1
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Dutta C, Lopez V, Preston C, Rudra N, Chavez AMV, Rogers AM, Solomon LA. Controlling heme redox properties in peptide amphiphile fibers with sequence and heme loading ratio. Biophys J 2024; 123:1781-1791. [PMID: 38783603 DOI: 10.1016/j.bpj.2024.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/10/2024] [Accepted: 05/21/2024] [Indexed: 05/25/2024] Open
Abstract
Controlling the reduction midpoint potential of heme B is a key factor in many bioelectrochemical reactions, including long-range electron transport. Currently, there are a number of globular model protein systems to study this biophysical parameter; however, there are none for large polymeric protein model systems (e.g., the OmcS protein from G. sulfurreducens). Peptide amphiphiles, short peptides with a lipid tail that polymerize into fibrous structures, fill this gap. Here, we show a peptide amphiphile model system where one can tune the electrochemical potential of heme B by changing the loading ratio and peptide sequence. Changing the loading ratio resulted in the most significant increase, with values as high as -22 mV down to -224 mV. Circular dichroism spectra of certain sequences show Cotton effects at lower loading ratios that disappear as more heme B is added, indicating an ordered environment that becomes disrupted if heme B is overpacked. These findings can contribute to the design of functional self-assembling biomaterials.
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Affiliation(s)
- Chiranjit Dutta
- Department of Chemistry and Biochemistry, George Mason University, Fairfax, Virginia
| | - Virginia Lopez
- Department of Chemistry and Biochemistry, George Mason University, Fairfax, Virginia
| | - Conner Preston
- Department of Chemistry and Biochemistry, George Mason University, Fairfax, Virginia
| | - Nimesh Rudra
- Thomas Jefferson High School for Science and Technology, Alexandria, Virginia
| | | | - Abigail M Rogers
- Department of Biology, George Mason University, Fairfax, Virginia
| | - Lee A Solomon
- Department of Chemistry and Biochemistry, George Mason University, Fairfax, Virginia.
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2
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Tang Y, Wang H, Liu S, Pu L, Hu X, Ding J, Xu G, Xu W, Xiang S, Yuan Z. A review of protein hydrogels: Protein assembly mechanisms, properties, and biological applications. Colloids Surf B Biointerfaces 2022. [DOI: 10.1016/j.colsurfb.2022.112973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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3
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Solomon LA, Witten J, Kodali G, Moser CC, Dutton PL. Tailorable Tetrahelical Bundles as a Toolkit for Redox Studies. J Phys Chem B 2022; 126:8177-8187. [PMID: 36219580 PMCID: PMC9589594 DOI: 10.1021/acs.jpcb.2c05119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Oxidoreductases have evolved over millions of years to perform a variety of metabolic tasks crucial for life. Understanding how these tasks are engineered relies on delivering external electron donors or acceptors to initiate electron transfer reactions. This is a challenge. Small-molecule redox reagents can act indiscriminately, poisoning the cell. Natural redox proteins are more selective, but finding the right partner can be difficult due to the limited number of redox potentials and difficulty tuning them. De novo proteins offer an alternative path. They are robust and can withstand mutations that allow for tailorable changes. They are also devoid of evolutionary artifacts and readily bind redox cofactors. However, no reliable set of engineering principles have been developed that allow for these proteins to be fine-tuned so their redox midpoint potential (Em) can form donor/acceptor pairs with any natural oxidoreductase. This work dissects protein-cofactor interactions that can be tuned to modulate redox potentials of acceptors and donors using a mutable de novo designed tetrahelical protein platform with iron tetrapyrrole cofactors as a test case. We show a series of engineered heme b-binding de novo proteins and quantify their resulting effect on Em. By focusing on the surface charge and buried charges, as well as cofactor placement, chemical modification, and ligation of cofactors, we are able to achieve a broad range of Em values spanning a range of 330 mV. We anticipate this work will guide the design of proteinaceous tools that can interface with natural oxidoreductases inside and outside the cell while shedding light on how natural proteins modulate Em values of bound cofactors.
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Affiliation(s)
- Lee A. Solomon
- Department
of Chemistry and Biochemistry, George Mason
University, Fairfax, Virginia22030, United States,
| | - Joshua Witten
- Department
of Biology, George Mason University, Fairfax, Virginia22030, United States
| | - Goutham Kodali
- Department
of Biochemistry and Biophysics, University
of Pennsylvania, Philadelphia, Pennsylvania19104, United States
| | - Christopher C. Moser
- Department
of Biochemistry and Biophysics, University
of Pennsylvania, Philadelphia, Pennsylvania19104, United States
| | - P. Leslie Dutton
- Department
of Biochemistry and Biophysics, University
of Pennsylvania, Philadelphia, Pennsylvania19104, United States
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4
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Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Protein Design: From the Aspect of Water Solubility and Stability. Chem Rev 2022; 122:14085-14179. [PMID: 35921495 PMCID: PMC9523718 DOI: 10.1021/acs.chemrev.1c00757] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.
