1
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Grove TZ, Magliery TJ. Editorial overview: From powerful tools to useful products: protein engineering after 35 years of directed evolution. Curr Opin Struct Biol 2020; 63:vi-viii. [PMID: 32690369 PMCID: PMC7367778 DOI: 10.1016/j.sbi.2020.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
| | - Thomas J Magliery
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.
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2
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Chen L, Tanimoto A, So BR, Bakhtina M, Magliery TJ, Wysocki VH, Musier-Forsyth K. Stoichiometry of triple-sieve tRNA editing complex ensures fidelity of aminoacyl-tRNA formation. Nucleic Acids Res 2019; 47:929-940. [PMID: 30418624 PMCID: PMC6344894 DOI: 10.1093/nar/gky1153] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/30/2018] [Indexed: 11/13/2022] Open
Abstract
Aminoacyl-tRNA synthetases catalyze the attachment of cognate amino acids onto tRNAs. To avoid mistranslation, editing mechanisms evolved to maintain tRNA aminoacylation fidelity. For instance, while rejecting the majority of non-cognate amino acids via discrimination in the synthetic active site, prolyl-tRNA synthetase (ProRS) misactivates and mischarges Ala and Cys, which are similar in size to cognate Pro. Ala-tRNAPro is specifically hydrolyzed by the editing domain of ProRS in cis, while YbaK, a free-standing editing domain, clears Cys-tRNAPro in trans. ProXp-ala is another editing domain that clears Ala-tRNAPro in trans. YbaK does not appear to possess tRNA specificity, readily deacylating Cys-tRNACysin vitro. We hypothesize that YbaK binds to ProRS to gain specificity for Cys-tRNAPro and avoid deacylation of Cys-tRNACys in the cell. Here, in vivo evidence for ProRS-YbaK interaction was obtained using a split-green fluorescent protein assay. Analytical ultracentrifugation and native mass spectrometry were used to investigate binary and ternary complex formation between ProRS, YbaK, and tRNAPro. Our combined results support the hypothesis that the specificity of YbaK toward Cys-tRNAPro is determined by the formation of a three-component complex with ProRS and tRNAPro and establish the stoichiometry of a 'triple-sieve' editing complex for the first time.
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Affiliation(s)
- Lin Chen
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Akiko Tanimoto
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Byung Ran So
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Marina Bakhtina
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Thomas J Magliery
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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3
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Goyal VD, Sullivan BJ, Magliery TJ. Phylogenetic spread of sequence data affects fitness of consensus enzymes: Insights from triosephosphate isomerase. Proteins 2019; 88:274-283. [PMID: 31407418 DOI: 10.1002/prot.25799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 07/26/2019] [Accepted: 08/08/2019] [Indexed: 11/08/2022]
Abstract
The concept of consensus in multiple sequence alignments (MSAs) has been used to design and engineer proteins previously with some success. However, consensus design implicitly assumes that all amino acid positions function independently, whereas in reality, the amino acids in a protein interact with each other and work cooperatively to produce the optimum structure required for its function. Correlation analysis is a tool that can capture the effect of such interactions. In a previously published study, we made consensus variants of the triosephosphate isomerase (TIM) protein using MSAs that included sequences form both prokaryotic and eukaryotic organisms. These variants were not completely native-like and were also surprisingly different from each other in terms of oligomeric state, structural dynamics, and activity. Extensive correlation analysis of the TIM database has revealed some clues about factors leading to the unusual behavior of the previously constructed consensus proteins. Among other things, we have found that the more ill-behaved consensus mutant had more broken correlations than the better-behaved consensus variant. Moreover, we report three correlation and phylogeny-based consensus variants of TIM. These variants were more native-like than the previous consensus mutants and considerably more stable than a wild-type TIM from a mesophilic organism. This study highlights the importance of choosing the appropriate diversity of MSA for consensus analysis and provides information that can be used to engineer stable enzymes.
