1
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Zorine D, Baker D. De novo design of alpha-beta repeat proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.15.590358. [PMID: 38915539 PMCID: PMC11195203 DOI: 10.1101/2024.06.15.590358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Proteins composed of a single structural unit tandemly repeated multiple times carry out a wide range of functions in biology. There has hence been considerable interest in designing such repeat proteins; previous approaches have employed strict constraints on secondary structure types and relative geometries, and most characterized designs either mimic a known natural topology, adhere closely to a parametric helical bundle architecture, or exploit very short repetitive sequences. Here, we describe Rosetta-based and deep learning hallucination methods for generating novel repeat protein architectures featuring mixed alpha-helix and beta-strand topologies, and 25 new highly stable alpha-beta proteins designed using these methods. We find that incorporation of terminal caps which prevent beta strand mediated intermolecular interactions increases the solubility and monomericity of individual designs as well as overall design success rate.
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Affiliation(s)
- Dmitri Zorine
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
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2
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Kim CS, Brown AM, Grove TZ, Etzkorn FA. Designed leucine-rich repeat proteins bind two muramyl dipeptide ligands. Protein Sci 2021; 30:804-817. [PMID: 33512005 DOI: 10.1002/pro.4031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 12/15/2022]
Abstract
Designed protein receptors hold diagnostic and therapeutic promise. We now report the design of five consensus leucine-rich repeat proteins (CLRR4-8) based on the LRR domain of nucleotide-binding oligomerization domain (NOD)-like receptors involved in the innate immune system. The CLRRs bind muramyl dipeptide (MDP), a bacterial cell wall component, with micromolar affinity. The overall Kd app values ranged from 1.0 to 57 μM as measured by fluorescence quenching experiments. Biphasic fluorescence quenching curves were observed in all CLRRs, with higher affinity Kd1 values ranging from 0.04 to 4.5 μM, and lower affinity Kd2 values ranging from 3.1 to 227 μM. These biphasic binding curves, along with the docking studies of MDP binding to CLRR4, suggest that at least two MDPs bind to each protein. Previously, only single MDP binding was reported. This high-capacity binding of MDP promises small, soluble, stable CLRR scaffolds as candidates for the future design of pathogen biosensors.
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Affiliation(s)
- Christina S Kim
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Anne M Brown
- University Libraries, Virginia Tech, Blacksburg, Virginia, USA
| | - Tijana Z Grove
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia, USA
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3
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Sternke M, Tripp KW, Barrick D. The use of consensus sequence information to engineer stability and activity in proteins. Methods Enzymol 2020; 643:149-179. [PMID: 32896279 DOI: 10.1016/bs.mie.2020.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The goal of protein design is to create proteins that are stable, soluble, and active. Here we focus on one approach to protein design in which sequence information is used to create a "consensus" sequence. Such consensus sequences comprise the most common residue at each position in a multiple sequence alignment (MSA). After describing some general ideas that relate MSA and consensus sequences and presenting a statistical thermodynamic framework that relates consensus and non-consensus sequences to stability, we detail the process of designing a consensus sequence and survey reports of consensus design and characterization from the literature. Many of these consensus proteins retain native biological activities including ligand binding and enzyme activity. Remarkably, in most cases the consensus protein shows significantly higher stability than extant versions of the protein, as measured by thermal or chemical denaturation, consistent with the statistical thermodynamic model. To understand this stability increase, we compare various features of consensus sequences with the extant MSA sequences from which they were derived. Consensus sequences show enrichment in charged residues (most notably glutamate and lysine) and depletion of uncharged polar residues (glutamine, serine, and asparagine). Surprisingly, a survey of stability changes resulting from point substitutions show little correlation with residue frequencies at the corresponding positions within the MSA, suggesting that the high stability of consensus proteins may result from interactions among residue pairs or higher-order clusters. Whatever the source, the large number of reported successes demonstrates that consensus design is a viable route to generating active and in many cases highly stabilized proteins.
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Affiliation(s)
- Matt Sternke
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, United States
| | - Katherine W Tripp
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States
| | - Doug Barrick
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States.