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Affiliation(s)
- Rui Qing
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shilei Hao
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Eva Smorodina
- Department
of Immunology, University of Oslo and Oslo
University Hospital, Oslo 0424, Norway
| | - David Jin
- Avalon GloboCare
Corp., Freehold, New Jersey 07728, United States
| | - Arthur Zalevsky
- Laboratory
of Bioinformatics Approaches in Combinatorial Chemistry and Biology, Shemyakin−Ovchinnikov Institute of Bioorganic
Chemistry RAS, Moscow 117997, Russia
| | - Shuguang Zhang
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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5
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Molecular Properties of β-Carotene Oxygenases and Their Potential in Industrial Production of Vitamin A and Its Derivatives. Antioxidants (Basel) 2022; 11:antiox11061180. [PMID: 35740077 PMCID: PMC9227343 DOI: 10.3390/antiox11061180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 11/16/2022] Open
Abstract
β-Carotene 15,15′-oxygenase (BCO1) and β-carotene 9′,10′-oxygenase (BCO2) are potential producers of vitamin A derivatives, since they can catalyze the oxidative cleavage of dietary provitamin A carotenoids to retinoids and derivative such as apocarotenal. Retinoids are a class of chemical compounds that are vitamers of vitamin A or are chemically related to it, and are essential nutrients for humans and highly valuable in the food and cosmetics industries. β-carotene oxygenases (BCOs) from various organisms have been overexpressed in heterogeneous bacteria, such as Escherichia coli, and their biochemical properties have been studied. For the industrial production of retinal, there is a need for increased production of a retinal producer and biosynthesis of retinal using biocatalyst systems improved by enzyme engineering. The current review aims to discuss BCOs from animal, plants, and bacteria, and to elaborate on the recent progress in our understanding of their functions, biochemical properties, substrate specificity, and enzyme activities with respect to the production of retinoids in whole-cell conditions. Moreover, we specifically propose ways to integrate BCOs into retinal biosynthetic bacterial systems to improve the performance of retinal production.
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Naudin EA, Albanese KI, Smith AJ, Mylemans B, Baker EG, Weiner OD, Andrews DM, Tigue N, Savery NJ, Woolfson DN. From peptides to proteins: coiled-coil tetramers to single-chain 4-helix bundles. Chem Sci 2022; 13:11330-11340. [PMID: 36320580 PMCID: PMC9533478 DOI: 10.1039/d2sc04479j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/24/2022] [Indexed: 11/21/2022] Open
Abstract
The design of completely synthetic proteins from first principles—de novo protein design—is challenging. This is because, despite recent advances in computational protein–structure prediction and design, we do not understand fully the sequence-to-structure relationships for protein folding, assembly, and stabilization. Antiparallel 4-helix bundles are amongst the most studied scaffolds for de novo protein design. We set out to re-examine this target, and to determine clear sequence-to-structure relationships, or design rules, for the structure. Our aim was to determine a common and robust sequence background for designing multiple de novo 4-helix bundles. In turn, this could be used in chemical and synthetic biology to direct protein–protein interactions and as scaffolds for functional protein design. Our approach starts by analyzing known antiparallel 4-helix coiled-coil structures to deduce design rules. In terms of the heptad repeat, abcdefg—i.e., the sequence signature of many helical bundles—the key features that we identify are: a = Leu, d = Ile, e = Ala, g = Gln, and the use of complementary charged residues at b and c. Next, we implement these rules in the rational design of synthetic peptides to form antiparallel homo- and heterotetramers. Finally, we use the sequence of the homotetramer to derive in one step a single-chain 4-helix-bundle protein for recombinant production in E. coli. All of the assembled designs are confirmed in aqueous solution using biophysical methods, and ultimately by determining high-resolution X-ray crystal structures. Our route from peptides to proteins provides an understanding of the role of each residue in each design. Rules for designing 4-helix bundles are defined, tested, and used to generate de novo peptide assemblies and a single-chain protein.![]()
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Affiliation(s)
- Elise A. Naudin
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Katherine I. Albanese
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Abigail J. Smith
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK
| | - Bram Mylemans
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Emily G. Baker
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK
| | - Orion D. Weiner
- Cardiovascular Research Institute, Department of Biochemistry and Biophysics, University of California, 555 Mission Bay Blvd. South, San Francisco, CA 94158, USA
| | - David M. Andrews
- Oncology R&D, AstraZeneca, Cambridge Science Park, Darwin Building, Cambridge CB4 0WG, UK
| | - Natalie Tigue
- BioPharmaceuticals R&D, AstraZeneca, Granta Park, Cambridge CB21 6GH, UK
| | - Nigel J. Savery
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK
- BrisEngBio, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Derek N. Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK
- BrisEngBio, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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7
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Neitz H, Paul NB, Häge FR, Lindner C, Graebner R, Kovermann M, Thomas F. Identification of novel functional mini-receptors by combinatorial screening of split-WW domains. Chem Sci 2022; 13:9079-9090. [PMID: 36091217 PMCID: PMC9365081 DOI: 10.1039/d2sc01078j] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 07/14/2022] [Indexed: 11/21/2022] Open
Abstract
A combinatorial approach toward novel functional WW domains based on coiled-coil-mediated reconstitution of split WW domains is presented. As such, an ATP-binding WW domain was found from a 4-by-6 library of N- and C-terminal WW domain fragments.