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Affiliation(s)
- Venuka Durani Goyal
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
| | - Brandon J Sullivan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio.,Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio
| | - Thomas J Magliery
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
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4
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Grunkemeyer TJ, Mata DG, Doddapaneni K, Murali S, Magliery TJ. Insights into the mechanism of paraoxonase-1: Comparing the reactivity of the six-bladed β-propeller hydrolases. Biochemistry 2018:acs.biochem.8b01115. [PMID: 30547569 DOI: 10.1021/acs.biochem.8b01115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mammalian protein paraoxonase-1 (PON1) has been explored as a promising bioscavenger treatment for organophosphorus (OP) agent poisoning, but it is not active enough to protect against many agents. Engineering is limited because PON1's catalytic mechanism is poorly understood; moreover, its native activity and substrate are unknown. PON1 is a calcium-bound six-bladed β-propeller hydrolase that shares high structural homology, a conserved metal-coordinating active site, and substrate specificity overlap with other members of a superfamily that includes squid diisopropylfluorophosphatase (DFPase), bacterial drug responsive protein 35 (Drp35), and mammalian senescence marker protein 30 (SMP30). We hypothesized that, by examining the reactivity of all four hydrolases using a common set of conservative mutations, we could gain further insight into the catalytic mechanism of PON1. We chose a set of mutations to examine conserved Asp and Glu residues in the hydrolase active sites, as well as the ligation sphere around the catalytic calcium and a His-His dyad seen in PON1. The wild-type (WT) and mutant hydrolases were assayed against a set of lactones, aryl esters, and OPs that PON1 is known to hydrolyze. Surprisingly, some mutations of Ca2+ coordinating residues, previously thought to be essential for turnover, resulted in significant activity toward all substrate classes examined. Additionally, merely maintaining WT-like charge in the active site of PON1 was insufficient for high activity. Finally, the H115-H134 dyad does not appear to be essential for catalysis against any substrate. Therefore, previously proposed mechanisms must be re-evaluated.
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5
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Bowles DP, Yuan C, Stephany KR, Lavinder JJ, Hansen AL, Magliery TJ. Resonance assignments of wild-type and two cysteine-free variants of the four-helix bundle protein, Rop. Biomol NMR Assign 2018; 12:345-350. [PMID: 30159810 DOI: 10.1007/s12104-018-9837-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/09/2018] [Indexed: 06/08/2023]
Abstract
Repressor of primer (Rop, or ROM, RNA I modulator) is a 63 amino acid four-helix bundle protein that exists in solution as an anti-parallel homodimer. This protein has been extensively studied, including by X-ray crystallography, NMR, rational design, and combinatorial mutagenesis. Previous NMR experiments with wild-type Rop were carried out at pH 2.3 and pH 6.3. In this paper, we report complete N-H backbone assignments for three variants of Rop under the same pH 6.3 conditions: wild-type Rop; a cysteine-free pseudo-wild type variant (C38A C52V); and a core-repacked variant of the Cys-free variant (T19V L41V C38A C52V). These assignments enable functional and dynamic studies of wild-type and Cys-free variants of Rop.
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Affiliation(s)
- David P Bowles
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, 43210, USA
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Ave., Columbus, OH, 43210, USA
| | - Chunhua Yuan
- Campus Chemical Instrument Center, The Ohio State University, 460 W. 12th Ave 209 Biomedical Research Tower, Columbus, OH, 43210, USA
| | - Kimberly R Stephany
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Ave., Columbus, OH, 43210, USA
| | - Jason J Lavinder
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, 43210, USA
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Ave., Columbus, OH, 43210, USA
| | - Alexandar L Hansen
- Campus Chemical Instrument Center, The Ohio State University, 460 W. 12th Ave 209 Biomedical Research Tower, Columbus, OH, 43210, USA
| | - Thomas J Magliery
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Ave., Columbus, OH, 43210, USA.