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4
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McCord JP, Grove TZ. Engineering repeat proteins of the immune system. Biopolymers 2020; 111:e23348. [PMID: 32031681 DOI: 10.1002/bip.23348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 08/30/2019] [Accepted: 09/06/2019] [Indexed: 11/06/2022]
Abstract
Limitations associated with immunoglobulins have motivated the search for novel binding scaffolds. Repeat proteins have emerged as one promising class of scaffolds, but often are limited to binding protein and peptide targets. An exception is the repeat proteins of the immune system, which have in recent years served as an inspiration for binding scaffolds which can bind glycans and other classes of biomolecule. Like other repeat proteins, these proteins can be very stable and have a monomeric mode of binding, with elongated and highly variable binding surfaces. The ability to target glycans and glycoproteins fill an important gap in current tools for research and biomedical applications.
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Affiliation(s)
- Jennifer P McCord
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, U.S.A
| | - Tijana Z Grove
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, U.S.A.,Zarkovic Grove Consulting, LLC, Blacksburg, VA, U.S.A
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5
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Vilariño-Güell C, Zimprich A, Martinelli-Boneschi F, Herculano B, Wang Z, Matesanz F, Urcelay E, Vandenbroeck K, Leyva L, Gris D, Massaad C, Quandt JA, Traboulsee AL, Encarnacion M, Bernales CQ, Follett J, Yee IM, Criscuoli MG, Deutschländer A, Reinthaler EM, Zrzavy T, Mascia E, Zauli A, Esposito F, Alcina A, Izquierdo G, Espino-Paisán L, Mena J, Antigüedad A, Urbaneja-Romero P, Ortega-Pinazo J, Song W, Sadovnick AD. Exome sequencing in multiple sclerosis families identifies 12 candidate genes and nominates biological pathways for the genesis of disease. PLoS Genet 2019; 15:e1008180. [PMID: 31170158 PMCID: PMC6553700 DOI: 10.1371/journal.pgen.1008180] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 05/07/2019] [Indexed: 12/12/2022] Open
Abstract
Multiple sclerosis (MS) is an inflammatory disease of the central nervous system characterized by myelin loss and neuronal dysfunction. Although the majority of patients do not present familial aggregation, Mendelian forms have been described. We performed whole-exome sequencing analysis in 132 patients from 34 multi-incident families, which nominated likely pathogenic variants for MS in 12 genes of the innate immune system that regulate the transcription and activation of inflammatory mediators. Rare missense or nonsense variants were identified in genes of the fibrinolysis and complement pathways (PLAU, MASP1, C2), inflammasome assembly (NLRP12), Wnt signaling (UBR2, CTNNA3, NFATC2, RNF213), nuclear receptor complexes (NCOA3), and cation channels and exchangers (KCNG4, SLC24A6, SLC8B1). These genes suggest a disruption of interconnected immunological and pro-inflammatory pathways as the initial event in the pathophysiology of familial MS, and provide the molecular and biological rationale for the chronic inflammation, demyelination and neurodegeneration observed in MS patients.