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Affiliation(s)
- Hermann Neitz
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Niels Benjamin Paul
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstr. 2, Göttingen 37077, Germany
| | - Florian R. Häge
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, Heidelberg 69120, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, Heidelberg 69120, Germany
| | - Christina Lindner
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, Heidelberg 69120, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, Heidelberg 69120, Germany
| | - Roman Graebner
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, Heidelberg 69120, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, Heidelberg 69120, Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
| | - Franziska Thomas
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, Heidelberg 69120, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, Heidelberg 69120, Germany
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8
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Curnow P, Anderson JLR. Expression and In Vivo Loading of De Novo Proteins with Tetrapyrrole Cofactors. Methods Mol Biol 2022; 2397:137-155. [PMID: 34813063 DOI: 10.1007/978-1-0716-1826-4_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Tetrapyrrole cofactors such as heme and chlorophyll imprint their intrinsic reactivity and properties on a multitude of natural proteins and enzymes, and there is much interest in exploiting their functional and catalytic capabilities within minimal, de novo designed protein scaffolds. Here we describe how, using only natural biosynthetic and post-translational modification pathways, de novo designed soluble and hydrophobic proteins can be equipped with tetrapyrrole cofactors within living Escherichia coli cells. We provide strategies to achieve covalent and non-covalent heme incorporation within the de novo proteins and describe how the heme biosynthetic pathway can be co-opted to produce the light sensitive zinc protoporphyrin IX for loading into proteins in vivo. In addition, we describe the imaging of hydrophobic proteins and cofactor-rich protein droplets by electron and fluorescence microscopy, and how cofactors can be stripped from the de novo proteins to aid in vitro identification.
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Affiliation(s)
- Paul Curnow
- School of Biochemistry, University of Bristol, University Walk, Bristol, UK
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Bristol, UK
| | - J L Ross Anderson
- School of Biochemistry, University of Bristol, University Walk, Bristol, UK.
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Bristol, UK.
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9
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van den Bent I, Makrodimitris S, Reinders M. The Power of Universal Contextualized Protein Embeddings in Cross-species Protein Function Prediction. Evol Bioinform Online 2021; 17:11769343211062608. [PMID: 34880594 PMCID: PMC8647222 DOI: 10.1177/11769343211062608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 11/03/2021] [Indexed: 11/16/2022] Open
Abstract
Computationally annotating proteins with a molecular function is a difficult problem that is made even harder due to the limited amount of available labeled protein training data. Unsupervised protein embeddings partly circumvent this limitation by learning a universal protein representation from many unlabeled sequences. Such embeddings incorporate contextual information of amino acids, thereby modeling the underlying principles of protein sequences insensitive to the context of species. We used an existing pre-trained protein embedding method and subjected its molecular function prediction performance to detailed characterization, first to advance the understanding of protein language models, and second to determine areas of improvement. Then, we applied the model in a transfer learning task by training a function predictor based on the embeddings of annotated protein sequences of one training species and making predictions on the proteins of several test species with varying evolutionary distance. We show that this approach successfully generalizes knowledge about protein function from one eukaryotic species to various other species, outperforming both an alignment-based and a supervised-learning-based baseline. This implies that such a method could be effective for molecular function prediction in inadequately annotated species from understudied taxonomic kingdoms.
