1
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Albayati SH, Nezhad NG, Taki AG, Rahman RNZRA. Efficient and easible biocatalysts: Strategies for enzyme improvement. A review. Int J Biol Macromol 2024; 276:133978. [PMID: 39038570 DOI: 10.1016/j.ijbiomac.2024.133978] [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] [Received: 04/18/2024] [Revised: 06/19/2024] [Accepted: 07/16/2024] [Indexed: 07/24/2024]
Abstract
Owing to the environmental friendliness and vast advantages that enzymes offer in the biotechnology and industry fields, biocatalysts are a prolific investigation field. However, the low catalytic activity, stability, and specific selectivity of the enzyme limit the range of the reaction enzymes involved in. A comprehensive understanding of the protein structure and dynamics in terms of molecular details enables us to tackle these limitations effectively and enhance the catalytic activity by enzyme engineering or modifying the supports and solvents. Along with different strategies including computational, enzyme engineering based on DNA recombination, enzyme immobilization, additives, chemical modification, and physicochemical modification approaches can be promising for the wide spread of industrial enzyme usage. This is attributed to the successful application of biocatalysts in industrial and synthetic processes requires a system that exhibits stability, activity, and reusability in a continuous flow process, thereby reducing the production cost. The main goal of this review is to display relevant approaches for improving enzyme characteristics to overcome their industrial application.
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Affiliation(s)
- Samah Hashim Albayati
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Nima Ghahremani Nezhad
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Anmar Ghanim Taki
- Department of Radiology Techniques, Health and Medical Techniques College, Alnoor University, Mosul, Iraq
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; Institute Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
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2
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Tule S, Foley G, Zhao C, Forbes M, Bodén M. Optimal phylogenetic reconstruction of insertion and deletion events. Bioinformatics 2024; 40:i277-i286. [PMID: 38940131 PMCID: PMC11211827 DOI: 10.1093/bioinformatics/btae254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024] Open
Abstract
MOTIVATION Insertions and deletions (indels) influence the genetic code in fundamentally distinct ways from substitutions, significantly impacting gene product structure and function. Despite their influence, the evolutionary history of indels is often neglected in phylogenetic tree inference and ancestral sequence reconstruction, hindering efforts to comprehend biological diversity determinants and engineer variants for medical and industrial applications. RESULTS We frame determining the optimal history of indel events as a single Mixed-Integer Programming (MIP) problem, across all branch points in a phylogenetic tree adhering to topological constraints, and all sites implied by a given set of aligned, extant sequences. By disentangling the impact on ancestral sequences at each branch point, this approach identifies the minimal indel events that jointly explain the diversity in sequences mapped to the tips of that tree. MIP can recover alternate optimal indel histories, if available. We evaluated MIP for indel inference on a dataset comprising 15 real phylogenetic trees associated with protein families ranging from 165 to 2000 extant sequences, and on 60 synthetic trees at comparable scales of data and reflecting realistic rates of mutation. Across relevant metrics, MIP outperformed alternative parsimony-based approaches and reported the fewest indel events, on par or below their occurrence in synthetic datasets. MIP offers a rational justification for indel patterns in extant sequences; importantly, it uniquely identifies global optima on complex protein data sets without making unrealistic assumptions of independence or evolutionary underpinnings, promising a deeper understanding of molecular evolution and aiding novel protein design. AVAILABILITY AND IMPLEMENTATION The implementation is available via GitHub at https://github.com/santule/indelmip.
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Affiliation(s)
- Sanjana Tule
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Gabriel Foley
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Chongting Zhao
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Michael Forbes
- School of Mathematics and Physics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
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3
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Notin P, Kollasch AW, Ritter D, van Niekerk L, Paul S, Spinner H, Rollins N, Shaw A, Weitzman R, Frazer J, Dias M, Franceschi D, Orenbuch R, Gal Y, Marks DS. ProteinGym: Large-Scale Benchmarks for Protein Design and Fitness Prediction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570727. [PMID: 38106144 PMCID: PMC10723403 DOI: 10.1101/2023.12.07.570727] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Predicting the effects of mutations in proteins is critical to many applications, from understanding genetic disease to designing novel proteins that can address our most pressing challenges in climate, agriculture and healthcare. Despite a surge in machine learning-based protein models to tackle these questions, an assessment of their respective benefits is challenging due to the use of distinct, often contrived, experimental datasets, and the variable performance of models across different protein families. Addressing these challenges requires scale. To that end we introduce ProteinGym, a large-scale and holistic set of benchmarks specifically designed for protein fitness prediction and design. It encompasses both a broad collection of over 250 standardized deep mutational scanning assays, spanning millions of mutated sequences, as well as curated clinical datasets providing high-quality expert annotations about mutation effects. We devise a robust evaluation framework that combines metrics for both fitness prediction and design, factors in known limitations of the underlying experimental methods, and covers both zero-shot and supervised settings. We report the performance of a diverse set of over 70 high-performing models from various subfields (eg., alignment-based, inverse folding) into a unified benchmark suite. We open source the corresponding codebase, datasets, MSAs, structures, model predictions and develop a user-friendly website that facilitates data access and analysis.
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Affiliation(s)
| | | | | | | | | | | | | | - Ada Shaw
- Applied Mathematics, Harvard University
| | | | | | - Mafalda Dias
- Centre for Genomic Regulation, Universitat Pompeu Fabra
| | | | | | - Yarin Gal
- Computer Science, University of Oxford
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4
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Sellés Vidal L, Isalan M, Heap JT, Ledesma-Amaro R. A primer to directed evolution: current methodologies and future directions. RSC Chem Biol 2023; 4:271-291. [PMID: 37034405 PMCID: PMC10074555 DOI: 10.1039/d2cb00231k] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/18/2023] [Indexed: 01/30/2023] Open
Abstract
Directed evolution is one of the most powerful tools for protein engineering and functions by harnessing natural evolution, but on a shorter timescale. It enables the rapid selection of variants of biomolecules with properties that make them more suitable for specific applications. Since the first in vitro evolution experiments performed by Sol Spiegelman in 1967, a wide range of techniques have been developed to tackle the main two steps of directed evolution: genetic diversification (library generation), and isolation of the variants of interest. This review covers the main modern methodologies, discussing the advantages and drawbacks of each, and hence the considerations for designing directed evolution experiments. Furthermore, the most recent developments are discussed, showing how advances in the handling of ever larger library sizes are enabling new research questions to be tackled.
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Affiliation(s)
- Lara Sellés Vidal
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Bioengineering, Imperial College London London SW7 2AZ UK
| | - Mark Isalan
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
| | - John T Heap
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Life Sciences, Imperial College London London SW7 2AZ UK
- School of Life Sciences, The University of Nottingham, University Park Nottingham NG7 2RD UK
| | - Rodrigo Ledesma-Amaro
- Imperial College Centre for Synthetic Biology, Imperial College London London SW7 2AZ UK
- Department of Bioengineering, Imperial College London London SW7 2AZ UK
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5
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Miton CM, Tokuriki N. Insertions and Deletions (Indels): A Missing Piece of the Protein Engineering Jigsaw. Biochemistry 2023; 62:148-157. [PMID: 35830609 DOI: 10.1021/acs.biochem.2c00188] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Over the years, protein engineers have studied nature and borrowed its tricks to accelerate protein evolution in the test tube. While there have been considerable advances, our ability to generate new proteins in the laboratory is seemingly limited. One explanation for these shortcomings may be that insertions and deletions (indels), which frequently arise in nature, are largely overlooked during protein engineering campaigns. The profound effect of indels on protein structures, by way of drastic backbone alterations, could be perceived as "saltation" events that bring about significant phenotypic changes in a single mutational step. Should we leverage these effects to accelerate protein engineering and gain access to unexplored regions of adaptive landscapes? In this Perspective, we describe the role played by indels in the functional diversification of proteins in nature and discuss their untapped potential for protein engineering, despite their often-destabilizing nature. We hope to spark a renewed interest in indels, emphasizing that their wider study and use may prove insightful and shape the future of protein engineering by unlocking unique functional changes that substitutions alone could never achieve.