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6
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Bowles DP, Hansen AL, Rhoads CA, Mohan S, Yuan C, Magliery TJ. 1H, 13C, 15N resonance assignment of recombinant Euplotes raikovi protein Er-23. Biomol NMR Assign 2018; 12:291-295. [PMID: 29876749 DOI: 10.1007/s12104-018-9825-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/31/2018] [Indexed: 06/08/2023]
Abstract
Er-23 is a small, 51 amino acid, disulfide-rich pheromone protein used for cell signaling by Euplotes raikovi. Ten of the 51 amino acids are cysteine, allowing up to five disulfide bonds. Previous NMR work with Er-23 utilized homologously expressed protein, prohibiting isotopic labeling, and consequently the chemical shift assignments were incomplete. We have expressed uniformly 15N and 13C-labeled Er-23 in an E. coli expression system. Here we report the full backbone and side chain resonance assignments for recombinant Er-23.
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Affiliation(s)
- David P Bowles
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, 43210, USA
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Ave., Columbus, OH, 43210, USA
| | - Alexandar L Hansen
- Campus Chemical Instrument Center, The Ohio State University, 460 W. 12th Ave 209 Biomedical Research Tower, Columbus, OH, 43210, USA
| | - Calvin A Rhoads
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Ave., Columbus, OH, 43210, USA
| | - Sidharth Mohan
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Ave., Columbus, OH, 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Chunhua Yuan
- Campus Chemical Instrument Center, The Ohio State University, 460 W. 12th Ave 209 Biomedical Research Tower, Columbus, OH, 43210, USA
| | - Thomas J Magliery
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Ave., Columbus, OH, 43210, USA.
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7
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Goyal VD, Magliery TJ. Cover Image, Volume 86, Issue 6. Proteins 2018. [DOI: 10.1002/prot.25515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Venuka Durani Goyal
- Department of Chemistry and Biochemistry; The Ohio State University; Columbus Ohio 43210
- Department of Chemistry; Indian Institute of Technology Bombay; Powai Mumbai 400076 India
| | - Thomas J. Magliery
- Department of Chemistry and Biochemistry; The Ohio State University; Columbus Ohio 43210
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8
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Long NE, Sullivan BJ, Ding H, Doll S, Ryan MA, Hitchcock CL, Martin EW, Kumar K, Tweedle MF, Magliery TJ. Linker engineering in anti-TAG-72 antibody fragments optimizes biophysical properties, serum half-life, and high-specificity tumor imaging. J Biol Chem 2018; 293:9030-9040. [PMID: 29669811 DOI: 10.1074/jbc.ra118.002538] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/05/2018] [Indexed: 12/24/2022] Open
Abstract
Antibody (Ab) fragments have great clinical potential as cancer therapeutics and diagnostics. Their small size allows for fast clearance from blood, low immunoreactivity, better tumor penetration, and simpler engineering and production. The smallest fragment derived from a full-length IgG that retains binding to its antigen, the single-chain variable fragment (scFV), is engineered by fusing the variable light and variable heavy domains with a peptide linker. Along with switching the domain orientation, altering the length and amino acid sequence of the linker can significantly affect scFV binding, stability, quaternary structure, and other biophysical properties. Comprehensive studies of these attributes in a single scaffold have not been reported, making design and optimization of Ab fragments challenging. Here, we constructed libraries of 3E8, an Ab specific to tumor-associated glycoprotein 72 (TAG-72), a mucinous glycoprotein overexpressed in 80% of adenocarcinomas. We cloned, expressed, and characterized scFVs, diabodies, and higher-order multimer constructs with varying linker compositions, linker lengths, and domain orientations. These constructs dramatically differed in their oligomeric states and stabilities, not only because of linker and orientation but also related to the purification method. For example, protein L-purified constructs tended to have broader distributions and higher oligomeric states than has been reported previously. From this library, we selected an optimal construct, 3E8.G4S, for biodistribution and pharmacokinetic studies and in vivo xenograft mouse PET imaging. These studies revealed significant tumor targeting of 3E8.G4S with a tumor-to-background ratio of 29:1. These analyses validated 3E8.G4S as a fast, accurate, and specific tumor-imaging agent.