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Affiliation(s)
- Irene van den Bent
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
| | - Stavros Makrodimitris
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands.,Keygene N.V., Wageningen, the Netherlands
| | - Marcel Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
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10
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A bound iron porphyrin is redox active in hybrid bacterial reaction centers modified to possess a four-helix bundle domain. Photochem Photobiol Sci 2021; 21:91-99. [PMID: 34850374 DOI: 10.1007/s43630-021-00142-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/16/2021] [Indexed: 10/19/2022]
Abstract
In this paper we report the design of hybrid reaction centers with a novel redox-active cofactor. Reaction centers perform the primary photochemistry of photosynthesis, namely the light-induced transfer of an electron from the bacteriochlorophyll dimer to a series of electron acceptors. Hybrid complexes were created by the fusion of an artificial four-helix bundle to the M-subunit of the reaction center. Despite the large modification, optical spectra show that the purified hybrid reaction centers assemble as active complexes that retain the characteristic cofactor absorption peaks and are capable of light-induced charge separation. The four-helix bundle could bind iron-protoporphyrin in either a reduced and oxidized state. After binding iron-protoporphyrin to the hybrid reaction centers, light excitation results in a new derivative signal with a maximum at 402 nm and minimum at 429 nm. This signal increases in amplitude with longer light durations and persists in the dark. No signal is observed when iron-protoporphyrin is added to reaction centers without the four-helix bundle domain or when a redox-inactive zinc-protoporphyrin is bound. The results are consistent with the signal arising from a new redox reaction, electron transfer from the iron-protoporphyrin to the oxidized bacteriochlorophyll dimer. These outcomes demonstrate the feasibility of binding porphyrins to the hybrid reaction centers to gain new light-driven functions.
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11
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Gomes LR, Durans AM, Napoleão-Pêgo P, Waterman JA, Freitas MS, De Sá NBR, Pereira LV, Furtado JS, Aquino RG, Machado MCR, Fintelman-Rodrigues N, Souza TML, Morel CM, Provance DW, De-Simone SG. Multiepitope Proteins for the Differential Detection of IgG Antibodies against RBD of the Spike Protein and Non-RBD Regions of SARS-CoV-2. Vaccines (Basel) 2021; 9:vaccines9090986. [PMID: 34579223 PMCID: PMC8473315 DOI: 10.3390/vaccines9090986] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 08/04/2021] [Accepted: 08/28/2021] [Indexed: 01/08/2023] Open
Abstract
The COVID-19 pandemic has exposed the extent of global connectivity and collective vulnerability to emerging diseases. From its suspected origins in Wuhan, China, it spread to all corners of the world in a matter of months. The absence of high-performance, rapid diagnostic methods that could identify asymptomatic carriers contributed to its worldwide transmission. Serological tests offer numerous benefits compared to other assay platforms to screen large populations. First-generation assays contain targets that represent proteins from SARS-CoV-2. While they could be quickly produced, each actually has a mixture of specific and non-specific epitopes that vary in their reactivity for antibodies. To generate the next generation of the assay, epitopes were identified in three SARS-Cov-2 proteins (S, N, and Orf3a) by SPOT synthesis analysis. After their similarity to other pathogen sequences was analyzed, 11 epitopes outside of the receptor-binding domain (RBD) of the spike protein that showed high reactivity and uniqueness to the virus. These were incorporated into a ß-barrel protein core to create a highly chimeric protein. Another de novo protein was designed that contained only epitopes in the RBD. In-house ELISAs suggest that both multiepitope proteins can serve as targets for high-performance diagnostic tests. Our approach to bioengineer chimeric proteins is highly amenable to other pathogens and immunological uses.
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Affiliation(s)
- Larissa R. Gomes
- FIOCRUZ, Center of Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (L.R.G.); (A.M.D.); (P.N.-P.); (J.A.W.); (M.S.F.); (N.F.-R.); (T.M.L.S.); (C.M.M.); (D.W.P.)
| | - Andressa M. Durans
- FIOCRUZ, Center of Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (L.R.G.); (A.M.D.); (P.N.-P.); (J.A.W.); (M.S.F.); (N.F.-R.); (T.M.L.S.); (C.M.M.); (D.W.P.)
- Interdisciplinary Medical Research Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-900, Brazil
| | - Paloma Napoleão-Pêgo
- FIOCRUZ, Center of Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (L.R.G.); (A.M.D.); (P.N.-P.); (J.A.W.); (M.S.F.); (N.F.-R.); (T.M.L.S.); (C.M.M.); (D.W.P.)
| | - Jessica A. Waterman
- FIOCRUZ, Center of Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (L.R.G.); (A.M.D.); (P.N.-P.); (J.A.W.); (M.S.F.); (N.F.-R.); (T.M.L.S.); (C.M.M.); (D.W.P.)
| | - Mariana S. Freitas
- FIOCRUZ, Center of Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (L.R.G.); (A.M.D.); (P.N.-P.); (J.A.W.); (M.S.F.); (N.F.-R.); (T.M.L.S.); (C.M.M.); (D.W.P.)
| | - Nathalia B. R. De Sá
- AIDS & Molecular Immunology Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-900, Brazil;
| | - Lilian V. Pereira
- Angra dos Reis Health Department, Angra dos Reis 23906-10, Brazil; (L.V.P.); (J.S.F.); (R.G.A.)
