1
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Fry HC, Liu Y, Taylor SK. Design and Function of α-Helix-Rich, Heme-Binding Peptide Materials. Biomacromolecules 2024; 25:3398-3408. [PMID: 38752597 DOI: 10.1021/acs.biomac.4c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Peptide materials often employ short peptides that self-assemble into unique nanoscale architectures and have been employed across many fields relevant to medicine and energy. A majority of peptide materials are high in β-sheet, secondary structure content, including heme-binding peptide materials. To broaden the structural diversity of heme-binding peptide materials, a small series of peptides were synthesized to explore the design criteria required for (1) folding into an α-helix structure, (2) assembling into a nanoscale material, (3) binding heme, and (4) demonstrating functions similar to that of heme proteins. One peptide was identified to meet all four criteria, including the heme protein function of CO binding and its microsecond-to-millisecond recombination rates, as measured by transient absorption spectroscopy. Implications of new design criteria and peptide material function through heme incorporation are discussed.
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Affiliation(s)
- H Christopher Fry
- Center for Nanoscale Materials, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, Illinois 60439, United States
| | - Yuzi Liu
- Center for Nanoscale Materials, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, Illinois 60439, United States
| | - Sunny K Taylor
- Pritzker School for Molecular Engineering, University of Chicago, 5640 S. Ellis Ave., Chicago, Illinois 60637, United States
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2
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Carrillo D, Duran-Meza E, Castillo-Caceres C, Alarcon DE, Guzman H, Diaz-Espinoza R. Catalytic amyloids for nucleotide hydrolysis. Methods Enzymol 2024; 697:269-291. [PMID: 38816126 DOI: 10.1016/bs.mie.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
The design of small peptides that assemble into catalytically active intermolecular structures has proven to be a successful strategy towards developing minimalistic catalysts that exhibit some of the unique functional features of enzymes. Among these, catalytic amyloids have emerged as a fruitful source to unravel many different activities. These assemblies can potentially have broad applications that range from biotechnology to prebiotic chemistry. Although many peptides that assemble into catalytic amyloids have been developed in recent years, the elucidation of convergent mechanistic aspects of the catalysis and the structure/function relationship is still a challenge. Novel catalytic activities are necessary to better address these issues and expand the current repertoire of applicability. In this chapter, we described a methodology to produce catalytic amyloids that are specifically active towards the hydrolysis of phosphoanhydride bonds of nucleotides. The design of potentially active amyloid-prone peptide sequences is explored using as template the active site of enzymes with nucleotidyltransferase activity. The procedures include an approach for sequence design, in vitro aggregation assays, morphological characterization of the amyloid state and a comprehensive methodology to measure activity in vitro using nucleoside and deoxynucleosides triphosphates as model substrates. The proposed strategy can also be implemented to explore different types of activities for the design of future catalytic amyloids.
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Affiliation(s)
- Daniel Carrillo
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile
| | - Eva Duran-Meza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile; Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Chile
| | - Claudio Castillo-Caceres
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile
| | - Diego Eduardo Alarcon
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile
| | - Hardy Guzman
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile
| | - Rodrigo Diaz-Espinoza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile.
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3
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Rathee P, Moorkkannur SN, Prabhakar R. Structural studies of catalytic peptides using molecular dynamics simulations. Methods Enzymol 2024; 697:151-180. [PMID: 38816122 DOI: 10.1016/bs.mie.2024.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Many self-assembling peptides can form amyloid like structures with different sizes and morphologies. Driven by non-covalent interactions, their aggregation can occur through distinct pathways. Additionally, they can bind metal ions to create enzyme like active sites that allow them to catalyze diverse reactions. Due to the non-crystalline nature of amyloids, it is quite challenging to elucidate their structures using experimental spectroscopic techniques. In this aspect, molecular dynamics (MD) simulations provide a useful tool to derive structures of these macromolecules in solution. They can be further validated by comparing with experimentally measured structural parameters. However, these simulations require a multi-step process starting from the selection of the initial structure to the analysis of MD trajectories. There are multiple force fields, parametrization protocols, equilibration processes, software and analysis tools available for this process. Therefore, it is complicated for non-experts to select the most relevant tools and perform these simulations effectively. In this chapter, a systematic methodology that covers all major aspects of modeling of catalytic peptides is provided in a user-friendly manner. It will be helpful for researchers in this critical area of research.
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Affiliation(s)
- Parth Rathee
- Department of Chemistry, University of Miami, Coral Gables, FL, United States
| | | | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, FL, United States.
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4
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Arad E, Pedersen KB, Malka O, Mambram Kunnath S, Golan N, Aibinder P, Schiøtt B, Rapaport H, Landau M, Jelinek R. Staphylococcus aureus functional amyloids catalyze degradation of β-lactam antibiotics. Nat Commun 2023; 14:8198. [PMID: 38081813 PMCID: PMC10713593 DOI: 10.1038/s41467-023-43624-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
Antibiotic resistance of bacteria is considered one of the most alarming developments in modern medicine. While varied pathways for bacteria acquiring antibiotic resistance have been identified, there still are open questions concerning the mechanisms underlying resistance. Here, we show that alpha phenol-soluble modulins (PSMαs), functional bacterial amyloids secreted by Staphylococcus aureus, catalyze hydrolysis of β-lactams, a prominent class of antibiotic compounds. Specifically, we show that PSMα2 and, particularly, PSMα3 catalyze hydrolysis of the amide-like bond of the four membered β-lactam ring of nitrocefin, an antibiotic β-lactam surrogate. Examination of the catalytic activities of several PSMα3 variants allowed mapping of the active sites on the amyloid fibrils' surface, specifically underscoring the key roles of the cross-α fibril organization, and the combined electrostatic and nucleophilic functions of the lysine arrays. Molecular dynamics simulations further illuminate the structural features of β-lactam association upon the fibril surface. Complementary experimental data underscore the generality of the functional amyloid-mediated catalytic phenomenon, demonstrating hydrolysis of clinically employed β-lactams by PSMα3 fibrils, and illustrating antibiotic degradation in actual S. aureus biofilms and live bacteria environments. Overall, this study unveils functional amyloids as catalytic agents inducing degradation of β-lactam antibiotics, underlying possible antibiotic resistance mechanisms associated with bacterial biofilms.
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Affiliation(s)
- Elad Arad
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Kasper B Pedersen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Orit Malka
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Sisira Mambram Kunnath
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Nimrod Golan
- Department of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Polina Aibinder
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Hanna Rapaport
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
- Centre for Structural Systems Biology (CSSB), and European Molecular Biology Laboratory (EMBL), Hamburg, 22607, Germany
| | - Raz Jelinek
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel.
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel.
