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OverFlap PCR: A reliable approach for generating plasmid DNA libraries containing random sequences without a template bias. PLoS One 2022; 17:e0262968. [PMID: 35939421 PMCID: PMC9359533 DOI: 10.1371/journal.pone.0262968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 07/17/2022] [Indexed: 11/19/2022] Open
Abstract
Over the decades, practical biotechnology researchers have aimed to improve naturally occurring proteins and create novel ones. It is widely recognized that coupling protein sequence randomization with various effect screening methodologies is one of the most powerful techniques for quickly, efficiently, and purposefully acquiring these desired improvements. Over the years, considerable advancements have been made in this field. However, developing PCR-based or template-guided methodologies has been hampered by resultant template sequence biases. Here, we present a novel whole plasmid amplification-based approach, which we named OverFlap PCR, for randomizing virtually any region of plasmid DNA without introducing a template sequence bias.
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Benjamin R, Giacoletto CJ, FitzHugh ZT, Eames D, Buczek L, Wu X, Newsome J, Han MV, Pearson T, Wei Z, Banerjee A, Brown L, Valente LJ, Shen S, Deng HW, Schiller MR. GigaAssay - An adaptable high-throughput saturation mutagenesis assay platform. Genomics 2022; 114:110439. [PMID: 35905834 PMCID: PMC9420302 DOI: 10.1016/j.ygeno.2022.110439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 07/12/2022] [Accepted: 07/24/2022] [Indexed: 11/17/2022]
Abstract
High-throughput assay systems have had a large impact on understanding the mechanisms of basic cell functions. However, high-throughput assays that directly assess molecular functions are limited. Herein, we describe the "GigaAssay", a modular high-throughput one-pot assay system for measuring molecular functions of thousands of genetic variants at once. In this system, each cell was infected with one virus from a library encoding thousands of Tat mutant proteins, with each viral particle encoding a random unique molecular identifier (UMI). We demonstrate proof of concept by measuring transcription of a GFP reporter in an engineered reporter cell line driven by binding of the HIV Tat transcription factor to the HIV long terminal repeat. Infected cells were flow-sorted into 3 bins based on their GFP fluorescence readout. The transcriptional activity of each Tat mutant was calculated from the ratio of signals from each bin. The use of UMIs in the GigaAssay produced a high average accuracy (95%) and positive predictive value (98%) determined by comparison to literature benchmark data, known C-terminal truncations, and blinded independent mutant tests. Including the substitution tolerance with structure/function analysis shows restricted substitution types spatially concentrated in the Cys-rich region. Tat has abundant intragenic epistasis (10%) when single and double mutants are compared.
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Affiliation(s)
- Ronald Benjamin
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA
| | - Christopher J Giacoletto
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA; School of Life Sciences, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA; Heligenics Inc., 833 Las Vegas Blvd. North, Suite B, Las Vegas, NV 89101, USA
| | - Zachary T FitzHugh
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA
| | - Danielle Eames
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA
| | - Lindsay Buczek
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA
| | - Xiaogang Wu
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA
| | - Jacklyn Newsome
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA
| | - Mira V Han
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA; School of Life Sciences, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA
| | - Tony Pearson
- School of Life Sciences, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA; Heligenics Inc., 833 Las Vegas Blvd. North, Suite B, Las Vegas, NV 89101, USA
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, GITC 4214C, University Heights, Newark, NJ 07102, USA
| | - Atoshi Banerjee
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA
| | - Lancer Brown
- Heligenics Inc., 833 Las Vegas Blvd. North, Suite B, Las Vegas, NV 89101, USA
| | - Liz J Valente
- Heligenics Inc., 833 Las Vegas Blvd. North, Suite B, Las Vegas, NV 89101, USA
| | - Shirley Shen
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA
| | - Hong-Wen Deng
- Center for Biomedical Informatics & Genomics Tulane University, 1440 Canal Street, Suite 1621, New Orleans, LA 70112, USA
| | - Martin R Schiller
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA; School of Life Sciences, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, Nevada 89154, USA; Heligenics Inc., 833 Las Vegas Blvd. North, Suite B, Las Vegas, NV 89101, USA.