| | - Jéssica S. Furtado
- Angra dos Reis Health Department, Angra dos Reis 23906-10, Brazil; (L.V.P.); (J.S.F.); (R.G.A.)
| | - Romário G. Aquino
- Angra dos Reis Health Department, Angra dos Reis 23906-10, Brazil; (L.V.P.); (J.S.F.); (R.G.A.)
| | | | - Natalia Fintelman-Rodrigues
- FIOCRUZ, Center of Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (L.R.G.); (A.M.D.); (P.N.-P.); (J.A.W.); (M.S.F.); (N.F.-R.); (T.M.L.S.); (C.M.M.); (D.W.P.)
- Immunopharmacology Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-900, Brazil
| | - Thiago M. L. Souza
- FIOCRUZ, Center of Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (L.R.G.); (A.M.D.); (P.N.-P.); (J.A.W.); (M.S.F.); (N.F.-R.); (T.M.L.S.); (C.M.M.); (D.W.P.)
- Immunopharmacology Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-900, Brazil
| | - Carlos M. Morel
- FIOCRUZ, Center of Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (L.R.G.); (A.M.D.); (P.N.-P.); (J.A.W.); (M.S.F.); (N.F.-R.); (T.M.L.S.); (C.M.M.); (D.W.P.)
| | - David W. Provance
- FIOCRUZ, Center of Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (L.R.G.); (A.M.D.); (P.N.-P.); (J.A.W.); (M.S.F.); (N.F.-R.); (T.M.L.S.); (C.M.M.); (D.W.P.)
- Interdisciplinary Medical Research Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-900, Brazil
| | - Salvatore G. De-Simone
- FIOCRUZ, Center of Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (L.R.G.); (A.M.D.); (P.N.-P.); (J.A.W.); (M.S.F.); (N.F.-R.); (T.M.L.S.); (C.M.M.); (D.W.P.)
- Department of Cellular and Molecular Biology, Biology Institute, Federal Fluminense University, Niterói 24020-141, Brazil
- Correspondence: ; Tel.: +55-213-865-8240
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12
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Lin B, Liu K, Qiu Y. Preparation of modified polysulfone material decorated by sulfonated citric chitosan for haemodialysis and its haemocompatibility. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210462. [PMID: 34540249 PMCID: PMC8437023 DOI: 10.1098/rsos.210462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/12/2021] [Indexed: 05/18/2023]
Abstract
Polysulfone (PSF) works potentially in haemodialysis due to its great mechanical and chemical stability, but performs poorly in haemocompatibility. For promoting the unpleasant haemocompatibility, sulfonated citric chitosan (SCACS) with the structure and groups similar to heparin was primarily synthesized by acylation and sulfonation. Furthermore, the chloroacylated PSF was pretreated by electrophilic chloroacetyl chloride to achieve more active sites for further reaction; the following membranes underwent the amination and were named amination polysulfone (AMPSF) membranes. Moreover, SCACS with abundant carboxyl and sulfonic groups was covalently grafted at the surface of pretreated PSF membranes, called PSF-SCACS membranes. The PSF-SCACS membranes were successfully synthesized and characterized by 1H NMR, ATR-FTIR and XPS. In addition, the water contact angle of PSF-SCACS membranes decreased by 47° and the morphologies of the membranes changed little compared with the unmodified PSF membranes. The haemocompatible testing results, including protein adsorption, platelet adhesion, haemolysis rate, plasma recalcification time, activated partial thromboplastin time (APTT), prothrombin time (PT) and thrombin time (TT), demonstrated that the PSF-SCACS membranes possessed excellent haemocompatible performances, and SCACS played an important role in the modification.
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Affiliation(s)
- Bingxian Lin
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, People's Republic of China
| | - Kaiming Liu
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, People's Republic of China
| | - Yunren Qiu
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, People's Republic of China
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13
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Unravelling the Structure of the Tetrahedral Metal-Binding Site in METP3 through an Experimental and Computational Approach. Molecules 2021; 26:molecules26175221. [PMID: 34500655 PMCID: PMC8434281 DOI: 10.3390/molecules26175221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 11/17/2022] Open
Abstract
Understanding the structural determinants for metal ion coordination in metalloproteins is a fundamental issue for designing metal binding sites with predetermined geometry and activity. In order to achieve this, we report in this paper the design, synthesis and metal binding properties of METP3, a homodimer made up of a small peptide, which self assembles in the presence of tetrahedrally coordinating metal ions. METP3 was obtained through a redesign approach, starting from the previously developed METP molecule. The undecapeptide sequence of METP, which dimerizes to house a Cys4 tetrahedral binding site, was redesigned in order to accommodate a Cys2His2 site. The binding properties of METP3 were determined toward different metal ions. Successful assembly of METP3 with Co(II), Zn(II) and Cd(II), in the expected 2:1 stoichiometry and tetrahedral geometry was proven by UV-visible spectroscopy. CD measurements on both the free and metal-bound forms revealed that the metal coordination drives the peptide chain to fold into a turned conformation. Finally, NMR data of the Zn(II)-METP3 complex, together with a retrostructural analysis of the Cys-X-X-His motif in metalloproteins, allowed us to define the model structure. All the results establish the suitability of the short METP sequence for accommodating tetrahedral metal binding sites, regardless of the first coordination ligands.