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Affiliation(s)
- Charlotte M Miton
- Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4 BC, Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4 BC, Canada
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6
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Emond S, Petek M, Kay EJ, Heames B, Devenish SRA, Tokuriki N, Hollfelder F. Accessing unexplored regions of sequence space in directed enzyme evolution via insertion/deletion mutagenesis. Nat Commun 2020; 11:3469. [PMID: 32651386 PMCID: PMC7351745 DOI: 10.1038/s41467-020-17061-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 06/01/2020] [Indexed: 11/22/2022] Open
Abstract
Insertions and deletions (InDels) are frequently observed in natural protein evolution, yet their potential remains untapped in laboratory evolution. Here we introduce a transposon-based mutagenesis approach (TRIAD) to generate libraries of random variants with short in-frame InDels, and screen TRIAD libraries to evolve a promiscuous arylesterase activity in a phosphotriesterase. The evolution exhibits features that differ from previous point mutagenesis campaigns: while the average activity of TRIAD variants is more compromised, a larger proportion has successfully adapted for the activity. Different functional profiles emerge: (i) both strong and weak trade-off between activities are observed; (ii) trade-off is more severe (20- to 35-fold increased kcat/KM in arylesterase with 60-400-fold decreases in phosphotriesterase activity) and (iii) improvements are present in kcat rather than just in KM, suggesting adaptive solutions. These distinct features make TRIAD an alternative to widely used point mutagenesis, accessing functional innovations and traversing unexplored fitness landscape regions.
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Affiliation(s)
- Stephane Emond
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
- Evonetix Ltd, Coldhams Business Park, Norman Way, Cambridge, CB1 3LH, UK.
| | - Maya Petek
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Emily J Kay
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
| | - Brennen Heames
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität, Hüfferstrasse 1, 48149, Münster, Germany
| | - Sean R A Devenish
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- Fluidic Analytics, The Paddocks Business Centre, Cherry Hinton Road, Cambridge, CB1 8DH, UK
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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7
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Gonzalez CE, Roberts P, Ostermeier M. Fitness Effects of Single Amino Acid Insertions and Deletions in TEM-1 β-Lactamase. J Mol Biol 2019; 431:2320-2330. [PMID: 31034887 DOI: 10.1016/j.jmb.2019.04.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 11/16/2022]
Abstract
Short insertions and deletions (InDels) are a common type of mutation found in nature and a useful source of variation in protein engineering. InDel events have important consequences in protein evolution, often opening new pathways for adaptation. However, much less is known about the effects of InDels compared to point mutations and amino acid substitutions. In particular, deep mutagenesis studies on the distribution of fitness effects of mutations have focused almost exclusively on amino acid substitutions. Here, we present a near-comprehensive analysis of the fitness effects of single amino acid InDels in TEM-1 β-lactamase. While we found InDels to be largely deleterious, partially overlapping deletion-tolerant and insertion-tolerant regions were observed throughout the protein, especially in unstructured regions and at the end of helices. The signal sequence of TEM-1 tolerated InDels more than the mature protein. Most regions of the protein tolerated insertions more than deletions, but a few regions tolerated deletions more than insertions. We examined the relationship between InDel tolerance and a variety of measures to help understand its origin. These measures included evolutionary variation in β-lactamases, secondary structure identity, tolerance to amino acid substitutions, solvent accessibility, and side-chain weighted contact number. We found secondary structure, weighted contact number, and evolutionary variation in class A beta-lactamases to be the somewhat predictive of InDel fitness effects.
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Affiliation(s)
- Courtney E Gonzalez
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Paul Roberts
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Marc Ostermeier
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA.
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8
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Balasco N, Smaldone G, Ruggiero A, De Simone A, Vitagliano L. Local structural motifs in proteins: Detection and characterization of fragments inserted in helices. Int J Biol Macromol 2018; 118:1924-1930. [PMID: 30017977 DOI: 10.1016/j.ijbiomac.2018.07.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/06/2018] [Accepted: 07/11/2018] [Indexed: 11/26/2022]
Abstract
The global/local fold of protein structures is stabilized by a variety of specific interactions. A primary role in this context is played by hydrogen bonds. In order to identify novel motifs in proteins, we searched Protein Data Bank structures looking for backbone H-bonds formed by NH groups of two (or more) consecutive residues with consecutive CO groups of distant residues in the sequence. The present analysis unravels the occurrence of recurrent structural motifs that, to the best of our knowledge, had not been characterized in literature. Indeed, these H-bonding patterns are found (i) in a specific parallel β-sheet capping, (ii) in linking of β-hairpins to α-helices, and (iii) in α-helix insertions. Interestingly, structural analyses of these motifs indicate that Gly residues frequently occupy prominent positions. The formation of these motifs is likely favored by the limited propensity of Gly to be embodied in helices/sheets. Of particular interest is the motif corresponding to insertions in helices that was detected in 1% of analyzed structures. Inserted fragments may assume different structures and aminoacid compositions and usually display diversified evolutionary conservation. Since inserted regions are physically separated from the rest of the protein structure, they represent hot spots for ad-hoc protein functionalization.
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Affiliation(s)
- Nicole Balasco
- Institute of Biostructures and Bioimaging, C.N.R., Naples, Italy.
| | | | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, C.N.R., Naples, Italy
| | - Alfonso De Simone
- Division of Molecular Biosciences, Imperial College South Kensington Campus, London SW7 2AZ, UK
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, C.N.R., Naples, Italy.
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9
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Gaytán P, Roldán-Salgado A, Yáñez JA, Morales-Arrieta S, Juárez-González VR. CiPerGenesis, A Mutagenesis Approach that Produces Small Libraries of Circularly Permuted Proteins Randomly Opened at a Focused Region: Testing on the Green Fluorescent Protein. ACS COMBINATORIAL SCIENCE 2018; 20:400-413. [PMID: 29812897 DOI: 10.1021/acscombsci.7b00152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Circularly permuted proteins (cpPs) represent a novel type of mutant proteins with original termini that are covalently linked through a peptide connector and opened at any other place of the polypeptide backbone to create new ends. cpPs are finding wide applications in biotechnology because their properties may be quite different from those of the parental protein. However, the actual challenge for the creation of successful cpPs is to identify those peptide bonds that can be broken to create new termini and ensure functional and well-folded cpPs. Herein, we describe CiPerGenesis, a combinatorial mutagenesis approach that uses two oligonucleotide libraries to amplify a circularized gene by PCR, starting and ending from a focused target region. This approach creates small libraries of circularly permuted genes that are easily cloned in the correct direction and frame using two different restriction sites encoded in the oligonucleotides. Once expressed, the protein libraries exhibit a unique sequence diversity, comprising cpPs that exhibit ordinary breakpoints between adjacent amino acids localized at the target region as well as cpPs with new termini containing user-defined truncations and repeats of some amino acids. CiPerGenesis was tested at the lid region G134-H148 of green fluorescent protein (GFP), revealing that the most fluorescent variants were those starting at Leu141 and ending at amino acids Tyr145, Tyr143, Glu142, Leu141, Lys140, and H139. Purification and biochemical characterization of some variants suggested a differential expression, solubility and maturation extent of the mutant proteins as the likely cause for the variability in fluorescence intensity observed in colonies.