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Koukos P, Bonvin A. Integrative Modelling of Biomolecular Complexes. J Mol Biol 2020; 432:2861-2881. [DOI: 10.1016/j.jmb.2019.11.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022]
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Shankar V, Goddard WA, Kim SK, Abrol R, Liu F. The 3D Structure of Human DP Prostaglandin G-Protein-Coupled Receptor Bound to Cyclopentanoindole Antagonist, Predicted Using the DuplexBiHelix Modification of the GEnSeMBLE Method. J Chem Theory Comput 2018; 14:1624-1642. [PMID: 29268008 DOI: 10.1021/acs.jctc.7b00842] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Prostaglandins play a critical physiological role in both cardiovascular and immune systems, acting through their interactions with 9 prostanoid G protein-coupled receptors (GPCRs). These receptors are important therapeutic targets for a variety of diseases including arthritis, allergies, type 2 diabetes, and cancer. The DP prostaglandin receptor is of interest because it has unique structural and physiological properties. Most notably, DP does not have the 3-6 ionic lock common to Class A GPCRs. However, the lack of X-ray structures for any of the 9 prostaglandin GPCRs hampers the application of structure-based drug design methods to develop more selective and active medications to specific receptors. We predict here 3D structures for the DP prostaglandin GPCR, based on the GEnSeMBLE complete sampling with hierarchical scoring (CS-HS) methodology. This involves evaluating the energy of 13 trillion packings to finally select the best 20 that are stable enough to be relevant for binding to antagonists, agonists, and modulators. To validate the predicted structures, we predict the binding site for the Merck cyclopentanoindole (CPI) selective antagonist docked to DP. We find that the CPI binds vertically in the 1-2-7 binding pocket, interacting favorably with residues R3107.40 and K762.54 with additional interactions with S3137.43, S3167.46, S191.35, etc. This binding site differs significantly from that of antagonists to known Class A GPCRs where the ligand binds in the 3-4-5-6 region. We find that the predicted binding site leads to reasonable agreement with experimental Structure-Activity Relationship (SAR). We suggest additional mutation experiments including K762.54, E1293.49, L1233.43, M2706.40, F2746.44 to further validate the structure, function, and activation mechanism of receptors in the prostaglandin family. Our structures and binding sites are largely consistent and improve upon the predictions by Li et al. ( J. Am. Chem. Soc. 2007 , 129 ( 35 ), 10720 ) that used our earlier MembStruk prediction methodology.
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Affiliation(s)
- Vishnu Shankar
- Materials and Process Simulation Center (139-74) , California Institute of Technology , 1200 E. California Blvd. , Pasadena , California 91125 , United States
| | - William A Goddard
- Materials and Process Simulation Center (139-74) , California Institute of Technology , 1200 E. California Blvd. , Pasadena , California 91125 , United States
| | - Soo-Kyung Kim
- Materials and Process Simulation Center (139-74) , California Institute of Technology , 1200 E. California Blvd. , Pasadena , California 91125 , United States
| | - Ravinder Abrol
- Materials and Process Simulation Center (139-74) , California Institute of Technology , 1200 E. California Blvd. , Pasadena , California 91125 , United States
| | - Fan Liu
- Materials and Process Simulation Center (139-74) , California Institute of Technology , 1200 E. California Blvd. , Pasadena , California 91125 , United States
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High-throughput mutagenesis using a two-fragment PCR approach. Sci Rep 2017; 7:6787. [PMID: 28754896 PMCID: PMC5533798 DOI: 10.1038/s41598-017-07010-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/20/2017] [Indexed: 12/19/2022] Open
Abstract
Site-directed scanning mutagenesis is a powerful protein engineering technique which allows studies of protein functionality at single amino acid resolution and design of stabilized proteins for structural and biophysical work. However, creating libraries of hundreds of mutants remains a challenging, expensive and time-consuming process. The efficiency of the mutagenesis step is the key for fast and economical generation of such libraries. PCR artefacts such as misannealing and tandem primer repeats are often observed in mutagenesis cloning and reduce the efficiency of mutagenesis. Here we present a high-throughput mutagenesis pipeline based on established methods that significantly reduces PCR artefacts. We combined a two-fragment PCR approach, in which mutagenesis primers are used in two separate PCR reactions, with an in vitro assembly of resulting fragments. We show that this approach, despite being more laborious, is a very efficient pipeline for the creation of large libraries of mutants.