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Affiliation(s)
- Nicholas E Long
- From the Department of Chemistry and Biochemistry.,the Ohio State Biochemistry Program
| | | | - Haiming Ding
- the Laboratory for Translational Research in Imaging Pharmaceuticals, Wright Center of Innovation in Biomedical Imaging, Department of Radiology, College of Medicine
| | - Stephanie Doll
- the Laboratory for Translational Research in Imaging Pharmaceuticals, Wright Center of Innovation in Biomedical Imaging, Department of Radiology, College of Medicine
| | - Michael A Ryan
- From the Department of Chemistry and Biochemistry.,the Ohio State Biochemistry Program
| | | | - Edward W Martin
- the Department of Surgery, College of Medicine, The Ohio State University, Columbus, Ohio 43210
| | - Krishan Kumar
- the Laboratory for Translational Research in Imaging Pharmaceuticals, Wright Center of Innovation in Biomedical Imaging, Department of Radiology, College of Medicine
| | - Michael F Tweedle
- the Laboratory for Translational Research in Imaging Pharmaceuticals, Wright Center of Innovation in Biomedical Imaging, Department of Radiology, College of Medicine
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9
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Goyal VD, Magliery TJ. Phylogenetic spread of sequence data affects fitness of SOD1 consensus enzymes: Insights from sequence statistics and structural analyses. Proteins 2018; 86:609-620. [PMID: 29490429 DOI: 10.1002/prot.25486] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 01/25/2018] [Accepted: 02/24/2018] [Indexed: 12/19/2022]
Abstract
Non-natural protein sequences with native-like structures and functions can be constructed successfully using consensus design. This design strategy is relatively well understood in repeat proteins with simple binding function, however detailed studies are lacking in globular enzymes. The SOD1 family is a good model for such studies due to the availability of large amount of sequence and structure data motivated by involvement of human SOD1 in the fatal motor neuron disease amyotrophic lateral sclerosis (ALS). We constructed two consensus SOD1 enzymes from multiple sequence alignments from all organisms and eukaryotic organisms. A significant difference in their catalytic activities shows that the phylogenetic spread of the sequences used affects the fitness of the construct obtained. A mutation in an electrostatic loop and overall design incompatibilities between bacterial and eukaryotic sequences were implicated in this disparity. Based on this analysis, a bioinformatics approach was used to classify mutations thought to cause familial ALS providing a unique high level view of the physical basis of disease-causing aggregation of human SOD1.