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Affiliation(s)
- Paul Gaytán
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Abigail Roldán-Salgado
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Jorge A. Yáñez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Sandra Morales-Arrieta
- Departamento de Ingeniería en Biotecnología, Universidad Politécnica del Estado de Morelos, Boulevard Cuauhnáhuac No. 566, Col. Lomas del Texcal, Jiutepec, Morelos 62550, México
| | - Víctor R. Juárez-González
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, México
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10
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Halliwell LM, Jathoul AP, Bate JP, Worthy HL, Anderson JC, Jones DD, Murray JAH. ΔFlucs: Brighter Photinus pyralis firefly luciferases identified by surveying consecutive single amino acid deletion mutations in a thermostable variant. Biotechnol Bioeng 2017; 115:50-59. [PMID: 28921549 DOI: 10.1002/bit.26451] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 11/05/2022]
Abstract
The bright bioluminescence catalyzed by Photinus pyralis firefly luciferase (Fluc) enables a vast array of life science research such as bio imaging in live animals and sensitive in vitro diagnostics. The effectiveness of such applications is improved using engineered enzymes that to date have been constructed using amino acid substitutions. We describe ΔFlucs: consecutive single amino acid deletion mutants within six loop structures of the bright and thermostable ×11 Fluc. Deletion mutations are a promising avenue to explore new sequence and functional space and isolate novel mutant phenotypes. However, this method is often overlooked and to date there have been no surveys of the effects of consecutive single amino acid deletions in Fluc. We constructed a large semi-rational ΔFluc library and isolated significantly brighter enzymes after finding ×11 Fluc activity was largely tolerant to deletions. Targeting an "omega-loop" motif (T352-G360) significantly enhanced activity, altered kinetics, reduced Km for D-luciferin, altered emission colors, and altered substrate specificity for redshifted analog DL-infraluciferin. Experimental and in silico analyses suggested remodeling of the Ω-loop impacts on active site hydrophobicity to increase light yields. This work demonstrates the further potential of deletion mutations, which can generate useful Fluc mutants and broaden the palette of the biomedical and biotechnological bioluminescence enzyme toolbox.
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Affiliation(s)
| | - Amit P Jathoul
- School of Biosciences, University of Cardiff, Cardiff, UK
| | - Jack P Bate
- School of Biosciences, University of Cardiff, Cardiff, UK
| | | | | | - D Dafydd Jones
- School of Biosciences, University of Cardiff, Cardiff, UK
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11
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Arpino JAJ, Rizkallah PJ, Jones DD. Structural and dynamic changes associated with beneficial engineered single-amino-acid deletion mutations in enhanced green fluorescent protein. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2152-62. [PMID: 25084334 PMCID: PMC4118826 DOI: 10.1107/s139900471401267x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 05/31/2014] [Indexed: 01/23/2023]
Abstract
Single-amino-acid deletions are a common part of the natural evolutionary landscape but are rarely sampled during protein engineering owing to limited and prejudiced molecular understanding of mutations that shorten the protein backbone. Single-amino-acid deletion variants of enhanced green fluorescent protein (EGFP) have been identified by directed evolution with the beneficial effect of imparting increased cellular fluorescence. Biophysical characterization revealed that increased functional protein production and not changes to the fluorescence parameters was the mechanism that was likely to be responsible. The structure EGFP(D190Δ) containing a deletion within a loop revealed propagated changes only after the deleted residue. The structure of EGFP(A227Δ) revealed that a `flipping' mechanism was used to adjust for residue deletion at the end of a β-strand, with amino acids C-terminal to the deletion site repositioning to take the place of the deleted amino acid. In both variants new networks of short-range and long-range interactions are generated while maintaining the integrity of the hydrophobic core. Both deletion variants also displayed significant local and long-range changes in dynamics, as evident by changes in B factors compared with EGFP. Rather than being detrimental, deletion mutations can introduce beneficial structural effects through altering core protein properties, folding and dynamics, as well as function.
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Affiliation(s)
- James A. J. Arpino
- School of Biosciences, Cardiff University, Park Place, Cardiff CF10 3AT, Wales
| | | | - D. Dafydd Jones
- School of Biosciences, Cardiff University, Park Place, Cardiff CF10 3AT, Wales
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12
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Arpino JAJ, Reddington SC, Halliwell LM, Rizkallah PJ, Jones DD. Random single amino acid deletion sampling unveils structural tolerance and the benefits of helical registry shift on GFP folding and structure. Structure 2014; 22:889-98. [PMID: 24856363 PMCID: PMC4058518 DOI: 10.1016/j.str.2014.03.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 03/08/2014] [Accepted: 03/10/2014] [Indexed: 12/01/2022]
Abstract
Altering a protein’s backbone through amino acid deletion is a common evolutionary mutational mechanism, but is generally ignored during protein engineering primarily because its effect on the folding-structure-function relationship is difficult to predict. Using directed evolution, enhanced green fluorescent protein (EGFP) was observed to tolerate residue deletion across the breadth of the protein, particularly within short and long loops, helical elements, and at the termini of strands. A variant with G4 removed from a helix (EGFPG4Δ) conferred significantly higher cellular fluorescence. Folding analysis revealed that EGFPG4Δ retained more structure upon unfolding and refolded with almost 100% efficiency but at the expense of thermodynamic stability. The EGFPG4Δ structure revealed that G4 deletion caused a beneficial helical registry shift resulting in a new polar interaction network, which potentially stabilizes a cis proline peptide bond and links secondary structure elements. Thus, deletion mutations and registry shifts can enhance proteins through structural rearrangements not possible by substitution mutations alone. Using directed evolution, the impact of amino acid deletion on EGFP is explored Loops, helices, and strand termini are especially tolerant to amino acid deletion A deletion mutant that enhances cellular production and fluorescence is identified Structure reveals that a helical registry shift creates a new polar network
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Affiliation(s)
- James A J Arpino
- School of Biosciences, Main Building, Park Place, Cardiff University, Cardiff CF10 3AT, UK
| | - Samuel C Reddington
- School of Biosciences, Main Building, Park Place, Cardiff University, Cardiff CF10 3AT, UK
| | - Lisa M Halliwell
- School of Biosciences, Main Building, Park Place, Cardiff University, Cardiff CF10 3AT, UK
| | - Pierre J Rizkallah
- School of Medicine, Cardiff University, WHRI, Main Building, Heath Park, Cardiff CF14 4XN, UK
| | - D Dafydd Jones
- School of Biosciences, Main Building, Park Place, Cardiff University, Cardiff CF10 3AT, UK.
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13
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Fujii R, Kitaoka M, Hayashi K. Random insertional-deletional strand exchange mutagenesis (RAISE): a simple method for generating random insertion and deletion mutations. Methods Mol Biol 2014; 1179:151-158. [PMID: 25055776 DOI: 10.1007/978-1-4939-1053-3_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Although proteins can be artificially improved by random insertion and deletion mutagenesis methods, these procedures are technically difficult. Here we describe a simple method called random insertional-deletional strand exchange mutagenesis (RAISE). This method is based on gene shuffling and can be used to introduce a wide variety of insertions, deletions, and substitutions. RAISE involves three steps: DNA fragmentation, attachment of a random short sequence, and reconstruction. This yields unique mutants and can be a powerful technique for protein engineering.