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Affiliation(s)
| | | | - Filippo Martinelli-Boneschi
- Laboratory of Human Genetics of Neurological Disorders, CNS Inflammatory Unit, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- MS Unit and Department of Neurology, IRCCS Policlinico San Donato, Milan, Italy
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Bruno Herculano
- Townsend Family Laboratories, Department of Psychiatry, University of British Columbia, Vancouver, Canada
| | - Zhe Wang
- Townsend Family Laboratories, Department of Psychiatry, University of British Columbia, Vancouver, Canada
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of the Capital Medical University, Beijing, China
| | - Fuencisla Matesanz
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina López Neyra (IPBLN), CSIC, Granada, Spain
| | - Elena Urcelay
- Immunology Dept, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
- Red Española de Esclerosis Múltiple REEM, Madrid, Spain
| | - Koen Vandenbroeck
- Achucarro Basque Center for Neuroscience, Universidad del País Vasco (UPV/EHU), Leioa, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Laura Leyva
- Red Española de Esclerosis Múltiple REEM, Madrid, Spain
- Instituto de Investigación Biomédica de Málaga-IBIMA, Unidad de Gestion Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Denis Gris
- Division of Immunology, Department of Pediatrics, CR-CHUS, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Canada
| | - Charbel Massaad
- Toxicology, Pharmacology and Cell Signalisation—UMR-S 1124 Université Paris Descartes, Paris, France
| | - Jacqueline A. Quandt
- Department of Pathology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Anthony L. Traboulsee
- Division of Neurology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Mary Encarnacion
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Cecily Q. Bernales
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Jordan Follett
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Irene M. Yee
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Maria G. Criscuoli
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Angela Deutschländer
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, United States of America
- Department of Clinical Genomics, Mayo Clinic Florida, Jacksonville, FL, United States of America
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, United States of America
| | - Eva M. Reinthaler
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Tobias Zrzavy
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Elisabetta Mascia
- Laboratory of Human Genetics of Neurological Disorders, CNS Inflammatory Unit, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Zauli
- Laboratory of Human Genetics of Neurological Disorders, CNS Inflammatory Unit, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federica Esposito
- Laboratory of Human Genetics of Neurological Disorders, CNS Inflammatory Unit, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Antonio Alcina
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina López Neyra (IPBLN), CSIC, Granada, Spain
| | | | - Laura Espino-Paisán
- Immunology Dept, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
- Red Española de Esclerosis Múltiple REEM, Madrid, Spain
| | - Jorge Mena
- Achucarro Basque Center for Neuroscience, Universidad del País Vasco (UPV/EHU), Leioa, Spain
| | - Alfredo Antigüedad
- Neurology Department, Hospital Universitario de Cruces, S/N, Baracaldo, Spain
| | - Patricia Urbaneja-Romero
- Red Española de Esclerosis Múltiple REEM, Madrid, Spain
- Instituto de Investigación Biomédica de Málaga-IBIMA, Unidad de Gestion Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Jesús Ortega-Pinazo
- Instituto de Investigación Biomédica de Málaga-IBIMA, Unidad de Gestion Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Weihong Song
- Townsend Family Laboratories, Department of Psychiatry, University of British Columbia, Vancouver, Canada
| | - A. Dessa Sadovnick
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- Division of Neurology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
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6
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Sanchez-deAlcazar D, Mejias SH, Erazo K, Sot B, Cortajarena AL. Self-assembly of repeat proteins: Concepts and design of new interfaces. J Struct Biol 2018; 201:118-129. [DOI: 10.1016/j.jsb.2017.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/09/2017] [Accepted: 09/02/2017] [Indexed: 11/25/2022]
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7
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Collins BC, Gunn RJ, McKitrick TR, Cummings RD, Cooper MD, Herrin BR, Wilson IA. Structural Insights into VLR Fine Specificity for Blood Group Carbohydrates. Structure 2017; 25:1667-1678.e4. [PMID: 28988747 PMCID: PMC5677568 DOI: 10.1016/j.str.2017.09.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/16/2017] [Accepted: 09/01/2017] [Indexed: 12/28/2022]
Abstract
High-quality reagents to study and detect glycans with high specificity for research and clinical applications are severely lacking. Here, we structurally and functionally characterize several variable lymphocyte receptor (VLR)-based antibodies from lampreys immunized with O erythrocytes that specifically recognize the blood group H-trisaccharide type II antigen. Glycan microarray analysis and biophysical data reveal that these VLRs exhibit greater specificity for H-trisaccharide compared with the plant lectin UEA-1, which is widely used in blood typing. Among these antibodies, O13 exhibits superior specificity for H-trisaccharide, the basis for which is revealed by comparative analysis of high-resolution VLR:glycan crystal structures. Using a structure-guided approach, we designed an O13 mutant with further enhanced specificity for H-trisaccharide. These insights into glycan recognition by VLRs suggest that lampreys can produce highly specific glycan antibodies, and are a valuable resource for the production of next-generation glycan reagents for biological and biomedical research and as diagnostics and therapeutics.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Monoclonal/biosynthesis
