 229 Stanley Hall, Berkeley, California 94720, USA
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26
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Affiliation(s)
- K M Müller
- Department of Molecular and Cell Biology, University of California at Berkeley 94720-3206, USA
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27
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Ogihara NL, Ghirlanda G, Bryson JW, Gingery M, DeGrado WF, Eisenberg D. Design of three-dimensional domain-swapped dimers and fibrous oligomers. Proc Natl Acad Sci U S A 2001; 98:1404-9. [PMID: 11171963 PMCID: PMC29269 DOI: 10.1073/pnas.98.4.1404] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three-dimensional (3D) domain-swapped proteins are intermolecularly folded analogs of monomeric proteins; both are stabilized by the identical interactions, but the individual domains interact intramolecularly in monomeric proteins, whereas they form intermolecular interactions in 3D domain-swapped structures. The structures and conditions of formation of several domain-swapped dimers and trimers are known, but the formation of higher order 3D domain-swapped oligomers has been less thoroughly studied. Here we contrast the structural consequences of domain swapping from two designed three-helix bundles: one with an up-down-up topology, and the other with an up-down-down topology. The up-down-up topology gives rise to a domain-swapped dimer whose structure has been determined to 1.5 A resolution by x-ray crystallography. In contrast, the domain-swapped protein with an up-down-down topology forms fibrils as shown by electron microscopy and dynamic light scattering. This demonstrates that design principles can predict the oligomeric state of 3D domain-swapped molecules, which should aid in the design of domain-swapped proteins and biomaterials.
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Affiliation(s)
- N L Ogihara
- UCLA-DOE Laboratory of Structural Biology and the Department of Chemistry and Biochemistry, P.O. Box 951570, University of California, Los Angeles, CA 90095-1570, USA
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28
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Hill RB, Bracken C, DeGrado WF, Palmer AG. Molecular Motions and Protein Folding: Characterization of the Backbone Dynamics and Folding Equilibrium of α2D Using 13C NMR Spin Relaxation. J Am Chem Soc 2000. [DOI: 10.1021/ja001129b] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. Blake Hill
- Contribution from the Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021, and Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032
| | - Clay Bracken
- Contribution from the Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021, and Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032
| | - William F. DeGrado
- Contribution from the Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021, and Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032
| | - Arthur G. Palmer
- Contribution from the Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021, and Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032
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29
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DeGrado WF, Summa CM, Pavone V, Nastri F, Lombardi A. De novo design and structural characterization of proteins and metalloproteins. Annu Rev Biochem 2000; 68:779-819. [PMID: 10872466 DOI: 10.1146/annurev.biochem.68.1.779] [Citation(s) in RCA: 462] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
De novo protein design has recently emerged as an attractive approach for studying the structure and function of proteins. This approach critically tests our understanding of the principles of protein folding; only in de novo design must one truly confront the issue of how to specify a protein's fold and function. If we truly understand proteins, it should be possible to design receptors, enzymes, and ion channels from scratch. Further, as this understanding evolves and is further refined, it should be possible to design proteins and biomimetic polymers with properties unprecedented in nature.
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Affiliation(s)
- W F DeGrado
- Johnson Research Foundation, Pennsylvania, Philadelphia, USA.
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30
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Lombardi A, Summa CM, Geremia S, Randaccio L, Pavone V, DeGrado WF. Retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins. Proc Natl Acad Sci U S A 2000; 97:6298-305. [PMID: 10841536 PMCID: PMC18597 DOI: 10.1073/pnas.97.12.6298] [Citation(s) in RCA: 189] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2000] [Indexed: 11/18/2022] Open
Abstract
De novo protein design provides an attractive approach for the construction of models to probe the features required for function of complex metalloproteins. The metal-binding sites of many metalloproteins lie between multiple elements of secondary structure, inviting a retrostructural approach to constructing minimal models of their active sites. The backbone geometries comprising the metal-binding sites of zinc fingers, diiron proteins, and rubredoxins may be described to within approximately 1 A rms deviation by using a simple geometric model with only six adjustable parameters. These geometric models provide excellent starting points for the design of metalloproteins, as illustrated in the construction of Due Ferro 1 (DF1), a minimal model for the Glu-Xxx-Xxx-His class of dinuclear metalloproteins. This protein was synthesized and structurally characterized as the di-Zn(II) complex by x-ray crystallography, by using data that extend to 2.5 A. This four-helix bundle protein is comprised of two noncovalently associated helix-loop-helix motifs. The dinuclear center is formed by two bridging Glu and two chelating Glu side chains, as well as two monodentate His ligands. The primary ligands are mostly buried in the protein interior, and their geometries are stabilized by a network of hydrogen bonds to second-shell ligands. In particular, a Tyr residue forms a hydrogen bond to a chelating Glu ligand, similar to a motif found in the diiron-containing R2 subunit of Escherichia coli ribonucleotide reductase and the ferritins. DF1 also binds cobalt and iron ions and should provide an attractive model for a variety of diiron proteins that use oxygen for processes including iron storage, radical formation, and hydrocarbon oxidation.
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Affiliation(s)
- A Lombardi
- Department of Chemistry, University of Napoli "Federico II," Via Mezzocannone, 4, I-80134 Napoli, Italy
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