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14
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Ferrando J, Solomon LA. Recent Progress Using De Novo Design to Study Protein Structure, Design and Binding Interactions. Life (Basel) 2021; 11:life11030225. [PMID: 33802210 PMCID: PMC7999464 DOI: 10.3390/life11030225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 12/14/2022] Open
Abstract
De novo protein design is a powerful methodology used to study natural functions in an artificial-protein context. Since its inception, it has been used to reproduce a plethora of reactions and uncover biophysical principles that are often difficult to extract from direct studies of natural proteins. Natural proteins are capable of assuming a variety of different structures and subsequently binding ligands at impressively high levels of both specificity and affinity. Here, we will review recent examples of de novo design studies on binding reactions for small molecules, nucleic acids, and the formation of protein-protein interactions. We will then discuss some new structural advances in the field. Finally, we will discuss some advancements in computational modeling and design approaches and provide an overview of some modern algorithmic tools being used to design these proteins.
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Affiliation(s)
- Juan Ferrando
- Department of Biology, George Mason University, 4400 University Dr, Fairfax, VA 22030, USA;
| | - Lee A. Solomon
- Department of Chemistry and Biochemistry, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
- Correspondence: ; Tel.: +703-993-6418
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15
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Bhutani P, Joshi G, Raja N, Bachhav N, Rajanna PK, Bhutani H, Paul AT, Kumar R. U.S. FDA Approved Drugs from 2015-June 2020: A Perspective. J Med Chem 2021; 64:2339-2381. [PMID: 33617716 DOI: 10.1021/acs.jmedchem.0c01786] [Citation(s) in RCA: 241] [Impact Index Per Article: 80.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In the present work, we report compilation and analysis of 245 drugs, including small and macromolecules approved by the U.S. FDA from 2015 until June 2020. Nearly 29% of the drugs were approved for the treatment of various types of cancers. Other major therapeutic areas of focus were infectious diseases (14%); neurological conditions (12%); and genetic, metabolic, and cardiovascular disorders (7-8% each). Itemization of the approved drugs according to the year of approval, sponsor, target, chemical class, major drug-metabolizing enzyme(s), route of administration/elimination, and drug-drug interaction liability (perpetrator or/and victim) is presented and discussed. An effort has been made to analyze the pharmacophores to identify the structural (e.g., aromatic, heterocycle, and aliphatic), elemental (e.g., boron, sulfur, fluorine, phosphorus, and deuterium), and functional group (e.g., nitro drugs) diversity among the approved drugs. Further, descriptor-based chemical space analysis of FDA approved drugs and several strategies utilized for optimizing metabolism leading to their discoveries have been emphasized. Finally, an analysis of drug-likeness for the approved drugs is presented.
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Affiliation(s)
- Priyadeep Bhutani
- Pharmaceutical Candidate Optimization, Biocon Bristol-Myers Squibb R&D Centre, Syngene International Limited, Bangalore 560099, India.,Department of Pharmacy, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Rajasthan 333031, India
| | - Gaurav Joshi
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151001, India
| | - Nivethitha Raja
- Pharmaceutical Candidate Optimization, Biocon Bristol-Myers Squibb R&D Centre, Syngene International Limited, Bangalore 560099, India
| | - Namrata Bachhav
- 1015 E Cozza Drive # 12, Spokane Washington 99208, United States
| | - Prabhakar K Rajanna
- Pharmaceutical Candidate Optimization, Biocon Bristol-Myers Squibb R&D Centre, Syngene International Limited, Bangalore 560099, India
| | - Hemant Bhutani
- Pharmaceutical Development, Biocon Bristol-Myers Squibb R&D Centre, Bristol-Myers Squibb India Private Limited, Bangalore 560099, India
| | - Atish T Paul
- Department of Pharmacy, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Rajasthan 333031, India
| | - Raj Kumar
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151001, India
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16
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Abstract
Conventional influenza vaccines are based on predicting the circulating viruses year by year, conferring limited effectiveness since the antigenicity of vaccine strains does not always match the circulating viruses. This necessitates development of universal influenza vaccines that provide broader and lasting protection against pan-influenza viruses. The discovery of the highly conserved immunogens (epitopes) of influenza viruses provides attractive targets for universal vaccine design. Here we review the current understanding with broadly protective immunogens (epitopes) and discuss several important considerations to achieve the goal of universal influenza vaccines.