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/isolation & purification
- Antibody Specificity
- Binding Sites
- Blood Group Antigens/analysis
- Blood Group Antigens/immunology
- Blood Grouping and Crossmatching/methods
- Crystallography, X-Ray
- Erythrocytes/chemistry
- Erythrocytes/immunology
- Humans
- Immunization
- Lampreys/immunology
- Models, Molecular
- Plant Lectins/chemistry
- Plant Lectins/immunology
- Polysaccharides/chemistry
- Polysaccharides/immunology
- Polysaccharides/metabolism
- Protein Binding
- Protein Conformation
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Trisaccharides/chemistry
- Trisaccharides/immunology
- Trisaccharides/metabolism
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Affiliation(s)
- Bernard C Collins
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robin J Gunn
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tanya R McKitrick
- National Center for Functional Glycomics, Beth Israel Deaconess Medical Center Department of Surgery, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Richard D Cummings
- National Center for Functional Glycomics, Beth Israel Deaconess Medical Center Department of Surgery, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Max D Cooper
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, USA
| | - Brantley R Herrin
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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8
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Indramohan M, Stehlik C, Dorfleutner A. COPs and POPs Patrol Inflammasome Activation. J Mol Biol 2017; 430:153-173. [PMID: 29024695 DOI: 10.1016/j.jmb.2017.10.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/28/2017] [Accepted: 10/04/2017] [Indexed: 01/07/2023]
Abstract
Sensing and responding to pathogens and tissue damage is a core mechanism of innate immune host defense, and inflammasomes represent a central cytosolic pattern recognition receptor pathway leading to the generation of the pro-inflammatory cytokines interleukin-1β and interleukin-18 and pyroptotic cell death that causes the subsequent release of danger signals to propagate and perpetuate inflammatory responses. While inflammasome activation is essential for host defense, deregulated inflammasome responses and excessive release of inflammatory cytokines and danger signals are linked to an increasing spectrum of inflammatory diseases. In this review, we will discuss recent developments in elucidating the role of PYRIN domain-only proteins (POPs) and the related CARD-only proteins (COPs) in regulating inflammasome responses and their impact on inflammatory disease.
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Affiliation(s)
- Mohanalaxmi Indramohan
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Christian Stehlik
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Interdepartmental Immunobiology Center and Skin Disease Research Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| | - Andrea Dorfleutner
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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9
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Rämisch S, Pramhed A, Tillgren V, Aspberg A, Logan DT. Crystal structure of human chondroadherin: solving a difficult molecular-replacement problem usingde novomodels. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:53-63. [DOI: 10.1107/s205979831601980x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 12/12/2016] [Indexed: 02/08/2023]
Abstract
Chondroadherin (CHAD) is a cartilage matrix protein that mediates the adhesion of isolated chondrocytes. Its protein core is composed of 11 leucine-rich repeats (LRR) flanked by cysteine-rich domains. CHAD makes important interactions with collagen as well as with cell-surface heparin sulfate proteoglycans and α2β1integrins. The integrin-binding site is located in a region of hitherto unknown structure at the C-terminal end of CHAD. Peptides based on the C-terminal human CHAD (hCHAD) sequence have shown therapeutic potential for treating osteoporosis. This article describes a still-unconventional structure solution by phasing withde novomodels, the first of a β-rich protein. Structure determination of hCHAD using traditional, though nonsystematic, molecular replacement was unsuccessful in the hands of the authors, possibly owing to a combination of low sequence identity to other LRR proteins, four copies in the asymmetric unit and weak translational pseudosymmetry. However, it was possible to solve the structure by generating a large number ofde novomodels for the central LRR domain usingRosettaand multiple parallel molecular-replacement attempts usingAMPLE. The hCHAD structure reveals an ordered C-terminal domain belonging to the LRRCT fold, with the integrin-binding motif (WLEAK) being part of a regular α-helix, and suggests ways in which experimental therapeutic peptides can be improved. The crystal structure itself and docking simulations further support that hCHAD dimers form in a similar manner to other matrix LRR proteins.