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Affiliation(s)
- Ryota Fujii
- Synthetic Chemicals Laboratory, Mitsui Chemicals, Inc., 580-32 Nagaura, Sodegaura, Chiba, 299-0265, Japan
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14
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Jones DD, Arpino JAJ, Baldwin AJ, Edmundson MC. Transposon-based approaches for generating novel molecular diversity during directed evolution. Methods Mol Biol 2014; 1179:159-172. [PMID: 25055777 DOI: 10.1007/978-1-4939-1053-3_11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This chapter introduces a set of transposon-based methods that were developed to sample trinucleotide deletion, trinucleotide replacement, and domain insertion. Each approach has a common initial step that utilizes an engineered version of the Mu transposon called MuDel. The inherent low sequence specificity of MuDel results in its random insertion into target DNA during in vitro transposition. Removal of the transposon using a type IIS restriction endonuclease generates blunt-end random breaks at a frequency of one per target gene and the concomitant loss of 3 bp. Self-ligation or insertion of another DNA cassette results in the sampling of trinucleotide deletion or trinucleotide substitution/domain insertion, respectively.
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Affiliation(s)
- D Dafydd Jones
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AT, UK,
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15
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Stewart KL, Nelson MR, Eaton KV, Anderson WJ, Cordes MHJ. A role for indels in the evolution of Cro protein folds. Proteins 2013; 81:1988-96. [PMID: 23843258 DOI: 10.1002/prot.24358] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 05/30/2013] [Accepted: 06/10/2013] [Indexed: 11/06/2022]
Abstract
Insertions and deletions in protein sequences, or indels, can disrupt structure and may result in changes in protein folds during evolution or in association with alternative splicing. Pfl 6 and Xfaso 1 are two proteins in the Cro family that share a common ancestor but have different folds. Sequence alignments of the two proteins show two gaps, one at the N terminus, where the sequence of Xfaso 1 is two residues shorter, and one near the center of the sequence, where the sequence of Pfl 6 is five residues shorter. To test the potential importance of indels in Cro protein evolution, we generated hybrid variants of Pfl 6 and Xfaso 1 with indels in one or both regions, chosen according to several plausible sequence alignments. All but one deletion variant completely unfolded both proteins, showing that a longer N-terminal sequence was critical for Pfl 6 folding and a longer central region sequence was critical for Xfaso 1 folding. By contrast, Xfaso 1 tolerated a longer N-terminal sequence with little destabilization, and Pfl 6 tolerated central region insertions, albeit with substantial effects on thermal stability and some perturbation of the surrounding structure. None of the mutations appeared to convert one stable fold into the other. On the basis of this two-protein comparison, short insertion and deletion mutations probably played a role in evolutionary fold change in the Cro family, but were also not the only factors.
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Affiliation(s)
- Katie L Stewart
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, 85721-0088
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16
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Leucine to proline substitution by SNP at position 197 in Caspase-9 gene expression leads to neuroblastoma: a bioinformatics analysis. 3 Biotech 2013; 3:225-234. [PMID: 28324374 PMCID: PMC3646108 DOI: 10.1007/s13205-012-0088-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2012] [Accepted: 08/24/2012] [Indexed: 11/24/2022] Open
Abstract
To understand the role of CASP9 (Caspase-9) gene products in relation to
neuroblastoma disease, we have analyzed the single nucleotide polymorphisms (SNPs)
associated with this gene. This can help us understand the genetic variations that
can alter the function of the gene products. A total of 941 SNPs are investigated
for CASP9 gene. To determine whether a non-synonymous SNP (nsSNP) in this gene
affects its protein product, we used certain computational tools which predicted one
nsSNP, rs1052574, to have deleterious phenotypic effect. This polymorphic variant
results in amino acid substitution from leucine to proline at 197 position, i.e.,
from acyclic amino acid to a 5-membered amino acid which resides in the buried area
of the protein with a high level of conservation. This amino acid substitution shows
a transition from helix to coil in the mutant protein. Hence, due to the complete
alteration in the structural property of the amino acid side chain, the stability of
the protein is reduced which may affect the function of CASP9 protein, leading to
deregulation of apoptosis and neuroblastoma development.
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17
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Raghunathan G, Soundrarajan N, Sokalingam S, Yun H, Lee SG. Deletional protein engineering based on stable fold. PLoS One 2012; 7:e51510. [PMID: 23240034 PMCID: PMC3519881 DOI: 10.1371/journal.pone.0051510] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 11/01/2012] [Indexed: 12/14/2022] Open
Abstract
Diversification of protein sequence-structure space is a major concern in protein engineering. Deletion mutagenesis can generate a protein sequence-structure space different from substitution mutagenesis mediated space, but it has not been widely used in protein engineering compared to substitution mutagenesis, because it causes a relatively huge range of structural perturbations of target proteins which often inactivates the proteins. In this study, we demonstrate that, using green fluorescent protein (GFP) as a model system, the drawback of the deletional protein engineering can be overcome by employing the protein structure with high stability. The systematic dissection of N-terminal, C-terminal and internal sequences of GFPs with two different stabilities showed that GFP with high stability (s-GFP), was more tolerant to the elimination of amino acids compared to a GFP with normal stability (n-GFP). The deletion studies of s-GFP enabled us to achieve three interesting variants viz. s-DL4, s-N14, and s-C225, which could not been obtained from n-GFP. The deletion of 191–196 loop sequences led to the variant s-DL4 that was expressed predominantly as insoluble form but mostly active. The s-N14 and s-C225 are the variants without the amino acid residues involving secondary structures around N- and C-terminals of GFP fold respectively, exhibiting comparable biophysical properties of the n-GFP. Structural analysis of the variants through computational modeling study gave a few structural insights that can explain the spectral properties of the variants. Our study suggests that the protein sequence-structure space of deletion mutants can be more efficiently explored by employing the protein structure with higher stability.
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Affiliation(s)
- Govindan Raghunathan
- Department of Chemical Engineering, Pusan National University, Busan, South Korea
| | | | - Sriram Sokalingam
- Department of Chemical Engineering, Pusan National University, Busan, South Korea
| | - Hyungdon Yun
- School of Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Sun-Gu Lee
- Department of Chemical Engineering, Pusan National University, Busan, South Korea
- * E-mail:
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18
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Joseph AP, Valadié H, Srinivasan N, de Brevern AG. Local structural differences in homologous proteins: specificities in different SCOP classes. PLoS One 2012; 7:e38805. [PMID: 22745680 PMCID: PMC3382195 DOI: 10.1371/journal.pone.0038805] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 05/10/2012] [Indexed: 11/19/2022] Open
Abstract
The constant increase in the number of solved protein structures is of great help in understanding the basic principles behind protein folding and evolution. 3-D structural knowledge is valuable in designing and developing methods for comparison, modelling and prediction of protein structures. These approaches for structure analysis can be directly implicated in studying protein function and for drug design. The backbone of a protein structure favours certain local conformations which include α-helices, β-strands and turns. Libraries of limited number of local conformations (Structural Alphabets) were developed in the past to obtain a useful categorization of backbone conformation. Protein Block (PB) is one such Structural Alphabet that gave a reasonable structure approximation of 0.42 Å. In this study, we use PB description of local structures to analyse conformations that are preferred sites for structural variations and insertions, among group of related folds. This knowledge can be utilized in improving tools for structure comparison that work by analysing local structure similarities. Conformational differences between homologous proteins are known to occur often in the regions comprising turns and loops. Interestingly, these differences are found to have specific preferences depending upon the structural classes of proteins. Such class-specific preferences are mainly seen in the all-β class with changes involving short helical conformations and hairpin turns. A test carried out on a benchmark dataset also indicates that the use of knowledge on the class specific variations can improve the performance of a PB based structure comparison approach. The preference for the indel sites also seem to be confined to a few backbone conformations involving β-turns and helix C-caps. These are mainly associated with short loops joining the regular secondary structures that mediate a reversal in the chain direction. Rare β-turns of type I’ and II’ are also identified as preferred sites for insertions.