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5
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Pankaew C, Supdensong K, Tothong C, Roytrakul S, Phaonakrop N, Kongbangkerd A, Limmongkon A. Combining elicitor treatment of chitosan, methyl jasmonate, and cyclodextrin to induce the generation of immune response bioactive peptides in peanut hairy root culture. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 331:111670. [PMID: 36914116 DOI: 10.1016/j.plantsci.2023.111670] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/15/2023] [Accepted: 03/10/2023] [Indexed: 06/18/2023]
Abstract
The endogenous peptides from peanut hairy root culture were induced upon elicitor treatment with chitosan (CHT), methyl jasmonate (MeJA), and cyclodextrin (CD): CHT+MeJA+CD. The peptides secreted into the liquid culture medium play an important role in plant signaling and stress responses. By performing gene ontology (GO) analysis, a number of plant proteins involved in biotic and abiotic defense responses were identified, such as endochitinase, defensin, antifungal protein, cationic peroxidase and Bowman-Birk type protease inhibitor A-II. The bioactivity of 14 peptides synthesized from secretome analysis was determined. Peptide BBP1-4, derived from the diverse region of Bowman-Birk type protease inhibitor, displayed high antioxidant activity and mimicked the property of chitinase and β-1,3-glucanase enzymes. The antimicrobial activity against S. aureus, S. typhimurium, and E. coli was evidenced with different peptide concentrations. Additionally, peptide BBP1-4 has the potential to be a useful candidate for an immune response property, as it was found to increase the expression of some pathogenesis-related (PR) proteins and stilbene biosynthesis genes in peanut hairy root tissues. The findings indicate that secreted peptides may play a role in plant responses to both abiotic and biotic stresses. These peptides, which possess bioactive properties, could be considered as potential candidates for use in the pharmaceutical, agricultural, and food industries.
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Affiliation(s)
- Chanyanut Pankaew
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Kanitha Supdensong
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Chonnikan Tothong
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Sittiruk Roytrakul
- Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani 12120, Thailand
| | - Narumon Phaonakrop
- Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani 12120, Thailand
| | - Anupan Kongbangkerd
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Apinun Limmongkon
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand.
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6
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Villard J, Kılıç M, Rothlisberger U. Surrogate Based Genetic Algorithm Method for Efficient Identification of Low-Energy Peptide Structures. J Chem Theory Comput 2023; 19:1080-1097. [PMID: 36692853 PMCID: PMC9933449 DOI: 10.1021/acs.jctc.2c01078] [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] [Indexed: 01/25/2023]
Abstract
Identification of the most stable structure(s) of a system is a prerequisite for the calculation of any of its properties from first-principles. However, even for relatively small molecules, exhaustive explorations of the potential energy surface (PES) are severely hampered by the dimensionality bottleneck. In this work, we address the challenging task of efficiently sampling realistic low-lying peptide coordinates by resorting to a surrogate based genetic algorithm (GA)/density functional theory (DFT) approach (sGADFT) in which promising candidates provided by the GA are ultimately optimized with DFT. We provide a benchmark of several computational methods (GAFF, AMOEBApro13, PM6, PM7, DFTB3-D3(BJ)) as possible prescanning surrogates and apply sGADFT to two test case systems that are (i) two isomer families of the protonated Gly-Pro-Gly-Gly tetrapeptide (Masson, A.; J. Am. Soc. Mass Spectrom.2015, 26, 1444-1454) and (ii) the doubly protonated cyclic decapeptide gramicidin S (Nagornova, N. S.; J. Am. Chem. Soc.2010, 132, 4040-4041). We show that our GA procedure can correctly identify low-energy minima in as little as a few hours. Subsequent refinement of surrogate low-energy structures within a given energy threshold (≤10 kcal/mol (i), ≤5 kcal/mol (ii)) via DFT relaxation invariably led to the identification of the most stable structures as determined from high-resolution infrared (IR) spectroscopy at low temperature. The sGADFT method therefore constitutes a highly efficient route for the screening of realistic low-lying peptide structures in the gas phase as needed for instance for the interpretation and assignment of experimental IR spectra.
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7
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Jain A, Kassem S, Fisher RS, Wang B, Li TD, Wang T, He Y, Elbaum-Garfinkle S, Ulijn RV. Connected Peptide Modules Enable Controlled Co-Existence of Self-Assembled Fibers Inside Liquid Condensates. J Am Chem Soc 2022; 144:15002-15007. [PMID: 35946870 DOI: 10.1021/jacs.2c05897] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Supramolecular self-assembly of fibrous components and liquid-liquid phase separation are at the extremes of the order-to-disorder spectrum. They collectively play key roles in cellular organization. It is still a major challenge to design systems where both highly ordered nanostructures and liquid-liquid phase-separated domains can coexist. We present a three-component assembly approach that generates fibrous domains that exclusively form inside globally disordered, liquid condensates. This is achieved by creating amphiphilic peptides that combine the features of fibrillar assembly (the amyloid domain LVFFA) and complex coacervation (oligo-arginine and adenosine triphosphate (ATP)) in one peptide, namely, LVFFAR9. When this hybrid peptide is mixed in different ratios with R9 and ATP, we find that conditions can be created where fibrous assembly is exclusively observed inside liquid coacervates. Through fluorescence and atomic force microscopy characterization, we investigate the dynamic evolution of ordered and disordered features over time. It was observed that the fibers nucleate and mature inside the droplets and that these fiber-containing liquid droplets can also undergo fusion, showing that the droplets remain liquid-like. Our work thus generates opportunities for the design of ordered structures within the confined environment of biomolecular condensates, which may be useful to create supramolecular materials in defined compartments and as model systems that can enhance understanding of ordering principles in biology.
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Affiliation(s)
- Ankit Jain
- Nanoscience Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, New York 10031, United States
| | - Salma Kassem
- Nanoscience Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, New York 10031, United States
| | - Rachel S Fisher
- Structural Biology Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, New York 10031, United States
| | - Biran Wang
- Molecular Cytology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Tai-De Li
- Nanoscience Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, New York 10031, United States.,Department of Physics, City College of New York, City University of New York, New York, New York 10031, United States
| | - Tong Wang
- Nanoscience Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, New York 10031, United States
| | - Ye He
- Neuroscience Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, New York 10031, United States.,Division of Science, The City College of New York, New York, New York 10031, United States
| | - Shana Elbaum-Garfinkle
- Structural Biology Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, New York 10031, United States.,Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Rein V Ulijn
- Nanoscience Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, New York 10031, United States.,Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States.,Department of Chemistry Hunter College, City University of New York, New York, New York 10065, United States
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8
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Gupta S, Azadvari N, Hosseinzadeh P. Design of Protein Segments and Peptides for Binding to Protein Targets. BIODESIGN RESEARCH 2022; 2022:9783197. [PMID: 37850124 PMCID: PMC10521657 DOI: 10.34133/2022/9783197] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/16/2022] [Indexed: 10/19/2023] Open
Abstract
Recent years have witnessed a rise in methods for accurate prediction of structure and design of novel functional proteins. Design of functional protein fragments and peptides occupy a small, albeit unique, space within the general field of protein design. While the smaller size of these peptides allows for more exhaustive computational methods, flexibility in their structure and sparsity of data compared to proteins, as well as presence of noncanonical building blocks, add additional challenges to their design. This review summarizes the current advances in the design of protein fragments and peptides for binding to targets and discusses the challenges in the field, with an eye toward future directions.