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Affiliation(s)
- Venuka Durani Goyal
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210.,Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Thomas J Magliery
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210
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10
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Sun SB, Sen S, Kim NJ, Magliery TJ, Schultz PG, Wang F. Retraction of "Mutational Analysis of 48G7 Reveals that Somatic Hypermutation Affects Both Antibody Stability and Binding Affinity". J Am Chem Soc 2018; 140:1976. [PMID: 29376652 DOI: 10.1021/jacs.7b08106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Choudhary D, Kumar A, Magliery TJ, Sotomayor M. Using thermal scanning assays to test protein-protein interactions of inner-ear cadherins. PLoS One 2017; 12:e0189546. [PMID: 29261728 PMCID: PMC5736220 DOI: 10.1371/journal.pone.0189546] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/27/2017] [Indexed: 12/15/2022] Open
Abstract
Protein-protein interactions play a crucial role in biological processes such as cell-cell adhesion, immune system-pathogen interactions, and sensory perception. Understanding the structural determinants of protein-protein complex formation and obtaining quantitative estimates of their dissociation constant (KD) are essential for the study of these interactions and for the discovery of new therapeutics. At the same time, it is equally important to characterize protein-protein interactions in a high-throughput fashion. Here, we use a modified thermal scanning assay to test interactions of wild type (WT) and mutant variants of N-terminal fragments (EC1+2) of cadherin-23 and protocadherin-15, two proteins essential for inner-ear mechanotransduction. An environmentally sensitive fluorescent dye (SYPRO orange) is used to monitor melting temperature (Tm) shifts of protocadherin-15 EC1+2 (pcdh15) in the presence of increasing concentrations of cadherin-23 EC1+2 (cdh23). These Tm shifts are absent when we use proteins containing deafness-related missense mutations known to disrupt cdh23 binding to pcdh15, and are increased for some rationally designed mutants expected to enhance binding. In addition, surface plasmon resonance binding experiments were used to test if the Tm shifts correlated with changes in binding affinity. We used this approach to find a double mutation (cdh23(T15E)- pcdh15(G16D)) that enhances binding affinity of the cadherin complex by 1.98 kJ/mol, roughly two-fold that of the WT complex. We suggest that the thermal scanning methodology can be used in high-throughput format to quickly compare binding affinities (KD from nM up to 100 μM) for some heterodimeric protein complexes and to screen small molecule libraries to find protein-protein interaction inhibitors and enhancers.
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Affiliation(s)
- Deepanshu Choudhary
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Anusha Kumar
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Thomas J. Magliery
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
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12
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Ray WC, Wolock SL, Callahan NW, Dong M, Li QQ, Liang C, Magliery TJ, Bartlett CW. Addressing the unmet need for visualizing conditional random fields in biological data. BMC Bioinformatics 2014; 15:202. [PMID: 25000815 PMCID: PMC4227292 DOI: 10.1186/1471-2105-15-202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 06/10/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The biological world is replete with phenomena that appear to be ideally modeled and analyzed by one archetypal statistical framework - the Graphical Probabilistic Model (GPM). The structure of GPMs is a uniquely good match for biological problems that range from aligning sequences to modeling the genome-to-phenome relationship. The fundamental questions that GPMs address involve making decisions based on a complex web of interacting factors. Unfortunately, while GPMs ideally fit many questions in biology, they are not an easy solution to apply. Building a GPM is not a simple task for an end user. Moreover, applying GPMs is also impeded by the insidious fact that the "complex web of interacting factors" inherent to a problem might be easy to define and also intractable to compute upon. DISCUSSION We propose that the visualization sciences can contribute to many domains of the bio-sciences, by developing tools to address archetypal representation and user interaction issues in GPMs, and in particular a variety of GPM called a Conditional Random Field(CRF). CRFs bring additional power, and additional complexity, because the CRF dependency network can be conditioned on the query data. CONCLUSIONS In this manuscript we examine the shared features of several biological problems that are amenable to modeling with CRFs, highlight the challenges that existing visualization and visual analytics paradigms induce for these data, and document an experimental solution called StickWRLD which, while leaving room for improvement, has been successfully applied in several biological research projects. Software and tutorials are available at http://www.stickwrld.org/.