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Affiliation(s)
- Agnel Praveen Joseph
- INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, UMR 665, Paris, France
- Institut National de la Transfusion Sanguine (INTS), Paris, France
| | - Hélène Valadié
- INSERM UMR-S 726, DSIMB, Université Paris Diderot - Paris 7, Paris, France
| | | | - Alexandre G. de Brevern
- INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, UMR 665, Paris, France
- Institut National de la Transfusion Sanguine (INTS), Paris, France
- * E-mail:
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19
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Berrondo M, Gray JJ. Computed structures of point deletion mutants and their enzymatic activities. Proteins 2011; 79:2844-60. [PMID: 21905110 DOI: 10.1002/prot.23109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 04/08/2011] [Accepted: 05/13/2011] [Indexed: 11/11/2022]
Abstract
Point deletions in enzymes can vary in effect from negligible to complete loss of activity; however, these effects are not generally predictable. Deletions are widely observed in nature and often result in diseases such as cancer, cystic fibrosis, or osteogenesis imperfecta. Here, we have developed an algorithm to model the perturbed structures of deletion mutants with the ultimate goal of predicting their activities. The algorithm works by deleting the specified residue from the wild-type structure, creating a gap that is closed using a combination of local and global moves that change the backbone torsion angles of the protein structure. On a set of five proteins for which both wild-type and deletion mutant x-ray crystal structures are available, the algorithm produces deep, narrow energy funnels within 1.5 Å of the crystal structure for the deletion mutants. To assess the ability of our algorithm to predict activity from the predicted structures, we tested the correlation of experimental activity with several measures of the predicted structure ensemble using a set of 45 point deletions from ricin. Estimates incorporating likely prevalence of active and inactive deletion sites suggest that activity can be predicted correctly over 60% of the time from the active site root-mean squared deviation of the lowest energy predicted structures. The predictions are stronger than simple sequence organization measures, but more fundamental work is required in structure prediction and enzyme activity determination to allow consistent prediction of activity.
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Affiliation(s)
- Monica Berrondo
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
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20
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Lee SC. Implications of available design space for identification of non-immunogenic protein therapeutics. Biomed Microdevices 2009; 12:283-6. [PMID: 20012559 DOI: 10.1007/s10544-009-9383-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Immunogenicity/antibody responses are major issues for parenteral proteins and nanotherapeutics (nanovectors, diagnostics, theranostics, etc.), and robust antibody responses require T-helper epitopes. T-helper epitopes consist of specific amino acids at specific positions (anchor positions) in immunogens which contact the major histocompatibility complex (MHC), provide most of the energy for MHC binding and constitute the binding motif for the corresponding MHC alleles. We developed an algorithm that considers motifs to design vaccines lacking unwanted T-cell epitopes, and found numbers of such vaccines can be astronomical (Lee et al. 2009). The algorithm can be used to design reduced immunogenicity proteins, and numbers of predicted proteins are also immense. Reducing T-helper epitope content reduces protein immunogenicity, but the depth of mutagensis needed to eliminate immunogenicity is commonly assumed to be too great for retention of protein bioactivity. However, very deep, but successful substitution, insertion and deletion mutagenesis have been reported. These reports and design space the algorithm reveals suggest development of non-immunogenic therapeutics might be more feasible than commonly assumed.
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Affiliation(s)
- Stephen Craig Lee
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH 43210, USA.
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21
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Ferraro DM, Robertson AD. Predicting the magnitude of the reflex response to insertions in ubiquitin. J Mol Biol 2007; 375:764-72. [PMID: 18036541 DOI: 10.1016/j.jmb.2007.10.068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Revised: 10/25/2007] [Accepted: 10/26/2007] [Indexed: 10/22/2022]
Abstract
The ability to predict the structural response of a protein to an insertion would be a significant advance for the fields of homology modeling and protein design. However, the effects of insertions on protein conformation are not well understood. Previous work has demonstrated that for two loops in ubiquitin, the primary determinant of the structural adaptation to insertions is the insertion site rather than the sequence of the insertion; this phenomenon was termed the reflex response of loops to insertions. We report herein the analysis of ubiquitin mutants with insertions in two other loops. This study demonstrates that the insertion site is the primary determinant of the response to insertions for these two new loops as well, which further supports the reflex response hypothesis. We also attempted to predict the relative magnitudes of the responses at each site but were unsuccessful. Using the additional data collected in this work, we have refined our predictive hypothesis.
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Affiliation(s)
- Debra M Ferraro
- Department of Biochemistry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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22
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Simm AM, Baldwin AJ, Busse K, Jones DD. Investigating protein structural plasticity by surveying the consequence of an amino acid deletion from TEM-1 beta-lactamase. FEBS Lett 2007; 581:3904-8. [PMID: 17662719 DOI: 10.1016/j.febslet.2007.07.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2007] [Revised: 06/28/2007] [Accepted: 07/09/2007] [Indexed: 11/19/2022]
Abstract
While the deletion of an amino acid is a common mutation observed in nature, it is generally thought to be disruptive to protein structure. Using a directed evolution approach, we find that the enzyme TEM-1 beta-lactamase was broadly tolerant to the deletion mutations sampled. Circa 73% of the variants analysed retained activity towards ampicillin, with deletion mutations observed in helices and strands as well as regions important for structure and function. Several deletion variants had enhanced activity towards ceftazidime compared to the wild-type TEM-1 demonstrating that removal of an amino acid can have a beneficial outcome.
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Affiliation(s)
- Alan M Simm
- School of Biosciences, Biomedical Sciences Building, Museum Avenue, Cardiff University, Cardiff CF10 3US, UK
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23
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Talavera D, Vogel C, Orozco M, Teichmann SA, de la Cruz X. The (in)dependence of alternative splicing and gene duplication. PLoS Comput Biol 2007; 3:e33. [PMID: 17335345 PMCID: PMC1808492 DOI: 10.1371/journal.pcbi.0030033] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Accepted: 01/04/2007] [Indexed: 11/18/2022] Open
Abstract
Alternative splicing (AS) and gene duplication (GD) both are processes that diversify the protein repertoire. Recent examples have shown that sequence changes introduced by AS may be comparable to those introduced by GD. In addition, the two processes are inversely correlated at the genomic scale: large gene families are depleted in splice variants and vice versa. All together, these data strongly suggest that both phenomena result in interchangeability between their effects. Here, we tested the extent to which this applies with respect to various protein characteristics. The amounts of AS and GD per gene are anticorrelated even when accounting for different gene functions or degrees of sequence divergence. In contrast, the two processes appear to be independent in their influence on variation in mRNA expression. Further, we conducted a detailed comparison of the effect of sequence changes in both alternative splice variants and gene duplicates on protein structure, in particular the size, location, and types of sequence substitutions and insertions/deletions. We find that, in general, alternative splicing affects protein sequence and structure in a more drastic way than gene duplication and subsequent divergence. Our results reveal an interesting paradox between the anticorrelation of AS and GD at the genomic level, and their impact at the protein level, which shows little or no equivalence in terms of effects on protein sequence, structure, and function. We discuss possible explanations that relate to the order of appearance of AS and GD in a gene family, and to the selection pressure imposed by the environment.