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Affiliation(s)
- Suchetana Gupta
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
| | - Noora Azadvari
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
| | - Parisa Hosseinzadeh
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
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9
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Yan K, Triana V, Kalmady SV, Aku-Dominguez K, Memon S, Brown A, Greiner R, Derda R. Learning the structure-activity relationship (SAR) of the Wittig reaction from genetically-encoded substrates. Chem Sci 2021; 12:14301-14308. [PMID: 34760216 PMCID: PMC8565473 DOI: 10.1039/d1sc04146k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/08/2021] [Indexed: 12/31/2022] Open
Abstract
The Wittig reaction can be used for late stage functionalization of proteins and peptides to ligate glycans, pharmacophores, and many other functionalities. In this manuscript, we modified 160 000 N-terminal glyoxaldehyde peptides displayed on phage with the Wittig reaction by using a biotin labeled ylide under conditions that functionalize only 1% of the library population. Deep-sequencing of the biotinylated and input populations estimated the rate of conversion for each sequence. This “deep conversion” (DC) from deep sequencing correlates with rate constants measured by HPLC. Peptide sequences with fast and slow reactivity highlighted the critical role of primary backbone amides (N–H) in accelerating the rate of the aqueous Wittig reaction. Experimental measurement of reaction rates and density functional theory (DFT) computation of the transition state geometries corroborated this relationship. We also collected deep-sequencing data to build structure–activity relationship (SAR) models that can predict the DC value of the Wittig reaction. By using these data, we trained two classifier models based on gradient boosted trees. These classifiers achieved area under the ROC (receiver operating characteristic) curve (ROC AUC) of 81.2 ± 0.4 and 73.7 ± 0.8 (90–92% accuracy) in determining whether a sequence belonged to the top 5% or the bottom 5% in terms of its reactivity. This model can suggest new peptides never observed experimentally with ‘HIGH’ or ‘LOW’ reactivity. Experimental measurement of reaction rates for 11 new sequences corroborated the predictions for 8 of them. We anticipate that phage-displayed peptides and related mRNA or DNA-displayed substrates can be employed in a similar fashion to study the substrate scope and mechanisms of many other chemical reactions. 160 000 peptides displayed on phage were subjected to the Wittig reaction with a biotinylated ylide. Deep-sequencing estimated the conversion rate for each sequence and unveiled the relationship between sequences and the rate of the Wittig reaction.![]()
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Affiliation(s)
- Kejia Yan
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Vivian Triana
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Sunil Vasu Kalmady
- Department of Computer Science, University of Alberta Alberta AB T6G 2E8 Canada
| | | | - Sharyar Memon
- Department of Electrical and Computer Engineering, University of Alberta Edmonton AB T6G 1H9 Canada
| | - Alex Brown
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
| | - Russell Greiner
- Department of Computer Science, University of Alberta Alberta AB T6G 2E8 Canada.,Alberta Machine Intelligence Institute Alberta AB T5J 3B1 Canada
| | - Ratmir Derda
- Department of Chemistry, University of Alberta Edmonton AB T6G 2G2 Canada
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10
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Piast RW, Wieczorek RM, Marzec N, Garstka M, Misicka A. A Phage Display-Identified Short Peptide Capable of Hydrolyzing Calcium Pyrophosphate Crystals-The Etiological Factor of Chondrocalcinosis. Molecules 2021; 26:molecules26195777. [PMID: 34641321 PMCID: PMC8510196 DOI: 10.3390/molecules26195777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/10/2021] [Accepted: 09/20/2021] [Indexed: 11/22/2022] Open
Abstract
Chondrocalcinosis is a metabolic disease caused by the presence of calcium pyrophosphate dihydrate crystals in the synovial fluid. The goal of our endeavor was to find out whether short peptides could be used as a dissolving factor for such crystals. In order to identify peptides able to dissolve crystals of calcium pyrophosphate, we screened through a random library of peptides using a phage display. The first screening was designed to select phages able to bind the acidic part of alendronic acid (pyrophosphate analog). The second was a catalytic assay in the presence of crystals. The best-performing peptides were subsequently chemically synthesized and rechecked for catalytic properties. One peptide, named R25, turned out to possess some hydrolytic activity toward crystals. Its catalysis is Mg2+-dependent and also works against soluble species of pyrophosphate.
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Affiliation(s)
- Radosław W. Piast
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
- Correspondence: (R.W.P.); (A.M.)
| | - Rafał M. Wieczorek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
| | - Nicola Marzec
- Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Stefana Banacha 2C, 02-087 Warsaw, Poland;
| | - Maciej Garstka
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland;
| | - Aleksandra Misicka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
- Correspondence: (R.W.P.); (A.M.)
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11
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Tanaka M, Hayashi M, Roach L, Kiriki Y, Kadonosono T, Nomoto T, Nishiyama N, Choi J, Critchley K, Evans SD, Okochi M. Synthesis of near-infrared absorbing triangular Au nanoplates using biomineralisation peptides. Acta Biomater 2021; 131:519-531. [PMID: 34144213 DOI: 10.1016/j.actbio.2021.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/24/2021] [Accepted: 06/01/2021] [Indexed: 12/27/2022]
Abstract
Triangular Au nanoplates (TrAuNPls) possessing strong plasmonic properties can be used as photothermal agents in cancer therapy. However, the controlled preparation of such morphologies typically requires harsh synthetic conditions. Biomolecules offer an alternative route to developing biocompatible synthetic protocols. In particular, peptides offer a novel route for inorganic synthesis under ambient conditions. Herein, using the previously isolated peptide, ASHQWAWKWE, for Au nanoparticle (AuNP) synthesis, the conditions for preparing TrAuNPls via a one-pot synthetic process of mixing HAuCl4 and peptides at room temperature were investigated to effectively obtain particles possessing near-infrared absorbance for non-invasive optical diagnosis and phototherapy. By adjusting the peptide concentration, the size and property of TrAuNPls were controlled under neutral pH conditions. The synthesised particles showed potential as photothermal therapeutic agents in vitro. In addition, peptide characterisation using B3 derivatives revealed the importance of the third amino acid histidine in morphological regulation and potential circular Au nanoplates (AuNPl) synthesis with ASEQWAWKWE and ASAQWAWKWE peptides. These findings provide not only an easy and green synthetic method for TrAuNPls and circular AuNPls, but also some insight to help elucidate the regulation of peptide-based nanoparticle synthesis for use in cancer therapy. STATEMENT OF SIGNIFICANCE: Biological molecules have received increasing attention as a vehicle to synthesise inorganic materials with specific properties under ambient conditions; particularly, short peptides have the potential to control the synthesis of nanoscale materials with tailored functions. Here, the application of a previously isolated peptide was assessed in synthesising Au nanoparticles containing decahedral and triangular nanoplates with near-infrared absorbance. The size and absorbance peaks of the triangular nanoplates observed were peptide concentration-dependent. In addition, these fine-tuned triangular nanoplates exhibited potential as a phototherapeutic agent. Moreover, the peptide derivatives indicated the possibility of synthesising circular nanoplates. These findings may offer insight into development of new techniques for synthesising functional nanoparticles having biological applications using non-toxic molecules under mild conditions stituted in the original B3 peptide is underlined.
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12
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Vishweshwaraiah YL, Acharya A, Hegde V, Prakash B. Rational design of hyperstable antibacterial peptides for food preservation. NPJ Sci Food 2021; 5:26. [PMID: 34471114 PMCID: PMC8410836 DOI: 10.1038/s41538-021-00109-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023] Open
Abstract
We describe the design of peptides with properties like thermostability, pH stability, and antibacterial activity against a few bacterial food pathogens. Insights obtained from classical structure-function analysis of natural peptides and their mutants through antimicrobial and enzymatic assays are used to rationally develop a set of peptides. pH and thermostability assays were performed to demonstrate robust antimicrobial activity post-treatment with high temperatures and at wide pH ranges. We have also investigated the mode of action of these hyperstable peptides using membrane permeability assays, electron microscopy, and molecular dynamics simulations. Notably, through mutational studies, we show that these peptides elicit their antibacterial action via both membrane destabilization and inhibition of intracellular trypsin-the two functions attributable to separate peptide segments. Finally, toxicity studies and food preservation assays demonstrate the safety and efficacy of the designed peptides for food preservation. Overall, the study provides a general 'blueprint' for the development of stable antimicrobial peptides (AMPs). Insights obtained from this work may also be combined with combinatorial methods in high-throughput studies for future development of antimicrobials for various applications.