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Groot-Kormelink PJ, Ferrand S, Kelley N, Bill A, Freuler F, Imbert PE, Marelli A, Gerwin N, Sivilotti LG, Miraglia L, Orth AP, Oakeley EJ, Schopfer U, Siehler S. High Throughput Random Mutagenesis and Single Molecule Real Time Sequencing of the Muscle Nicotinic Acetylcholine Receptor. PLoS One 2016; 11:e0163129. [PMID: 27649498 PMCID: PMC5029940 DOI: 10.1371/journal.pone.0163129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/03/2016] [Indexed: 12/15/2022] Open
Abstract
High throughput random mutagenesis is a powerful tool to identify which residues are important for the function of a protein, and gain insight into its structure-function relation. The human muscle nicotinic acetylcholine receptor was used to test whether this technique previously used for monomeric receptors can be applied to a pentameric ligand-gated ion channel. A mutant library for the α1 subunit of the channel was generated by error-prone PCR, and full length sequences of all 2816 mutants were retrieved using single molecule real time sequencing. Each α1 mutant was co-transfected with wildtype β1, δ, and ε subunits, and the channel function characterized by an ion flux assay. To test whether the strategy could map the structure-function relation of this receptor, we attempted to identify mutations that conferred resistance to competitive antagonists. Mutant hits were defined as receptors that responded to the nicotinic agonist epibatidine, but were not inhibited by either α-bungarotoxin or tubocurarine. Eight α1 subunit mutant hits were identified, six of which contained mutations at position Y233 or V275 in the transmembrane domain. Three single point mutations (Y233N, Y233H, and V275M) were studied further, and found to enhance the potencies of five channel agonists tested. This suggests that the mutations made the channel resistant to the antagonists, not by impairing antagonist binding, but rather by producing a gain-of-function phenotype, e.g. increased agonist sensitivity. Our data show that random high throughput mutagenesis is applicable to multimeric proteins to discover novel functional mutants, and outlines the benefits of using single molecule real time sequencing with regards to quality control of the mutant library as well as downstream mutant data interpretation.
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Affiliation(s)
- Paul J. Groot-Kormelink
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Sandrine Ferrand
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Nicholas Kelley
- Analytical Sciences and Imaging, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Anke Bill
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Felix Freuler
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Pierre-Eloi Imbert
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Anthony Marelli
- Genomics Institute of the Novartis Research Foundation, Novartis Institutes for BioMedical Research, San Diego, California, United States of America
| | - Nicole Gerwin
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Lucia G. Sivilotti
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom
| | - Loren Miraglia
- Genomics Institute of the Novartis Research Foundation, Novartis Institutes for BioMedical Research, San Diego, California, United States of America
| | - Anthony P. Orth
- Genomics Institute of the Novartis Research Foundation, Novartis Institutes for BioMedical Research, San Diego, California, United States of America
| | - Edward J. Oakeley
- Analytical Sciences and Imaging, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Ulrich Schopfer
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Sandra Siehler
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
- * E-mail:
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Molinski SV, Ahmadi S, Hung M, Bear CE. Facilitating Structure-Function Studies of CFTR Modulator Sites with Efficiencies in Mutagenesis and Functional Screening. ACTA ACUST UNITED AC 2015; 20:1204-17. [PMID: 26385858 DOI: 10.1177/1087057115605834] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/23/2015] [Indexed: 12/20/2022]
Abstract
There are nearly 2000 mutations in the CFTR gene associated with cystic fibrosis disease, and to date, the only approved drug, Kalydeco, has been effective in rescuing the functional expression of a small subset of these mutant proteins with defects in channel activation. However, there is currently an urgent need to assess other mutations for possible rescue by Kalydeco, and further, definition of the binding site of such modulators on CFTR would enhance our understanding of the mechanism of action of such therapeutics. Here, we describe a simple and rapid one-step PCR-based site-directed mutagenesis method to generate mutations in the CFTR gene. This method was used to generate CFTR mutants bearing deletions (p.Gln2_Trp846del, p.Ser700_Asp835del, p.Ile1234_Arg1239del) and truncation with polyhistidine tag insertion (p.Glu1172-3Gly-6-His*), which either recapitulate a disease phenotype or render tools for modulator binding site identification, with subsequent evaluation of drug responses using a high-throughput (384-well) membrane potential-sensitive fluorescence assay of CFTR channel activity within a 1 wk time frame. This proof-of-concept study shows that these methods enable rapid and quantitative comparison of multiple CFTR mutants to emerging drugs, facilitating future large-scale efforts to stratify mutants according to their "theratype" or most promising targeted therapy.