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Affiliation(s)
- David Talavera
- Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Barcelona, Spain
- Protein Structure and Modelling Node, Instituto Nacional de Bioinfomática, Genoma España, Parc Científic de Barcelona, Barcelona, Spain
| | - Christine Vogel
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
- Institute for Cellular and Molecular Biology, University of Texas Austin, Austin, Texas, United States of America
- * To whom correspondence should be addressed. E-mail: (XdlC); (CV)
| | - Modesto Orozco
- Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Barcelona, Spain
- Protein Structure and Modelling Node, Instituto Nacional de Bioinfomática, Genoma España, Parc Científic de Barcelona, Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat de Barcelona, Barcelona, Spain
- Institut per a la Recerca i Estudis Avançats (IRCA), Barcelona, Spain
| | - Sarah A Teichmann
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Xavier de la Cruz
- Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Barcelona, Spain
- Protein Structure and Modelling Node, Instituto Nacional de Bioinfomática, Genoma España, Parc Científic de Barcelona, Barcelona, Spain
- Computational Biology Program, Barcelona Supercomputing Center, Barcelona, Spain
- * To whom correspondence should be addressed. E-mail: (XdlC); (CV)
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24
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Ferraro DM, Ferraro DJ, Ramaswamy S, Robertson AD. Structures of ubiquitin insertion mutants support site-specific reflex response to insertions hypothesis. J Mol Biol 2006; 359:390-402. [PMID: 16647719 DOI: 10.1016/j.jmb.2006.03.047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2005] [Revised: 03/17/2006] [Accepted: 03/21/2006] [Indexed: 11/29/2022]
Abstract
We previously concluded that, judging from NMR chemical shifts, the effects of insertions into ubiquitin on its conformation appear to depend primarily on the site of insertion rather than the sequence of the insertion. To obtain a more complete and atomic-resolution understanding of how these insertions modulate the conformation of ubiquitin, we have solved the crystal structures of four insertional mutants of ubiquitin. Insertions between residues 9 and 10 of ubiquitin are minimally perturbing to the remainder of the protein, while larger alterations occur when the insertion is between residues 35 and 36. Further, the alterations in response to insertions are very similar for each mutant at a given site. Two insertions, one at each site, were designed from structurally homologous proteins. Interestingly, the secondary structure within these five to seven amino acid residue insertions is conserved in the new protein. Overall, the crystal structures support the previous conclusion that the conformational effects of these insertions are determined largely by the site of insertion and only secondarily by the sequence of the insert.
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Affiliation(s)
- Debra M Ferraro
- Department of Biochemistry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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25
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Fujii R, Kitaoka M, Hayashi K. RAISE: a simple and novel method of generating random insertion and deletion mutations. Nucleic Acids Res 2006; 34:e30. [PMID: 16493137 PMCID: PMC1380258 DOI: 10.1093/nar/gnj032] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Revised: 01/24/2006] [Accepted: 02/04/2006] [Indexed: 11/12/2022] Open
Abstract
Although proteins may be artificially improved by random insertion and deletion mutagenesis methods, these procedures are technically difficult, and the mutations introduced are no more variable than those introduced by the introduction of random point mutations. We describe here a three-step method called RAISE, which is based on gene shuffling and can introduce a wide variety of insertions, deletions and substitutions. To test the efficacy of this method, we used it to mutate TEM beta-lactamase to generate improved antibiotic resistance. Some unique insertion or deletion mutations were observed in the improved mutants, some of which caused higher activities than point mutations. Our findings indicate that the RAISE method can yield unique mutants and may be a powerful technique of protein engineering.
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Affiliation(s)
- Ryota Fujii
- National Food Research Institute2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
| | - Motomitsu Kitaoka
- National Food Research Institute2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
| | - Kiyoshi Hayashi
- National Food Research Institute2-1-12 Kannondai, Tsukuba, Ibaraki, 305-8642, Japan
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26
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Swift S, Leger AJ, Talavera J, Zhang L, Bohm A, Kuliopulos A. Role of the PAR1 receptor 8th helix in signaling: the 7-8-1 receptor activation mechanism. J Biol Chem 2005; 281:4109-16. [PMID: 16354660 DOI: 10.1074/jbc.m509525200] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The protease-activated receptors are tethered ligand G protein-coupled receptors that are activated by proteolytic cleavage of the extracellular domain of the receptor. The archetypic protease-activated receptor PAR1 strongly activates G(q) signaling pathways, but very little is known regarding the mechanism of signal transference between receptor and internally located G protein. The recent x-ray structure of rhodopsin revealed the presence of a highly conserved amphipathic 8th helix that is likely to be physically interposed between receptor and G protein. We found that the analogous 8th helix region of PAR1 was critical for activation of G(q)-dependent signaling. Engineering an 8th helix alpha-aneurysm with a downwards-directed alanine residue markedly interfered with signal transference to G(q). The 8th helix-anchoring cysteine palmitoylation sites were important for the affinity of ligand-dependent G protein coupling but did not affect the maximal signal. A network of H-bond and ionic interactions was found to connect the N-terminal portion of the 8th helix to the nearby NPXXY motif on transmembrane helix 7 and also to the adjacent intracellular loop-1. Disruption of these pairwise interactions caused additive defects in coupling to G protein, indicating that the transmembrane 7-8th helix-i1 loop may move in a coordinated manner to transfer the signal from PAR1 to G protein. This "7-8-1" interaction network was found to be prevalent in G protein-coupled receptors involved in endothelial signaling and angiogenesis.
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Affiliation(s)
- Steven Swift
- Molecular Oncology Research Institute, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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27
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Ferraro DM, Hope EK, Robertson AD. Site-specific Reflex Response of Ubiquitin to Loop Insertions. J Mol Biol 2005; 352:575-84. [PMID: 16081099 DOI: 10.1016/j.jmb.2005.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2005] [Revised: 07/01/2005] [Accepted: 07/06/2005] [Indexed: 11/16/2022]
Abstract
Predicting the structural effects of insertions in proteins by homology modeling remains a challenge. To investigate the molecular basis for conformational adaptations to insertions, ten mutants of ubiquitin were generated by introducing five different inserts, varying from five to 11 residues in size, at two different sites. Most insertion sequences were derived from homologous positions in structurally homologous ubiquitin-like proteins; to test sequence specificity, insertions were made into both homologous and non-homologous sites in ubiquitin. Structural inferences from NMR data suggest that each insertion site shows a reflex response to insertions: the sequence of the insertion has much less impact on structural adaptations than does the site of the insertion. Further, each site responds to insertions in a unique but consistent manner. For a given insertion site, different inserted sequences give rise to different stabilities, but the relationship between stability and sequence is not yet clear. However, the change in stability is similar for all insertions in a given site.
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Affiliation(s)
- Debra M Ferraro
- Department of Biochemistry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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28
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Tabtiang RK, Cezairliyan BO, Grant RA, Cochrane JC, Sauer RT. Consolidating critical binding determinants by noncyclic rearrangement of protein secondary structure. Proc Natl Acad Sci U S A 2005; 102:2305-9. [PMID: 15689399 PMCID: PMC548995 DOI: 10.1073/pnas.0409562102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We designed a single-chain variant of the Arc repressor homodimer in which the beta strands that contact operator DNA are connected by a hairpin turn and the alpha helices that form the tetrahelical scaffold of the dimer are attached by a short linker. The designed protein represents a noncyclic permutation of secondary structural elements in another single-chain Arc molecule (Arc-L1-Arc), in which the two subunits are fused by a single linker. The permuted protein binds operator DNA with nanomolar affinity, refolds on the sub-millisecond time scale, and is as stable as Arc-L1-Arc. The crystal structure of the permuted protein reveals an essentially wild-type fold, demonstrating that crucial folding information is not encoded in the wild-type order of secondary structure. Noncyclic rearrangement of secondary structure may allow grouping of critical active-site residues in other proteins and could be a useful tool for protein design and minimization.