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Affiliation(s)
- Yashavantha L. Vishweshwaraiah
- grid.417629.f0000 0004 0501 5711Department of Molecular Nutrition, CSIR-Central Food Technological Research Institute, Mysore, India
| | - Abhishek Acharya
- grid.417629.f0000 0004 0501 5711Department of Molecular Nutrition, CSIR-Central Food Technological Research Institute, Mysore, India
| | - Vinayak Hegde
- grid.417629.f0000 0004 0501 5711Department of Molecular Nutrition, CSIR-Central Food Technological Research Institute, Mysore, India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh India
| | - Balaji Prakash
- grid.417629.f0000 0004 0501 5711Department of Molecular Nutrition, CSIR-Central Food Technological Research Institute, Mysore, India ,grid.448607.90000 0004 1781 3606Division of Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, Gujarat India
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13
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Hamley IW. Biocatalysts Based on Peptide and Peptide Conjugate Nanostructures. Biomacromolecules 2021; 22:1835-1855. [PMID: 33843196 PMCID: PMC8154259 DOI: 10.1021/acs.biomac.1c00240] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/31/2021] [Indexed: 12/15/2022]
Abstract
Peptides and their conjugates (to lipids, bulky N-terminals, or other groups) can self-assemble into nanostructures such as fibrils, nanotubes, coiled coil bundles, and micelles, and these can be used as platforms to present functional residues in order to catalyze a diversity of reactions. Peptide structures can be used to template catalytic sites inspired by those present in natural enzymes as well as simpler constructs using individual catalytic amino acids, especially proline and histidine. The literature on the use of peptide (and peptide conjugate) α-helical and β-sheet structures as well as turn or disordered peptides in the biocatalysis of a range of organic reactions including hydrolysis and a variety of coupling reactions (e.g., aldol reactions) is reviewed. The simpler design rules for peptide structures compared to those of folded proteins permit ready ab initio design (minimalist approach) of effective catalytic structures that mimic the binding pockets of natural enzymes or which simply present catalytic motifs at high density on nanostructure scaffolds. Research on these topics is summarized, along with a discussion of metal nanoparticle catalysts templated by peptide nanostructures, especially fibrils. Research showing the high activities of different classes of peptides in catalyzing many reactions is highlighted. Advances in peptide design and synthesis methods mean they hold great potential for future developments of effective bioinspired and biocompatible catalysts.
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Affiliation(s)
- Ian W. Hamley
- Department of Chemistry, University of Reading, RG6 6AD Reading, United Kingdom
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14
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Pagar AD, Patil MD, Flood DT, Yoo TH, Dawson PE, Yun H. Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet. Chem Rev 2021; 121:6173-6245. [PMID: 33886302 DOI: 10.1021/acs.chemrev.0c01201] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.
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Affiliation(s)
- Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D Patil
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Dillon T Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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15
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Kurbasic M, Garcia AM, Viada S, Marchesan S. Heterochiral tetrapeptide self-assembly into hydrogel biomaterials for hydrolase mimicry. J Pept Sci 2021; 28:e3304. [PMID: 33521995 DOI: 10.1002/psc.3304] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 12/23/2022]
Abstract
Self-assembling short peptides have attracted great interest as enzyme mimics, especially if the catalytic activity resides solely in the supramolecular structure so that it can be switched on/off as needed by controlling assembly/disassembly. Among the various enzyme classes, hydrolases find wide application in biomaterials, and their mimetics often contain His residues, in addition to either divalent cations or other amino acids to mimic the catalytic site. This work reports two self-assembling tetrapeptides based on the Ser-His motif for catalysis and the Phe-Phe motif to drive amyloid structure formation. Both peptides form thermoreversible hydrogels in phosphate buffer at neutral pH that display a mild esterase-like activity, as demonstrated on the hydrolysis of 4-nitrophenyl acetate as a model substrate, although presence of Ser did not enhance catalytic activity. The systems are characterised by circular dichroism, transmission electron microscopy, oscillatory rheology and Thioflavin T fluorescence as an amyloid stain, to provide further insights that may assist the future design of improved supramolecular catalysts.
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Affiliation(s)
- Marina Kurbasic
- Chemical and Pharmaceutical Sciences Department, University of Trieste, Trieste, 34127, Italy
| | - Ana M Garcia
- Chemical and Pharmaceutical Sciences Department, University of Trieste, Trieste, 34127, Italy
| | - Simone Viada
- Chemical and Pharmaceutical Sciences Department, University of Trieste, Trieste, 34127, Italy
| | - Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department, University of Trieste, Trieste, 34127, Italy
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16
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Kurbasic M, Garcia AM, Viada S, Marchesan S. Tripeptide Self-Assembly into Bioactive Hydrogels: Effects of Terminus Modification on Biocatalysis. Molecules 2020; 26:E173. [PMID: 33396543 PMCID: PMC7794889 DOI: 10.3390/molecules26010173] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/25/2020] [Accepted: 12/28/2020] [Indexed: 12/21/2022] Open
Abstract
Bioactive hydrogels based on the self-assembly of tripeptides have attracted great interest in recent years. In particular, the search is active for sequences that are able to mimic enzymes when they are self-organized in a nanostructured hydrogel, so as to provide a smart catalytic (bio)material whose activity can be switched on/off with assembly/disassembly. Within the diverse enzymes that have been targeted for mimicry, hydrolases find wide application in biomaterials, ranging from their use to convert prodrugs into active compounds to their ability to work in reverse and catalyze a plethora of reactions. We recently reported the minimalistic l-His-d-Phe-d-Phe for its ability to self-organize into thermoreversible and biocatalytic hydrogels for esterase mimicry. In this work, we analyze the effects of terminus modifications that mimic the inclusion of the tripeptide in a longer sequence. Therefore, three analogues, i.e., N-acetylated, C-amidated, or both, were synthesized, purified, characterized by several techniques, and probed for self-assembly, hydrogelation, and esterase-like biocatalysis. This work provides useful insights into how chemical modifications at the termini affect self-assembly into biocatalytic hydrogels, and these data may become useful for the future design of supramolecular catalysts for enhanced performance.
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Affiliation(s)
| | | | | | - Silvia Marchesan
- Chemical & Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (M.K.); (A.M.G.); (S.V.)
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17
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Sawada T, Oyama R, Tanaka M, Serizawa T. Discovery of Surfactant-Like Peptides from a Phage-Displayed Peptide Library. Viruses 2020; 12:E1442. [PMID: 33333956 PMCID: PMC7765448 DOI: 10.3390/v12121442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/09/2020] [Accepted: 12/12/2020] [Indexed: 11/17/2022] Open
Abstract
Peptides with specific affinities for various materials have been identified in the past three decades and utilized in materials science and engineering. A peptide's capability to specifically interact with materials is not naturally derived but screened from a biologically constructed peptide library displayed on phages or cells. To date, due to limitations in the screening procedure, the function of screened peptides has been primarily limited to the affinity for target materials. Herein, we demonstrated the screening of surfactant-like peptides from a phage-displayed peptide library. A screened phage clone displaying a peptide showed high activity for accumulating at emulsion surfaces with certain assembled structures, resulting in stable emulsions. The surface tension for the solution of the chemically synthesized peptide decreased with increasing peptide concentration, demonstrating certain surface activity, which corresponded to the ability to decrease the surface tension of liquids (e.g., water), owing to the accumulation of molecules at the air-liquid or liquid-liquid interface. Peptides with a randomized sequence did not lower the surface tension, indicating the essential role of amino acid sequences in surface activity. Our strategy for identifying novel functional peptides from a phage-displayed peptide library can be used to expand the applicability of peptidyl materials and biosurfactants.