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Affiliation(s)
- William C Ray
- Nationwide Children’s Hospital, 575 Children’s Crossroad, 43215 Columbus, OH, USA
- The Ohio State University, 100 W. 18th Ave, 43210 Columbus, OH, USA
| | - Samuel L Wolock
- Nationwide Children’s Hospital, 575 Children’s Crossroad, 43215 Columbus, OH, USA
| | | | - Min Dong
- Miami University, 501 E. High St., 45056 Oxford, OH, USA
| | - Q Quinn Li
- Miami University, 501 E. High St., 45056 Oxford, OH, USA
| | - Chun Liang
- Miami University, 501 E. High St., 45056 Oxford, OH, USA
| | | | - Christopher W Bartlett
- Nationwide Children’s Hospital, 575 Children’s Crossroad, 43215 Columbus, OH, USA
- The Ohio State University, 100 W. 18th Ave, 43210 Columbus, OH, USA
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13
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Caleca L, Putignano AL, Colombo M, Congregati C, Sarkar M, Magliery TJ, Ripamonti CB, Foglia C, Peissel B, Zaffaroni D, Manoukian S, Tondini C, Barile M, Pensotti V, Bernard L, Papi L, Radice P. Characterization of an Italian founder mutation in the RING-finger domain of BRCA1. PLoS One 2014; 9:e86924. [PMID: 24516540 PMCID: PMC3916327 DOI: 10.1371/journal.pone.0086924] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 12/16/2013] [Indexed: 12/17/2022] Open
Abstract
The identification of founder mutations in cancer predisposing genes is important to improve risk assessment in geographically defined populations, since it may provide specific targets resulting in cost-effective genetic testing. Here, we report the characterization of the BRCA1 c.190T>C (p.Cys64Arg) mutation, mapped to the RING-finger domain coding region, that we detected in 43 hereditary breast/ovarian cancer (HBOC) families, for the large part originating from the province of Bergamo (Northern Italy). Haplotype analysis was performed in 21 families, and led to the identification of a shared haplotype extending over three BRCA1-associated marker loci (0.4 cM). Using the DMLE+2.2 software program and regional population demographic data, we were able to estimate the age of the mutation to vary between 3,100 and 3,350 years old. Functional characterization of the mutation was carried out at both transcript and protein level. Reverse transcriptase-PCR analysis on lymphoblastoid cells revealed expression of full length mRNA from the mutant allele. A green fluorescent protein (GFP)-fragment reassembly assay showed that the p.Cys64Arg substitution prevents the binding of the BRCA1 protein to the interacting protein BARD1, in a similar way as proven deleterious mutations in the RING-domain. Overall, 55 of 83 (66%) female mutation carriers had a diagnosis of breast and/or ovarian cancer. Our observations indicate that the BRCA1 c.190T>C is a pathogenic founder mutation present in the Italian population. Further analyses will evaluate whether screening for this mutation can be suggested as an effective strategy for the rapid identification of at-risk individuals in the Bergamo area.
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Affiliation(s)
- Laura Caleca
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), c/o Amadeolab, Milano, Italy
- * E-mail:
| | - Anna Laura Putignano
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
- FiorGen Foundation for Pharmacogenomics, Sesto Fiorentino, Italy
| | - Mara Colombo
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), c/o Amadeolab, Milano, Italy
| | - Caterina Congregati
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Mohosin Sarkar
- Department of Chemistry and Department of Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Thomas J. Magliery
- Department of Chemistry and Department of Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Carla B. Ripamonti
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), c/o Amadeolab, Milano, Italy
| | - Claudia Foglia
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), c/o Amadeolab, Milano, Italy
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Daniela Zaffaroni
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Carlo Tondini
- Unit of Medical Oncology, Azienda Ospedaliera Papa Giovanni XXIII, Bergamo, Italy
| | - Monica Barile
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, Milan, Italy
| | - Valeria Pensotti
- COGENTECH-Cancer Genetic Testing Laboratory, Milan, Italy
- Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Loris Bernard
- COGENTECH-Cancer Genetic Testing Laboratory, Milan, Italy
- Department of Experimental Oncology, Istituto Europeo di Oncologia, Milan, Italy
| | - Laura Papi
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), c/o Amadeolab, Milano, Italy
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Zhang Y, Goswami D, Wang D, Wang TSA, Sen S, Magliery TJ, Griffin PR, Wang F, Schultz PG. An antibody with a variable-region coiled-coil "knob" domain. Angew Chem Int Ed Engl 2013; 53:132-5. [PMID: 24254636 DOI: 10.1002/anie.201307939] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Indexed: 01/24/2023]
Abstract
The X-ray crystal structure of a bovine antibody (BLV1H12) revealed a unique structure in its ultralong heavy chain complementarity determining region 3 (CDR3H) that folds into a solvent-exposed β-strand "stalk" fused to a disulfide crosslinked "knob" domain. We have substituted an antiparallel heterodimeric coiled-coil motif for the β-strand stalk in this antibody. The resulting antibody (Ab-coil) expresses in mammalian cells and has a stability similar to that of the parent bovine antibody. MS analysis of H-D exchange supports the coiled-coil structure of the substituted peptides. Substitution of the knob-domain of Ab-coil with bovine granulocyte colony-stimulating factor (bGCSF) results in a stably expressed chimeric antibody, which proliferates mouse NFS-60 cells with a potency comparable to that of bGCSF. This work demonstrates the utility of this novel coiled-coil CDR3 motif as a means for generating stable, potent antibody fusion proteins with useful pharmacological properties.