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Affiliation(s)
- Ramon K Tabtiang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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29
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García-Mayoral MF, García-Ortega L, Lillo MP, Santoro J, Martínez del Pozo A, Gavilanes JG, Rico M, Bruix M. NMR structure of the noncytotoxic alpha-sarcin mutant Delta(7-22): the importance of the native conformation of peripheral loops for activity. Protein Sci 2004; 13:1000-11. [PMID: 15044731 PMCID: PMC2280062 DOI: 10.1110/ps.03532204] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The deletion mutant Delta(7-22) of alpha-sarcin, unlike its wild-type protein counterpart, lacks the specific ability to degrade rRNA in intact ribosomes and exhibits an increased unspecific ribonuclease activity and decreased interaction with lipid vesicles. In trying to shed light on these differences, we report here on the three-dimensional structure of the Delta(7-22) alpha-sarcin mutant using NMR methods. We also evaluated its dynamic properties on the basis of theoretical models and measured its correlation time (6.2 nsec) by time-resolved fluorescence anisotropy. The global fold characteristic of ribotoxins is preserved in the mutant. The most significant differences with respect to the alpha-sarcin structure are concentrated in (1) loop 2, (2) loop 3, which adopts a new orientation, and (3) loop 5, which shows multiple conformations and an altered dynamics. The interactions between loop 5 and the N-terminal hairpin are lost in the mutant, producing increased solvent accessibility of the active-site residues. The degree of solvent exposure of the catalytic His 137 is similar to that shown by His 92 in RNase T1. Additionally, the calculated order parameters of residues belonging to loop 5 in the mutant correspond to an internal dynamic behavior more similar to RNase T1 than alpha-sarcin. On the other hand, changes in the relative orientation of loop 3 move the lysine-rich region 111-114, crucial for substrate recognition, away from the active site. All of the structural and dynamic data presented here reveal that the mutant is a hybrid of ribotoxins and noncytotoxic ribonucleases, consistent with its biological properties.
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Affiliation(s)
- Ma Flor García-Mayoral
- Departamento de Espectroscopía y Estructura Molecular, Instituto de Química Física Rocasolano, Serrano 119, CSIC, 28006 Madrid, Spain
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30
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Osuna J, Yáñez J, Soberón X, Gaytán P. Protein evolution by codon-based random deletions. Nucleic Acids Res 2004; 32:e136. [PMID: 15459282 PMCID: PMC521680 DOI: 10.1093/nar/gnh135] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2004] [Revised: 09/10/2004] [Accepted: 09/15/2004] [Indexed: 11/14/2022] Open
Abstract
A method to delete in-phase codons throughout a defined target region of a gene has been developed. This approach, named the codon-based random deletion (COBARDE) method, is able to delete complete codons in a random and combinatorial mode. Robustness, automation and fine-tuning of the mutagenesis rate are essential characteristics of the method, which is based on the assembly of oligonucleotides and on the use of two transient orthogonal protecting groups during the chemical synthesis. The performance of the method for protein function evolution was demonstrated by changing the substrate specificity of TEM-1 beta-lactamase. Functional ceftazidime-resistant beta-lactamase variants containing several deleted residues inside the catalytically important omega-loop region were found. The results show that the COBARDE method is a useful new molecular tool to access previously unexplorable sequence space.
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Affiliation(s)
- Joel Osuna
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología/UNAM, Ap. Postal 510-3 Cuernavaca, Morelos 62250, México
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31
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Abstract
Strategies for growing protein crystals have for many years been essentially empirical, the protein, once purified to a certain homogeneity, being mixed with a selection of crystallization agents selected in a more or less trial-and-error fashion. Screening for the correct conditions has been made easier through automation and by the introduction of commercially available crystallization kits. Many parameters can be changed in these experiments, such as temperature, pH, and ionic strength, but perhaps the most important variable has been ignored, namely the protein. The crystallization properties of a protein vary greatly: some crystallize readily, whereas others have proven extremely difficult or even impossible to obtain in a crystalline state. The possibility of altering the intrinsic characteristics of a protein for crystallization has become a feasible strategy. Some historical perspectives and advances in this area will be reviewed.
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32
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Valenzuela A, Talavera D, Orozco M, de la Cruz X. Alternative splicing mechanisms for the modulation of protein function: conservation between human and other species. J Mol Biol 2004; 335:495-502. [PMID: 14672658 DOI: 10.1016/j.jmb.2003.10.061] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Alternative splicing (AS) is an important process in eukaryotic organisms by which a given gene may express a set of different protein isoforms depending on the tissue, or the developmental stage of the individual. In the present work, we have compared AS among species, focusing on the conservation of AS mechanisms for the modulation of protein function. For this purpose, we first analysed the frequency with which different species, human, mouse, rat and fruitfly, utilise them. Second, we focused more directly on the conservation among species of the mechanisms themselves. To this end, we compared biologically equivalent AS events between human and mouse, or rat. Our results indicate only minor differences in the frequency of use of these mechanisms, as well as a high degree of conservation among the species studied.
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Affiliation(s)
- Abel Valenzuela
- Unitat de Modelització Molecular i Bioinformática, Institut de Recerca Biomèdica de Barcelona, Parc Científic de Barcelona, C/Josep Samitier, 1-5, 08028 Barcelona, Spain
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33
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Reddy BV, Li WW, Shindyalov IN, Bourne PE. Conserved key amino acid positions (CKAAPs) derived from the analysis of common substructures in proteins. Proteins 2001. [DOI: 10.1002/1097-0134(20010201)42:2%3c148::aid-prot20%3e3.0.co;2-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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34
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Reddy BV, Li WW, Shindyalov IN, Bourne PE. Conserved key amino acid positions (CKAAPs) derived from the analysis of common substructures in proteins. Proteins 2001; 42:148-63. [PMID: 11119639 DOI: 10.1002/1097-0134(20010201)42:2<148::aid-prot20>3.0.co;2-r] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
An all-against-all protein structure comparison using the Combinatorial Extension (CE) algorithm applied to a representative set of PDB structures revealed a gallery of common substructures in proteins (http://cl.sdsc.edu/ce.html). These substructures represent commonly identified folds, domains, or components thereof. Most of the subsequences forming these similar substructures have no significant sequence similarity. We present a method to identify conserved amino acid positions and residue-dependent property clusters within these subsequences starting with structure alignments. Each of the subsequences is aligned to its homologues in SWALL, a nonredundant protein sequence database. The most similar sequences are purged into a common frequency matrix, and weighted homologues of each one of the subsequences are used in scoring for conserved key amino acid positions (CKAAPs). We have set the top 20% of the high-scoring positions in each substructure to be CKAAPs. It is hypothesized that CKAAPs may be responsible for the common folding patterns in either a local or global view of the protein-folding pathway. Where a significant number of structures exist, CKAAPs have also been identified in structure alignments of complete polypeptide chains from the same protein family or superfamily. Evidence to support the presence of CKAAPs comes from other computational approaches and experimental studies of mutation and protein-folding experiments, notably the Paracelsus challenge. Finally, the structural environment of CKAAPs versus non-CKAAPs is examined for solvent accessibility, hydrogen bonding, and secondary structure. The identification of CKAAPs has important implications for protein engineering, fold recognition, modeling, and structure prediction studies and is dependent on the availability of structures and an accurate structure alignment methodology. Proteins 2001;42:148-163.
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Affiliation(s)
- B V Reddy
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093-0505, USA
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35
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Hayes F, Hallet B. Pentapeptide scanning mutagenesis: encouraging old proteins to execute unusual tricks. Trends Microbiol 2000; 8:571-7. [PMID: 11115754 DOI: 10.1016/s0966-842x(00)01857-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Pentapeptide scanning mutagenesis is a facile transposon-based procedure for the random insertion of a variable five amino acid cassette into a target protein. The analysis of a library of proteins harbouring pentapeptide insertions can provide invaluable information on the essential and inessential regions of a target protein, as well as revealing surprising aspects of target protein function and activity.
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Affiliation(s)
- F Hayes
- Dept of Biomolecular Sciences, University of Manchester Institute of Science and Technology (UMIST), PO Box 88, M60 1QD, Manchester, UK.