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Affiliation(s)
- Toshiki Sawada
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1-H121 Ookayama, Meguro-ku, Tokyo 152-8550, Japan; (R.O.); (M.T.)
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Rina Oyama
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1-H121 Ookayama, Meguro-ku, Tokyo 152-8550, Japan; (R.O.); (M.T.)
| | - Michihiro Tanaka
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1-H121 Ookayama, Meguro-ku, Tokyo 152-8550, Japan; (R.O.); (M.T.)
| | - Takeshi Serizawa
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1-H121 Ookayama, Meguro-ku, Tokyo 152-8550, Japan; (R.O.); (M.T.)
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18
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Choi W, Sun H, Battistella C, Berger O, Vratsanos MA, Wang MM, Gianneschi NC. Biomolecular Densely Grafted Brush Polymers: Oligonucleotides, Oligosaccharides and Oligopeptides. Angew Chem Int Ed Engl 2020; 59:19762-19772. [PMID: 32436259 PMCID: PMC11042487 DOI: 10.1002/anie.202005379] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Indexed: 01/19/2023]
Abstract
In this Minireview, we describe synthetic polymers densely functionalized with sequence-defined biomolecular sidechains. We focus on synthetic brush polymers of oligonucleotides, oligosaccharides, and oligopeptides, prepared via graft-through polymerization from biomolecule functionalized monomers. The resulting structures are brush polymers wherein a biomolecular graft is positioned at each monomer backbone unit. We describe key synthetic milestones, identify synthetic opportunities, and highlight recent advances in the field, including biological applications.
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Affiliation(s)
- Wonmin Choi
- Department Department of Chemistry, Materials Science & Engineering, Biomedical Engineering, Pharmacology, International Institute for Nanotechnology, Simpson Querrey Institute, Chemistry of Life Processes Institute, Lurie Cancer Center, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 (USA)
| | - Hao Sun
- Department Department of Chemistry, Materials Science & Engineering, Biomedical Engineering, Pharmacology, International Institute for Nanotechnology, Simpson Querrey Institute, Chemistry of Life Processes Institute, Lurie Cancer Center, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 (USA)
| | - Claudia Battistella
- Department Department of Chemistry, Materials Science & Engineering, Biomedical Engineering, Pharmacology, International Institute for Nanotechnology, Simpson Querrey Institute, Chemistry of Life Processes Institute, Lurie Cancer Center, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 (USA)
| | - Or Berger
- Department Department of Chemistry, Materials Science & Engineering, Biomedical Engineering, Pharmacology, International Institute for Nanotechnology, Simpson Querrey Institute, Chemistry of Life Processes Institute, Lurie Cancer Center, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 (USA)
| | - Maria A. Vratsanos
- Department Department of Chemistry, Materials Science & Engineering, Biomedical Engineering, Pharmacology, International Institute for Nanotechnology, Simpson Querrey Institute, Chemistry of Life Processes Institute, Lurie Cancer Center, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 (USA)
| | - Max M. Wang
- Department Department of Chemistry, Materials Science & Engineering, Biomedical Engineering, Pharmacology, International Institute for Nanotechnology, Simpson Querrey Institute, Chemistry of Life Processes Institute, Lurie Cancer Center, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 (USA)
| | - Nathan C. Gianneschi
- Department Department of Chemistry, Materials Science & Engineering, Biomedical Engineering, Pharmacology, International Institute for Nanotechnology, Simpson Querrey Institute, Chemistry of Life Processes Institute, Lurie Cancer Center, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 (USA)
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19
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Choi W, Sun H, Battistella C, Berger O, Vratsanos MA, Wang MM, Gianneschi NC. Biomolecular Densely Grafted Brush Polymers: Oligonucleotides, Oligosaccharides and Oligopeptides. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Wonmin Choi
- Department Department of Chemistry Materials Science & Engineering Biomedical Engineering, Pharmacology International Institute for Nanotechnology Simpson Querrey Institute Chemistry of Life Processes Institute Lurie Cancer Center Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
| | - Hao Sun
- Department Department of Chemistry Materials Science & Engineering Biomedical Engineering, Pharmacology International Institute for Nanotechnology Simpson Querrey Institute Chemistry of Life Processes Institute Lurie Cancer Center Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
| | - Claudia Battistella
- Department Department of Chemistry Materials Science & Engineering Biomedical Engineering, Pharmacology International Institute for Nanotechnology Simpson Querrey Institute Chemistry of Life Processes Institute Lurie Cancer Center Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
| | - Or Berger
- Department Department of Chemistry Materials Science & Engineering Biomedical Engineering, Pharmacology International Institute for Nanotechnology Simpson Querrey Institute Chemistry of Life Processes Institute Lurie Cancer Center Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
| | - Maria A. Vratsanos
- Department Department of Chemistry Materials Science & Engineering Biomedical Engineering, Pharmacology International Institute for Nanotechnology Simpson Querrey Institute Chemistry of Life Processes Institute Lurie Cancer Center Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
| | - Max M. Wang
- Department Department of Chemistry Materials Science & Engineering Biomedical Engineering, Pharmacology International Institute for Nanotechnology Simpson Querrey Institute Chemistry of Life Processes Institute Lurie Cancer Center Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
| | - Nathan C. Gianneschi
- Department Department of Chemistry Materials Science & Engineering Biomedical Engineering, Pharmacology International Institute for Nanotechnology Simpson Querrey Institute Chemistry of Life Processes Institute Lurie Cancer Center Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
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20
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Chien CY, Yu SS. Ester-mediated peptide formation promoted by deep eutectic solvents: a facile pathway to proto-peptides. Chem Commun (Camb) 2020; 56:11949-11952. [PMID: 32929424 DOI: 10.1039/d0cc03319g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The ester-amide exchange reaction enables spontaneous formation of prebiotic proto-peptides under mild conditions. However, this reaction also leads to oligomers with a vast sequence diversity of ester and amide linkages. Here, we demonstrate using deep eutectic solvents as a universal strategy to regulate the reaction pathways and promote the formation of amino acid-enriched oligomers with peptide backbones.
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Affiliation(s)
- Chen-Yu Chien
- Department of Chemical Engineering, National Cheng Kung University, No. 1 University Road, Tainan City, 70101, Taiwan, Republic of China.
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21
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Carlomagno T, Cringoli MC, Kralj S, Kurbasic M, Fornasiero P, Pengo P, Marchesan S. Biocatalysis of D,L-Peptide Nanofibrillar Hydrogel. Molecules 2020; 25:E2995. [PMID: 32630001 PMCID: PMC7411710 DOI: 10.3390/molecules25132995] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 01/30/2023] Open
Abstract
Self-assembling peptides are attracting wide interest as biodegradable building blocks to achieve functional nanomaterials that do not persist in the environment. Amongst the many applications, biocatalysis is gaining momentum, although a clear structure-to-activity relationship is still lacking. This work applied emerging design rules to the heterochiral octapeptide sequence His-Leu-DLeu-Ile-His-Leu-DLeu-Ile for self-assembly into nanofibrils that, at higher concentration, give rise to a supramolecular hydrogel for the mimicry of esterase-like activity. The peptide was synthesized by solid-phase and purified by HPLC, while its identity was confirmed by 1H-NMR and electrospray ionization (ESI)-MS. The hydrogel formed by this peptide was studied with oscillatory rheometry, and the supramolecular behavior of the peptide was investigated with transmission electron microscopy (TEM) analysis, circular dichroism (CD) spectroscopy, thioflavin T amyloid fluorescence assay, and attenuated total reflectance (ATR) Fourier-transform infrared (FT-IR) spectroscopy. The biocatalytic activity was studied by monitoring the hydrolysis of p-nitrophenyl acetate (pNPA) at neutral pH, and the reaction kinetics followed an apparent Michaelis-Menten model, for which a Lineweaver-Burk plot was produced to determine its enzymatic parameters for a comparison with the literature. Finally, LC-MS analysis was conducted on a series of experiments to evaluate the extent of, if any, undesired peptide acetylation at the N-terminus. In conclusion, we provide new insights that allow gaining a clearer picture of self-assembling peptide design rules for biocatalysis.