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17
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Quijano-Rubio A, Ulge UY, Walkey CD, Silva DA. The advent of de novo proteins for cancer immunotherapy. Curr Opin Chem Biol 2020; 56:119-128. [PMID: 32371023 DOI: 10.1016/j.cbpa.2020.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 12/22/2022]
Abstract
Engineered proteins are revolutionizing immunotherapy, but advances are still needed to harness their full potential. Traditional protein engineering methods use naturally existing proteins as a starting point, and therefore, are intrinsically limited to small alterations of a protein's natural structure and function. Conversely, computational de novo protein design is free of such limitation, and can produce a virtually infinite number of novel protein sequences, folds, and functions. Recently, we used de novo protein engineering to create Neoleukin-2/15 (Neo-2/15), a protein mimetic of the function of both interleukin-2 (IL-2) and interleukin-15 (IL-15). To our knowledge, Neo-2/15 is the first de novo protein with immunotherapeutic activity, and in murine cancer models, it has demonstrated enhanced therapeutic potency and reduced toxicity compared to IL-2. De novo protein design is already showcasing its tremendous potential for driving the next wave of protein-based therapeutics that are explicitly engineered to treat disease.
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Affiliation(s)
| | - Umut Y Ulge
- Neoleukin Therapeutics Inc., Seattle, WA, USA
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18
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Grupi A, Ashur I, Degani-Katzav N, Yudovich S, Shapira Z, Marzouq A, Morgenstein L, Mandel Y, Weiss S. Interfacing the Cell with "Biomimetic Membrane Proteins". SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1903006. [PMID: 31765076 DOI: 10.1002/smll.201903006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Integral membrane proteins mediate a myriad of cellular processes and are the target of many therapeutic drugs. Enhancement and extension of the functional scope of membrane proteins can be realized by membrane incorporation of engineered nanoparticles designed for specific diagnostic and therapeutic applications. In contrast to hydrophobic insertion of small amphiphilic molecules, delivery and membrane incorporation of particles on the nanometric scale poses a crucial barrier for technological development. In this perspective, the transformative potential of biomimetic membrane proteins (BMPs), current state of the art, and the barriers that need to be overcome in order to advance the field are discussed.
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Affiliation(s)
- Asaf Grupi
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Idan Ashur
- Agricultural Research Organization, The Volcani Center, Institute of Agricultural Engineering, Rishon LeZion, 7505101, Israel
| | - Nurit Degani-Katzav
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Shimon Yudovich
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Zehavit Shapira
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Adan Marzouq
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Lion Morgenstein
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Yossi Mandel
- Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- School of Optometry and Vision Science, Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Shimon Weiss
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, 90095, USA
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19
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Kim S, Nam HY, Lee J, Seo J. Mitochondrion-Targeting Peptides and Peptidomimetics: Recent Progress and Design Principles. Biochemistry 2019; 59:270-284. [PMID: 31696703 DOI: 10.1021/acs.biochem.9b00857] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mitochondria are multifunctional subcellular organelles whose operations encompass energy production, signal transduction, and metabolic regulation. Given their wide range of roles, they have been studied extensively as a potential therapeutic target for the treatment of various diseases, including cancer, diabetes, and neurodegenerative diseases. Mitochondrion-mediated pathways have been identified as promising targets in the context of these diseases. However, the delivery of specific probes and drugs to the mitochondria is one of the major problems that remains to be solved. Over the past decade, much effort has been devoted to developing mitochondrion-targeted delivery methods based on the membrane characteristics and the protein import machinery of mitochondria. While various methods utilizing small molecules to polymeric particles have been introduced, it is notable that many of these compounds share common structural elements and physicochemical properties for optimal selectivity and efficiency. In this Perspective, we will review the most recently developed mitochondrion-targeting peptides and peptidomimetics to outline the key aspects of structural requirements and design principles. We will also discuss successful and potential applications of mitochondrial delivery to assess opportunities and challenges in the targeting of mitochondria.