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36
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Abstract
We describe the NMR structure of a deletion mutant of the B1 IgG-binding domain from Group G Streptococcus. The deletion occurs within the last beta-strand of the protein, where it may potentially have a deleterious effect on the stability of the protein if the protein were not able to conformationally adjust to the perturbation. In particular, the deletion changes the registry of the final three residues in the sheet, forcing a polar Thr to be buried in the interior of the protein and exposing a hydrophobic Val to solvent. The deletion could also potentially create a large cavity in the beta-sheet and force the alpha- and gamma-carboxylates of the C-terminal Glu residue into a partially buried region of the sheet. The structure of the mutant illustrates how the conformation of the protein adjusts to the deletion, thereby mitigating some of the potentially deleterious consequences. Although the elements of secondary structure are retained between the mutant and the wt domain, there are multiple small adjustments in the segments connecting secondary structure elements. In particular, a hydrogen bond between the Glu57 carboxylates and two main chain amides is introduced that alters the conformation in the loop connecting the helix to strand 3. In addition, to minimize hydrophobic surface exposure, the turn connecting strands 1 and 2 folds toward the core so that the molecular volume is decreased.
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Affiliation(s)
- K T O'Neil
- Department of Biochemistry and Biophysics, The University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania, USA
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37
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Seitz T, Berger B, Nguyen VT, Tricot C, Villeret V, Schmid S, Stalon V, Haas D. Linker insertion mutagenesis based on IS21 transposition: isolation of an AMP-insensitive variant of catabolic ornithine carbamoyltransferase from Pseudomonas aeruginosa. PROTEIN ENGINEERING 2000; 13:329-37. [PMID: 10835106 DOI: 10.1093/protein/13.5.329] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The bacterial insertion sequence IS21 when repeated in tandem efficiently promotes non-replicative cointegrate formation in Escherichia coli. An IS21-IS21 junction region which had been engineered to contain unique SalI and BglII sites close to the IS21 termini was not affected in the ability to form cointegrates with target plasmids. Based on this finding, a novel procedure of random linker insertion mutagenesis was devised. Suicide plasmids containing the engineered junction region (pME5 and pME6) formed cointegrates with target plasmids in an E.coli host strain expressing the IS21 transposition proteins in trans. Cointegrates were resolved in vitro by restriction with SalI or BglII and ligation; thus, insertions of four or 11 codons, respectively, were created in the target DNA, practically at random. The cloned Pseudomonas aeruginosa arcB gene encoding catabolic ornithine carbamoyltransferase was used as a target. Of 20 different four-codon insertions in arcB, 11 inactivated the enzyme. Among the remaining nine insertion mutants which retained enzyme activity, three enzyme variants had reduced affinity for the substrate ornithine and one had lost recognition of the allosteric activator AMP. The linker insertions obtained illustrate the usefulness of the method in the analysis of structure-function relationships of proteins.
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Affiliation(s)
- T Seitz
- Laboratoire de Biologie Microbienne, Universit¿e de Lausanne, CH-1015 Lausanne, Switzerland, Institut de Recherches Microbiologiques Jean-Marie Wiame, B-1070 Brussels, Belgium
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38
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Fetrow JS, Dreher U, Wiland DJ, Schaak DL, Boose TL. Mutagenesis of histidine 26 demonstrates the importance of loop-loop and loop-protein interactions for the function of iso-1-cytochrome c. Protein Sci 1998; 7:994-1005. [PMID: 9568906 PMCID: PMC2143970 DOI: 10.1002/pro.5560070417] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In yeast iso-1-cytochrome c, the side chain of histidine 26 (His26) attaches omega loop A to the main body of the protein by forming a hydrogen bond to the backbone atom carbonyl of glutamic acid 44. The His26 side chain also forms a stabilizing intra-loop interaction through a hydrogen bond to the backbone amide of asparagine 31. To investigate the importance of loop-protein attachment and intra-loop interactions to the structure and function of this protein, a series of site-directed and random-directed mutations were produced at His26. Yeast strains expressing these variant proteins were analyzed for their ability to grow on non-fermentable carbon sources and for their intracellular production of cytochrome c. While the data show that mutations at His26 lead to slightly decreased intracellular amounts of cytochrome c, the level of cytochrome c function is decreased more. The data suggest that cytochrome c reductase binding is affected more than cytochrome c oxidase or lactate dehydrogenase binding. We propose that mutations at this residue increase loop mobility, which, in turn, decreases the protein's ability to bind redox partners.
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Affiliation(s)
- J S Fetrow
- Department of Biological Sciences, Center for Biochemistry and Biophysical Chemistry, State University of New York, Albany 12222, USA.
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39
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Singh IR, Crowley RA, Brown PO. High-resolution functional mapping of a cloned gene by genetic footprinting. Proc Natl Acad Sci U S A 1997; 94:1304-9. [PMID: 9037048 PMCID: PMC19786 DOI: 10.1073/pnas.94.4.1304] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We describe an efficient method for introducing and analyzing a comprehensive set of mutations in a cloned gene to map its functional organization. The technique, genetic footprinting, uses a retroviral integrase to generate a comprehensive library of mutants, each of which bears a single insertion of a defined oligonucleotide at a random position in the gene of interest. This mutant library is selected for gene function en masse. DNA samples are isolated from the library both before and after selection, and the mutations represented in each sample are then analyzed. The analysis is designed so that a mutation at a particular location gives rise to an electrophoretic band of discrete mobility. For the whole library, this results in a ladder of bands, each band representing a specific mutation. Mutants in which the inserted sequence disrupts a feature that is required for the selected function, ipso facto, fail the selection. The corresponding bands are therefore absent from the ladder of bands obtained from the library after selection, giving rise to a footprint representing features of the gene that are essential for the selected function. Because the sequence of the inserted oligonucleotide is known, and its position can be inferred precisely from the electrophoretic mobility of the corresponding band, the precise location and sequence of mutations that disrupt gene function can be determined without isolating or sequencing individual mutants. This method should be generally applicable for saturation mutagenesis and high-resolution functional mapping of cloned DNA sequences.
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Affiliation(s)
- I R Singh
- Department of Biochemistry, Stanford University Medical Center, CA 94305-5428, USA
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40
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Muir TW, Dawson PE, Fitzgerald MC, Kent SB. Probing the chemical basis of binding activity in an SH3 domain by protein signature analysis. CHEMISTRY & BIOLOGY 1996; 3:817-25. [PMID: 8939700 DOI: 10.1016/s1074-5521(96)90067-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND Modifying the covalent structure of a protein is an effective empirical route to probing three-dimensional structure and biological function. Here we describe a combinatorial protein chemistry strategy for studying structure-activity relationships in proteins. Our approach (termed 'protein signature analysis') involves functional selection from an array of self-encoded protein analogs prepared by total synthesis, coupled to a simple chemical readout that unambiguously identifies the modified proteins in the resulting active and inactive populations. RESULTS Protein signature analysis was used to study the interaction of the amino-terminal SH3 domain from the cellular adaptor protein c-Crk with its cognate proline-rich peptide, C3G. Using a functional selection assay, the qualitative effects of scanning a series of synthetic analog units through the amino-acid sequence of the SH3 domain were evaluated. The analog units were designed to alter both amino-acid sidechains and the polypeptide backbone within the protein. These chemical studies revealed that the sidechain of Asp 150 in the SH3 domain is essential for ligand binding and that changes in the structure of the polypeptide backbone can also result in loss of binding activity. CONCLUSIONS These chemical studies have provided new insight into how ligand binding is related to the covalent structure of the SH3 domain. Protein signature analysis is a powerful and conceptually novel way of studying the molecular and chemical basis of protein function; it combines the advantages of systematic modification of a protein's chemical structure with the practical convenience of combinatorial synthesis.
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Affiliation(s)
- T W Muir
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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