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Affiliation(s)
- Tiziano Carlomagno
- Chemical & Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (T.C.); (M.C.C.); (M.K.); (P.F.)
| | - Maria C. Cringoli
- Chemical & Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (T.C.); (M.C.C.); (M.K.); (P.F.)
- INSTM Trieste Research Unit, 34127 Trieste, Italy
| | - Slavko Kralj
- Materials Synthesis Department, Jožef Stefan Institute, 1000 Ljubljana, Slovenia;
| | - Marina Kurbasic
- Chemical & Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (T.C.); (M.C.C.); (M.K.); (P.F.)
| | - Paolo Fornasiero
- Chemical & Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (T.C.); (M.C.C.); (M.K.); (P.F.)
- INSTM Trieste Research Unit, 34127 Trieste, Italy
- ICCOM-CNR Trieste Research Unit, 34127 Trieste, Italy
| | - Paolo Pengo
- Chemical & Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (T.C.); (M.C.C.); (M.K.); (P.F.)
| | - Silvia Marchesan
- Chemical & Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (T.C.); (M.C.C.); (M.K.); (P.F.)
- INSTM Trieste Research Unit, 34127 Trieste, Italy
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22
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Tanaka M, Saito S, Kita R, Jang J, Choi Y, Choi J, Okochi M. Array-Based Screening of Silver Nanoparticle Mineralization Peptides. Int J Mol Sci 2020; 21:E2377. [PMID: 32235567 PMCID: PMC7178033 DOI: 10.3390/ijms21072377] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/26/2020] [Accepted: 03/26/2020] [Indexed: 12/24/2022] Open
Abstract
The use of biomolecules in nanomaterial synthesis has received increasing attention, because they can function as a medium to produce inorganic materials in ambient conditions. Short peptides are putative ligands that interact with metallic surfaces, as they have the potential to control the synthesis of nanoscale materials. Silver nanoparticle (AgNP) mineralization using peptides has been investigated; however, further comprehensive analysis must be carried out, because the design of peptide mediated-AgNP properties is still highly challenging. Herein, we employed an array comprising 200 spot synthesis-based peptides, which were previously isolated as gold nanoparticle (AuNP)-binding and/or mineralization peptides, and the AgNP mineralization activity of each peptide was broadly evaluated. Among 10 peptides showing the highest AgNP-synthesis activity (TOP10), nine showed the presence of EE and E[X]E (E: glutamic acid, and X: any amino acid), whereas none of these motifs were found in the WORST25 (25 peptides showing the lowest AgNP synthesis activity) peptides. The size and morphology of the particles synthesized by TOP3 peptides were dependent on their sequences. These results suggested not only that array-based techniques are effective for the peptide screening of AgNP mineralization, but also that AgNP mineralization regulated by peptides has the potential for the synthesis of AgNPs, with controlled morphology in environmentally friendly conditions.
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Affiliation(s)
- Masayoshi Tanaka
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8552, Japan; (M.T.); (S.S.)
| | - Shogo Saito
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8552, Japan; (M.T.); (S.S.)
| | - Reo Kita
- School of Science; Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8552, Japan;
| | - Jaehee Jang
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (J.J.); (Y.C.); (J.C.)
| | - Yonghyun Choi
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (J.J.); (Y.C.); (J.C.)
| | - Jonghoon Choi
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (J.J.); (Y.C.); (J.C.)
| | - Mina Okochi
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8552, Japan; (M.T.); (S.S.)
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23
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Blanco C, Verbanic S, Seelig B, Chen IA. High throughput sequencing of in vitro selections of mRNA-displayed peptides: data analysis and applications. Phys Chem Chem Phys 2020; 22:6492-6506. [PMID: 31967131 PMCID: PMC8219182 DOI: 10.1039/c9cp05912a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In vitro selection using mRNA display is currently a widely used method to isolate functional peptides with desired properties. The analysis of high throughput sequencing (HTS) data from in vitro evolution experiments has proven to be a powerful technique but only recently has it been applied to mRNA display selections. In this Perspective, we introduce aspects of mRNA display and HTS that may be of interest to physical chemists. We highlight the potential of HTS to analyze in vitro selections of peptides and review recent advances in the application of HTS analysis to mRNA display experiments. We discuss some possible issues involved with HTS analysis and summarize some strategies to alleviate them. Finally, the potential for future impact of advancing HTS analysis on mRNA display experiments is discussed.
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Affiliation(s)
- Celia Blanco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA.
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24
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Novel silica forming peptide, RSGH, from Equus caballus: Its unique biosilica formation under acidic conditions. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2019.107389] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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25
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Fischer J, Renn D, Quitterer F, Radhakrishnan A, Liu M, Makki A, Ghorpade S, Rueping M, Arold ST, Groll M, Eppinger J. Robust and Versatile Host Protein for the Design and Evaluation of Artificial Metal Centers. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02896] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Johannes Fischer
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
| | - Dominik Renn
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
| | - Felix Quitterer
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
| | | | | | | | | | | | - Stefan T. Arold
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, 34090 Montpellier, France
| | - Michael Groll
- Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München (TUM), D-85747 Garching, Germany
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26
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Antifungal Agents in Agriculture: Friends and Foes of Public Health. Biomolecules 2019; 9:biom9100521. [PMID: 31547546 PMCID: PMC6843326 DOI: 10.3390/biom9100521] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 09/12/2019] [Accepted: 09/19/2019] [Indexed: 12/14/2022] Open
Abstract
Fungal diseases have been underestimated worldwide but constitute a substantial threat to several plant and animal species as well as to public health. The increase in the global population has entailed an increase in the demand for agriculture in recent decades. Accordingly, there has been worldwide pressure to find means to improve the quality and productivity of agricultural crops. Antifungal agents have been widely used as an alternative for managing fungal diseases affecting several crops. However, the unregulated use of antifungals can jeopardize public health. Application of fungicides in agriculture should be under strict regulation to ensure the toxicological safety of commercialized foods. This review discusses the use of antifungals in agriculture worldwide, the need to develop new antifungals, and improvement of regulations regarding antifungal use.