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10
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Abstract
Repeat proteins are an attractive target for protein engineering and design. We have focused our attention on the design and engineering of one particular class: tetratricopeptide repeat (TPR) proteins. In previous work, we have shown that the structure and stability of TPR proteins can be manipulated in a rational fashion [Cortajarena (2011) Prot. Sci. 20: , 1042-1047; Main (2003) Structure 11: , 497-508]. Building on those studies, we have designed and characterized a number of different peptide-binding TPR modules and we have also assembled these modules into supramolecular arrays [Cortajarena (2009) ACS Chem. Biol. 5: , 545-552; Cortajarena (2008) ACS Chem. Biol. 3: , 161-166; Jackrel (2009) Prot. Sci. 18: , 762-774; Kajander (2007) Acta Crystallogr. D Biol. Crystallogr. 63: , 800-811]. Here we focus on the development of one such TPR-peptide interaction for a practical application, affinity purification. We illustrate the general utility of our designed protein interaction. Furthermore, this example highlights how basic research on protein-peptide interactions can lead to the development of novel reagents with important practical applications.
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11
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Biomolecular templating of functional hybrid nanostructures using repeat protein scaffolds. Biochem Soc Trans 2016; 43:825-31. [PMID: 26517889 DOI: 10.1042/bst20150077] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The precise synthesis of materials and devices with tailored complex structures and properties is a requisite for the development of the next generation of products based on nanotechnology. Nowadays, the technology for the generation of this type of devices lacks the precision to determine their properties and is accomplished mostly by 'trial and error' experimental approaches. The use of bottom-up approaches that rely on highly specific biomolecular interactions of small and simple components is an attractive approach for the templating of nanoscale elements. In nature, protein assemblies define complex structures and functions. Engineering novel bio-inspired assemblies by exploiting the same rules and interactions that encode the natural diversity is an emerging field that opens the door to create nanostructures with numerous potential applications in synthetic biology and nanotechnology. Self-assembly of biological molecules into defined functional structures has a tremendous potential in nano-patterning and the design of novel materials and functional devices. Molecular self-assembly is a process by which complex 3D structures with specified functions are constructed from simple molecular building blocks. Here we discuss the basis of biomolecular templating, the great potential of repeat proteins as building blocks for biomolecular templating and nano-patterning. In particular, we focus on the designed consensus tetratricopeptide repeats (CTPRs), the control on the assembly of these proteins into higher order structures and their potential as building blocks in order to generate functional nanostructures and materials.
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12
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Abstract
Advances in protein engineering tools, both computational and experimental, has afforded many new protein structures and functions. Here, we present a snapshot of repeat-protein engineering efforts towards new, versatile, alternative binding scaffolds for use in analytical sensors and as imaging agents. Analytical assays, sensors and imaging agents based on the direct binding of analyte are increasingly important for research and diagnostics in medicine, food safety, and national security.
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13
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Abstract
A popular and successful strategy in semi-rational design of protein stability is the use of evolutionary information encapsulated in homologous protein sequences. Consensus design is based on the hypothesis that at a given position, the respective consensus amino acid contributes more than average to the stability of the protein than non-conserved amino acids. Here, we review the consensus design approach, its theoretical underpinnings, successes, limitations and challenges, as well as providing a detailed guide to its application in protein engineering.
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Affiliation(s)
- Benjamin T Porebski
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Faculty of Medicine, Monash University, Clayton, Victoria 3800, Australia Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ashley M Buckle
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Faculty of Medicine, Monash University, Clayton, Victoria 3800, Australia
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14
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Design of Self-Assembling Protein-Polymer Conjugates. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 940:179-214. [PMID: 27677514 DOI: 10.1007/978-3-319-39196-0_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein-polymer conjugates are of particular interest for nanobiotechnology applications because of the various and complementary roles that each component may play in composite hybrid-materials. This chapter focuses on the design principles and applications of self-assembling protein-polymer conjugate materials. We address the general design methodology, from both synthetic and genetic perspective, conjugation strategies, protein vs. polymer driven self-assembly and finally, emerging applications for conjugate materials. By marrying proteins and polymers into conjugated bio-hybrid materials, materials scientists, chemists, and biologists alike, have at their fingertips a vast toolkit for material design. These inherently hierarchical structures give rise to useful patterning, mechanical and transport properties that may help realize new, more efficient materials for energy generation, catalysis, nanorobots, etc.