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Affiliation(s)
- Soyoung Kim
- Department of Chemistry, School of Physics and Chemistry , Gwangju Institute of Science and Technology , Gwangju 61005 , Republic of Korea
| | - Ho Yeon Nam
- Department of Chemistry, School of Physics and Chemistry , Gwangju Institute of Science and Technology , Gwangju 61005 , Republic of Korea
| | - Jiyoun Lee
- Department of Global Medical Science , Sungshin University , Seoul 01133 , Republic of Korea
| | - Jiwon Seo
- Department of Chemistry, School of Physics and Chemistry , Gwangju Institute of Science and Technology , Gwangju 61005 , Republic of Korea
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20
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O'Connor MB, Bennie SJ, Deeks HM, Jamieson-Binnie A, Jones AJ, Shannon RJ, Walters R, Mitchell TJ, Mulholland AJ, Glowacki DR. Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework. J Chem Phys 2019; 150:220901. [PMID: 31202243 DOI: 10.1063/1.5092590] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
As molecular scientists have made progress in their ability to engineer nanoscale molecular structure, we face new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs from the familiar mechanics of everyday objects because it involves a complicated, highly correlated, and three-dimensional many-body dynamical choreography which is often nonintuitive even for highly trained researchers. We recently described how interactive molecular dynamics in virtual reality (iMD-VR) can help to meet this challenge, enabling researchers to manipulate real-time MD simulations of flexible structures in 3D. In this article, we outline various efforts to extend immersive technologies to the molecular sciences, and we introduce "Narupa," a flexible, open-source, multiperson iMD-VR software framework which enables groups of researchers to simultaneously cohabit real-time simulation environments to interactively visualize and manipulate the dynamics of molecular structures with atomic-level precision. We outline several application domains where iMD-VR is facilitating research, communication, and creative approaches within the molecular sciences, including training machines to learn potential energy functions, biomolecular conformational sampling, protein-ligand binding, reaction discovery using "on-the-fly" quantum chemistry, and transport dynamics in materials. We touch on iMD-VR's various cognitive and perceptual affordances and outline how these provide research insight for molecular systems. By synergistically combining human spatial reasoning and design insight with computational automation, technologies such as iMD-VR have the potential to improve our ability to understand, engineer, and communicate microscopic dynamical behavior, offering the potential to usher in a new paradigm for engineering molecules and nano-architectures.
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Affiliation(s)
- Michael B O'Connor
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Simon J Bennie
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Helen M Deeks
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Alexander Jamieson-Binnie
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Alex J Jones
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Robin J Shannon
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Rebecca Walters
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Thomas J Mitchell
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - David R Glowacki
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
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21
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Rhys GG, Wood CW, Beesley JL, Zaccai NR, Burton AJ, Brady RL, Thomson AR, Woolfson DN. Navigating the Structural Landscape of De Novo α-Helical Bundles. J Am Chem Soc 2019; 141:8787-8797. [PMID: 31066556 DOI: 10.1021/jacs.8b13354] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The association of amphipathic α helices in water leads to α-helical-bundle protein structures. However, the driving force for this-the hydrophobic effect-is not specific and does not define the number or the orientation of helices in the associated state. Rather, this is achieved through deeper sequence-to-structure relationships, which are increasingly being discerned. For example, for one structurally extreme but nevertheless ubiquitous class of bundle-the α-helical coiled coils-relationships have been established that discriminate between all-parallel dimers, trimers, and tetramers. Association states above this are known, as are antiparallel and mixed arrangements of the helices. However, these alternative states are less well understood. Here, we describe a synthetic-peptide system that switches between parallel hexamers and various up-down-up-down tetramers in response to single-amino-acid changes and solution conditions. The main accessible states of each peptide variant are characterized fully in solution and, in most cases, to high resolution with X-ray crystal structures. Analysis and inspection of these structures helps rationalize the different states formed. This navigation of the structural landscape of α-helical coiled coils above the dimers and trimers that dominate in nature has allowed us to design rationally a well-defined and hyperstable antiparallel coiled-coil tetramer (apCC-Tet). This robust de novo protein provides another scaffold for further structural and functional designs in protein engineering and synthetic biology.
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Affiliation(s)
- Guto G Rhys
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
| | - Christopher W Wood
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
| | - Joseph L Beesley
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
| | - Nathan R Zaccai
- School of Biochemistry , University of Bristol , Medical Sciences Building, University Walk , Bristol BS8 1TD , United Kingdom
| | - Antony J Burton
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
- Frick Chemistry Laboratory , Princeton University , Princeton , New Jersey 08544 , United States
| | - R Leo Brady
- School of Biochemistry , University of Bristol , Medical Sciences Building, University Walk , Bristol BS8 1TD , United Kingdom
| | - Andrew R Thomson
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
- School of Chemistry , University of Glasgow , Glasgow G12 8QQ , United Kingdom
| | - Derek N Woolfson
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
- School of Biochemistry , University of Bristol , Medical Sciences Building, University Walk , Bristol BS8 1TD , United Kingdom
- BrisSynBio , University of Bristol , Life Sciences Building, Tyndall Avenue , Bristol BS8 1TQ , United Kingdom
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