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Bonk B, Weis JW, Tidor B. Machine Learning Identifies Chemical Characteristics That Promote Enzyme Catalysis. J Am Chem Soc 2019; 141:4108-4118. [PMID: 30761897 PMCID: PMC6407039 DOI: 10.1021/jacs.8b13879] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Indexed: 11/28/2022]
Abstract
Despite tremendous progress in understanding and engineering enzymes, knowledge of how enzyme structures and their dynamics induce observed catalytic properties is incomplete, and capabilities to engineer enzymes fall far short of industrial needs. Here, we investigate the structural and dynamic drivers of enzyme catalysis for the rate-limiting step of the industrially important enzyme ketol-acid reductoisomerase (KARI) and identify a region of the conformational space of the bound enzyme-substrate complex that, when populated, leads to large increases in reactivity. We apply computational statistical mechanical methods that implement transition interface sampling to simulate the kinetics of the reaction and combine this with machine learning techniques from artificial intelligence to select features relevant to reactivity and to build predictive models for reactive trajectories. We find that conformational descriptors alone, without the need for dynamic ones, are sufficient to predict reactivity with greater than 85% accuracy (90% AUC). Key descriptors distinguishing reactive from almost-reactive trajectories quantify substrate conformation, substrate bond polarization, and metal coordination geometry and suggest their role in promoting substrate reactivity. Moreover, trajectories constrained to visit a region of the reactant well, separated from the rest by a simple hyperplane defined by ten conformational parameters, show increases in computed reactivity by many orders of magnitude. This study provides evidence for the existence of reactivity promoting regions within the conformational space of the enzyme-substrate complex and develops methodology for identifying and validating these particularly reactive regions of phase space. We suggest that identification of reactivity promoting regions and re-engineering enzymes to preferentially populate them may lead to significant rate enhancements.
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Affiliation(s)
- Brian
M. Bonk
- Department
of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - James W. Weis
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Computational
and Systems Biology, Massachusetts Institute
of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department
of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Bruce Tidor
- Department
of Biological Engineering, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Computational
and Systems Biology, Massachusetts Institute
of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department
of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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29
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Tanaka M, Takahashi Y, Roach L, Critchley K, Evans SD, Okochi M. Rational screening of biomineralisation peptides for colour-selected one-pot gold nanoparticle syntheses. NANOSCALE ADVANCES 2019; 1:71-75. [PMID: 36132451 PMCID: PMC9473233 DOI: 10.1039/c8na00075a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 07/16/2018] [Indexed: 06/11/2023]
Abstract
Biomineralisation peptides that facilitate the one-pot synthesis of gold nanoparticles (AuNPs) with selected optical properties, were screened using a coherent peptide-spotted array consisting of a AuNP binding peptide library. As the biomineralised AuNPs were captured on each peptide spot, analysis of the images provided information on their collective optical properties.
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Affiliation(s)
- M Tanaka
- Department of Chemical Science and Engineering, Tokyo Institute of Technology 2-12-1, O-okayama, Meguro-ku Tokyo 152-8552 Japan +81-3-5734-2116 +81-3-5734-2116
| | - Y Takahashi
- Department of Chemical Science and Engineering, Tokyo Institute of Technology 2-12-1, O-okayama, Meguro-ku Tokyo 152-8552 Japan +81-3-5734-2116 +81-3-5734-2116
| | - L Roach
- School of Physics and Astronomy, University of Leeds Leeds LS2 9JT UK
| | - K Critchley
- School of Physics and Astronomy, University of Leeds Leeds LS2 9JT UK
| | - S D Evans
- School of Physics and Astronomy, University of Leeds Leeds LS2 9JT UK
| | - M Okochi
- Department of Chemical Science and Engineering, Tokyo Institute of Technology 2-12-1, O-okayama, Meguro-ku Tokyo 152-8552 Japan +81-3-5734-2116 +81-3-5734-2116
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30
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Baruch Leshem A, Isaacs S, Srivastava SK, Abdulhalim I, Kushmaro A, Rapaport H. Quantitative assessment of paraoxon adsorption to amphiphilic β-sheet peptides presenting the catalytic triad of esterases. J Colloid Interface Sci 2018; 530:328-337. [DOI: 10.1016/j.jcis.2018.06.065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/21/2018] [Accepted: 06/22/2018] [Indexed: 01/31/2023]
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31
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Gosavi PM, Jayachandran M, Rempillo JJL, Zozulia O, Makhlynets OV, Korendovych IV. A Designed Enzyme Promotes Selective Post-translational Acylation. Chembiochem 2018; 19:1605-1608. [PMID: 29756279 DOI: 10.1002/cbic.201800196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Indexed: 11/10/2022]
Abstract
A computationally designed, allosterically regulated catalyst (CaM M144H) produced by substituting a single residue in calmodulin, a non-enzymatic protein, is capable of efficient and site selective post-translational acylation of lysines in peptides with highly diverse sequences. Calmodulin's binding partners are involved in regulating a large number of cellular processes; this new chemical-biology tool will help to identify them and provide structural insight into their interactions with calmodulin.
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Affiliation(s)
- Pallavi M Gosavi
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Megha Jayachandran
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Joel J L Rempillo
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Oleksii Zozulia
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Olga V Makhlynets
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Ivan V Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
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32
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Lengyel Z, Rufo CM, Moroz YS, Makhlynets OV, Korendovych IV. Copper-Containing Catalytic Amyloids Promote Phosphoester Hydrolysis and Tandem Reactions. ACS Catal 2018; 8:59-62. [PMID: 30319881 PMCID: PMC6181230 DOI: 10.1021/acscatal.7b03323] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Self-assembly of short de novo designed peptides gives rise to catalytic amyloids capable of facilitating multiple chemical transformations. We show that catalytic amyloids can efficiently hydrolyze paraoxon, a widely used, highly toxic organophosphate pesticide. Moreover, these robust and inexpensive metal-containing materials can be easily deposited on various surfaces producing catalytic flow devices. Finally, functional promiscuity of catalytic amyloids promotes tandem hydrolysis/oxidation reactions. High efficiency discovered in a very small library of peptides suggests an enormous potential for further improvement of catalytic properties both in terms of catalytic efficiency and substrate scope.
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Affiliation(s)
- Zsófia Lengyel
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244
| | - Caroline M. Rufo
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244
| | | | - Olga V. Makhlynets
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244
| | - Ivan V. Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244
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33
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ten Brummelhuis N, Wilke P, Börner HG. Identification of Functional Peptide Sequences to Lead the Design of Precision Polymers. Macromol Rapid Commun 2017; 38. [DOI: 10.1002/marc.201700632] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 09/26/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Niels ten Brummelhuis
- Laboratory for Organic Synthesis of Functional Systems; Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 D-12489 Berlin Germany
| | - Patrick Wilke
- Laboratory for Organic Synthesis of Functional Systems; Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 D-12489 Berlin Germany
| | - Hans G. Börner
- Laboratory for Organic Synthesis of Functional Systems; Department of Chemistry; Humboldt-Universität zu Berlin; Brook-Taylor-Str. 2 D-12489 Berlin Germany
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34
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Reed JH, Shi Y, Zhu Q, Chakraborty S, Mirts EN, Petrik ID, Bhagi-Damodaran A, Ross M, Moënne-Loccoz P, Zhang Y, Lu Y. Manganese and Cobalt in the Nonheme-Metal-Binding Site of a Biosynthetic Model of Heme-Copper Oxidase Superfamily Confer Oxidase Activity through Redox-Inactive Mechanism. J Am Chem Soc 2017; 139:12209-12218. [PMID: 28768416 PMCID: PMC5673108 DOI: 10.1021/jacs.7b05800] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The presence of a nonheme metal, such as copper and iron, in the heme-copper oxidase (HCO) superfamily is critical to the enzymatic activity of reducing O2 to H2O, but the exact mechanism the nonheme metal ion uses to confer and fine-tune the activity remains to be understood. We herein report that manganese and cobalt can bind to the same nonheme site and confer HCO activity in a heme-nonheme biosynthetic model in myoglobin. While the initial rates of O2 reduction by the Mn, Fe, and Co derivatives are similar, the percentages of reactive oxygen species (ROS) formation are 7%, 4%, and 1% and the total turnovers are 5.1 ± 1.1, 13.4 ± 0.7, and 82.5 ± 2.5, respectively. These results correlate with the trends of nonheme-metal-binding dissociation constants (35, 22, and 9 μM) closely, suggesting that tighter metal binding can prevent ROS release from the active site, lessen damage to the protein, and produce higher total turnover numbers. Detailed spectroscopic, electrochemical, and computational studies found no evidence of redox cycling of manganese or cobalt in the enzymatic reactions and suggest that structural and electronic effects related to the presence of different nonheme metals lead to the observed differences in reactivity. This study of the roles of nonheme metal ions beyond the Cu and Fe found in native enzymes has provided deeper insights into nature's choice of metal ion and reaction mechanism and allows for finer control of the enzymatic activity, which is a basis for the design of efficient catalysts for the oxygen reduction reaction in fuel cells.