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15
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Designed Repeat Proteins as Building Blocks for Nanofabrication. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 940:61-81. [DOI: 10.1007/978-3-319-39196-0_4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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16
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Park K, Shen BW, Parmeggiani F, Huang PS, Stoddard BL, Baker D. Control of repeat-protein curvature by computational protein design. Nat Struct Mol Biol 2015; 22:167-74. [PMID: 25580576 PMCID: PMC4318719 DOI: 10.1038/nsmb.2938] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 11/25/2014] [Indexed: 01/07/2023]
Abstract
Shape complementarity is an important component of molecular recognition, and the ability to precisely adjust the shape of a binding scaffold to match a target of interest would greatly facilitate the creation of high-affinity protein reagents and therapeutics. Here we describe a general approach to control the shape of the binding surface on repeat-protein scaffolds and apply it to leucine-rich-repeat proteins. First, self-compatible building-block modules are designed that, when polymerized, generate surfaces with unique but constant curvatures. Second, a set of junction modules that connect the different building blocks are designed. Finally, new proteins with custom-designed shapes are generated by appropriately combining building-block and junction modules. Crystal structures of the designs illustrate the power of the approach in controlling repeat-protein curvature.
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Affiliation(s)
- Keunwan Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA, Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Betty W. Shen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Fabio Parmeggiani
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA, Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Po-Ssu Huang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA, Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Barry L. Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA, Institute for Protein Design, University of Washington, Seattle, WA 98195, USA,Correspondence:
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Computational design of a leucine-rich repeat protein with a predefined geometry. Proc Natl Acad Sci U S A 2014; 111:17875-80. [PMID: 25427795 DOI: 10.1073/pnas.1413638111] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Structure-based protein design offers a possibility of optimizing the overall shape of engineered binding scaffolds to match their targets better. We developed a computational approach for the structure-based design of repeat proteins that allows for adjustment of geometrical features like length, curvature, and helical twist. By combining sequence optimization of existing repeats and de novo design of capping structures, we designed leucine-rich repeats (LRRs) from the ribonuclease inhibitor (RI) family that assemble into structures with a predefined geometry. The repeat proteins were built from self-compatible LRRs that are designed to interact to form highly curved and planar assemblies. We validated the geometrical design approach by engineering a ring structure constructed from 10 self-compatible repeats. Protein design can also be used to increase our structural understanding of repeat proteins. We use our design constructs to demonstrate that buried Cys play a central role for stability and folding cooperativity in RI-type LRR proteins. The computational procedure presented here may be used to develop repeat proteins with various geometrical shapes for applications where greater control of the interface geometry is desired.
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Parmeggiani F, Huang PS, Vorobiev S, Xiao R, Park K, Caprari S, Su M, Seetharaman J, Mao L, Janjua H, Montelione GT, Hunt J, Baker D. A general computational approach for repeat protein design. J Mol Biol 2014; 427:563-75. [PMID: 25451037 PMCID: PMC4303030 DOI: 10.1016/j.jmb.2014.11.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 10/08/2014] [Accepted: 11/07/2014] [Indexed: 01/12/2023]
Abstract
Repeat proteins have considerable potential for use as modular binding reagents or biomaterials in biomedical and nanotechnology applications. Here we describe a general computational method for building idealized repeats that integrates available family sequences and structural information with Rosetta de novo protein design calculations. Idealized designs from six different repeat families were generated and experimentally characterized; 80% of the proteins were expressed and soluble and more than 40% were folded and monomeric with high thermal stability. Crystal structures determined for members of three families are within 1Å root-mean-square deviation to the design models. The method provides a general approach for fast and reliable generation of stable modular repeat protein scaffolds.
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Affiliation(s)
- Fabio Parmeggiani
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Po-Ssu Huang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Sergey Vorobiev
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027, USA
| | - Rong Xiao
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry and Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Keunwan Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Silvia Caprari
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Min Su
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027, USA
| | - Jayaraman Seetharaman
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027, USA
| | - Lei Mao
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry and Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Haleema Janjua
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry and Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry and Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - John Hunt
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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