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Affiliation(s)
- Steven V Molinski
- Molecular Structure and Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Saumel Ahmadi
- Molecular Structure and Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Maurita Hung
- Molecular Structure and Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Christine E Bear
- Molecular Structure and Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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Bill A, Popa MO, van Diepen MT, Gutierrez A, Lilley S, Velkova M, Acheson K, Choudhury H, Renaud NA, Auld DS, Gosling M, Groot-Kormelink PJ, Gaither LA. Variomics screen identifies the re-entrant loop of the calcium-activated chloride channel ANO1 that facilitates channel activation. J Biol Chem 2014; 290:889-903. [PMID: 25425649 DOI: 10.1074/jbc.m114.618140] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The calcium-activated chloride channel ANO1 regulates multiple physiological processes. However, little is known about the mechanism of channel gating and regulation of ANO1 activity. Using a high-throughput, random mutagenesis-based variomics screen, we generated and functionally characterized ∼6000 ANO1 mutants and identified novel mutations that affected channel activity, intracellular trafficking, or localization of ANO1. Mutations such as S741T increased ANO1 calcium sensitivity and rendered ANO1 calcium gating voltage-independent, demonstrating a critical role of the re-entrant loop in coupling calcium and voltage sensitivity of ANO1 and hence in regulating ANO1 activation. Our data present the first unbiased and comprehensive study of the structure-function relationship of ANO1. The novel ANO1 mutants reported have diverse functional characteristics, providing new tools to study ANO1 function in biological systems, paving the path for a better understanding of the function of ANO1 and its role in health and diseases.
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Affiliation(s)
- Anke Bill
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139
| | - M Oana Popa
- the Novartis Institutes for Biomedical Research, Horsham, West Sussex RH12 5AB, United Kingdom, and
| | - Michiel T van Diepen
- the Novartis Institutes for Biomedical Research, Horsham, West Sussex RH12 5AB, United Kingdom, and
| | - Abraham Gutierrez
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139
| | - Sarah Lilley
- the Novartis Institutes for Biomedical Research, Horsham, West Sussex RH12 5AB, United Kingdom, and
| | - Maria Velkova
- the Novartis Institutes for Biomedical Research, Horsham, West Sussex RH12 5AB, United Kingdom, and
| | - Kathryn Acheson
- the Novartis Institutes for Biomedical Research, Horsham, West Sussex RH12 5AB, United Kingdom, and
| | - Hedaythul Choudhury
- the Novartis Institutes for Biomedical Research, Horsham, West Sussex RH12 5AB, United Kingdom, and
| | - Nicole A Renaud
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139
| | - Douglas S Auld
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139
| | - Martin Gosling
- the Novartis Institutes for Biomedical Research, Horsham, West Sussex RH12 5AB, United Kingdom, and
| | | | - L Alex Gaither
- From the Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139,
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