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Affiliation(s)
- Julian H. Reed
- Department of Biochemistry, University of Illinois at
Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yelu Shi
- Department of Biomedical Engineering, Chemistry, and Biological
Sciences, Stevens Institute of Technology, Hoboken, NJ, 07030, USA
| | - Qianhong Zhu
- Division of Environmental & Biomolecular Systems, Institute
of Environmental Health, Oregon Health & Science University, Portland, OR,
97239, USA
| | - Saumen Chakraborty
- Department of Chemistry & Biochemistry, University of
Mississippi, Oxford, Mississippi, 38677, USA
| | - Evan N. Mirts
- Center for Biophysics and Quantitative Biology, University of
Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Igor D. Petrik
- Department of Chemistry, University of Illinois at Urbana-Champaign,
Urbana, IL, 61801, USA
| | - Ambika Bhagi-Damodaran
- Department of Pharmaceutical Chemistry, University of California,
San Francisco, San Francisco, CA, 94143, USA
| | - Matthew Ross
- Department of Chemistry, Northwestern University, Evanston, IL,
60208, USA
| | - Pierre Moënne-Loccoz
- Division of Environmental & Biomolecular Systems, Institute
of Environmental Health, Oregon Health & Science University, Portland, OR,
97239, USA
| | - Yong Zhang
- Department of Biomedical Engineering, Chemistry, and Biological
Sciences, Stevens Institute of Technology, Hoboken, NJ, 07030, USA
| | - Yi Lu
- Department of Biochemistry, University of Illinois at
Urbana-Champaign, Urbana, IL, 61801, USA
- Center for Biophysics and Quantitative Biology, University of
Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign,
Urbana, IL, 61801, USA
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35
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Bhagi-Damodaran A, Kahle M, Shi Y, Zhang Y, Ädelroth P, Lu Y. Insights Into How Heme Reduction Potentials Modulate Enzymatic Activities of a Myoglobin-based Functional Oxidase. Angew Chem Int Ed Engl 2017; 56:6622-6626. [PMID: 28470988 DOI: 10.1002/anie.201701916] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Indexed: 01/01/2023]
Abstract
Heme-copper oxidase (HCO) is a class of respiratory enzymes that use a heme-copper center to catalyze O2 reduction to H2 O. While heme reduction potential (E°') of different HCO types has been found to vary >500 mV, its impact on HCO activity remains poorly understood. Here, we use a set of myoglobin-based functional HCO models to investigate the mechanism by which heme E°' modulates oxidase activity. Rapid stopped-flow kinetic measurements show that increasing heme E°' by ca. 210 mV results in increases in electron transfer (ET) rates by 30-fold, rate of O2 binding by 12-fold, O2 dissociation by 35-fold, while decreasing O2 affinity by 3-fold. Theoretical calculations reveal that E°' modulation has significant implications on electronic charge of both heme iron and O2 , resulting in increased O2 dissociation and reduced O2 affinity at high E°' values. Overall, this work suggests that fine-tuning E°' in HCOs and other heme enzymes can modulate their substrate affinity, ET rate and enzymatic activity.
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Affiliation(s)
- Ambika Bhagi-Damodaran
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Maximilian Kahle
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-10691, Stockholm, Sweden
| | - Yelu Shi
- Department of Biomedical Engineering, Chemistry and Biological Sciences, Stevens Institute of Technology, Hoboken, New Jersey, NY, 07030, USA
| | - Yong Zhang
- Department of Biomedical Engineering, Chemistry and Biological Sciences, Stevens Institute of Technology, Hoboken, New Jersey, NY, 07030, USA
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-10691, Stockholm, Sweden
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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36
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Bhagi‐Damodaran A, Kahle M, Shi Y, Zhang Y, Ädelroth P, Lu Y. Insights Into How Heme Reduction Potentials Modulate Enzymatic Activities of a Myoglobin‐based Functional Oxidase. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Maximilian Kahle
- Department of Biochemistry and Biophysics Arrhenius Laboratories for Natural Sciences Stockholm University SE-10691 Stockholm Sweden
| | - Yelu Shi
- Department of Biomedical Engineering, Chemistry and Biological Sciences Stevens Institute of Technology Hoboken, New Jersey NY 07030 USA
| | - Yong Zhang
- Department of Biomedical Engineering, Chemistry and Biological Sciences Stevens Institute of Technology Hoboken, New Jersey NY 07030 USA
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics Arrhenius Laboratories for Natural Sciences Stockholm University SE-10691 Stockholm Sweden
| | - Yi Lu
- Department of Chemistry University of Illinois at Urbana-Champaign Urbana IL 61801 USA
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37
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Abstract
Amyloid-like fibrils assembled from de novo designed peptides lock ligands in a conformation optimal for metal binding and catalysis in a manner similar to how metalloenzymes provide proper coordination environment through fold. These supramolecular assemblies efficiently catalyze p-nitrophenyl ester hydrolysis in the presence of zinc and phenol oxidation by dioxygen in the presence of copper. The resulting heterogeneous catalysts are inherently switchable, as addition and removal of the metal ions turns the catalytic activity on and off, respectively. The ease of peptide preparation and self-assembly makes amyloid-like fibrils an attractive platform for developing catalysts for a broad range of chemical reactions. Here, we present a detailed protocol for the preparation of copper-containing fibrils and for kinetic characterization of their abilities to oxidize phenols.
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Affiliation(s)
- Alex Sternisha
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Olga Makhlynets
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA.
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38
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Makhlynets OV, Korendovych IV. Minimalist Design of Allosterically Regulated Protein Catalysts. Methods Enzymol 2016; 580:191-202. [PMID: 27586334 DOI: 10.1016/bs.mie.2016.05.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Nature facilitates chemical transformations with exceptional selectivity and efficiency. Despite a tremendous progress in understanding and predicting protein function, the overall problem of designing a protein catalyst for a given chemical transformation is far from solved. Over the years, many design techniques with various degrees of complexity and rational input have been developed. Minimalist approach to protein design that focuses on the bare minimum requirements to achieve activity presents several important advantages. By focusing on basic physicochemical properties and strategic placing of only few highly active residues one can feasibly evaluate in silico a very large variety of possible catalysts. In more general terms minimalist approach looks for the mere possibility of catalysis, rather than trying to identify the most active catalyst possible. Even very basic designs that utilize a single residue introduced into nonenzymatic proteins or peptide bundles are surprisingly active. Because of the inherent simplicity of the minimalist approach computational tools greatly enhance its efficiency. No complex calculations need to be set up and even a beginner can master this technique in a very short time. Here, we present a step-by-step protocol for minimalist design of functional proteins using basic, easily available, and free computational tools.
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