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Affiliation(s)
- Yong Zhang
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 (USA); Present address: California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
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15
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Zhang Y, Goswami D, Wang D, Wang TSA, Sen S, Magliery TJ, Griffin PR, Wang F, Schultz PG. An Antibody with a Variable-Region Coiled-Coil “Knob” Domain. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307939] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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16
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Sun SB, Sen S, Kim NJ, Magliery TJ, Schultz PG, Wang F. Mutational analysis of 48G7 reveals that somatic hypermutation affects both antibody stability and binding affinity. J Am Chem Soc 2013; 135:9980-3. [PMID: 23795814 DOI: 10.1021/ja402927u] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The monoclonal antibody 48G7 differs from its germline precursor by 10 somatic mutations, a number of which appear to be functionally silent. We analyzed the effects of individual somatic mutations and combinations thereof on both antibody binding affinity and thermal stability. Individual somatic mutations that enhance binding affinity to hapten decrease the stability of the germline antibody; combining these binding mutations produced a mutant with high affinity for hapten but exceptionally low stability. Adding back each of the remaining somatic mutations restored thermal stability. These results, in conjunction with recently published studies, suggest an expanded role for somatic hypermutation in which both binding affinity and stability are optimized during clonal selection.
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Affiliation(s)
- Sophie B Sun
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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Abstract
The concepts of consensus and correlation in multiple sequence alignments (MSAs) have been used in the past to understand and engineer proteins. However, there are multiple ways of acquiring MSA databases and also numerous mathematical metrics that can be applied to calculate each of the parameters. This chapter describes an overall methodology that we have chosen to employ for acquiring and statistically analyzing MSAs. We have provided a step-by-step protocol for calculating relative entropy and mutual information metrics and describe how they can be used to predict mutations that have a high probability of stabilizing a protein. This protocol allows for flexibility for modification of formulae and parameters without using anything more complicated than Microsoft Excel. We have also demonstrated various aspects of data analysis by carrying out a sample analysis on the BPTI-Kunitz family of proteins and identified mutations that would be predicted to stabilize this protein based on consensus and correlation values.
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Affiliation(s)
- Venuka Durani
- Department of Chemistry, The Ohio State University, Columbus, Ohio, USA
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18
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Muthukrishnan S, Shete VS, Sanan TT, Vyas S, Oottikkal S, Porter LM, Magliery TJ, Hadad CM. Mechanistic Insights into the Hydrolysis of Organophosphorus Compounds by Paraoxonase-1: Exploring the Limits of Substrate Tolerance in a Promiscuous Enzyme. J PHYS ORG CHEM 2012; 25:1247-1260. [PMID: 23946555 PMCID: PMC3740977 DOI: 10.1002/poc.3002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We designed, synthesized and screened a library of analogs of the organophosphate pesticide metabolite paraoxon against a recombinant variant of human serum paraoxonase-1. Alterations of both the aryloxy leaving group and the retained alkyl chains of paraoxon analogs resulted in substantial changes to binding and hydrolysis, as measured directly by spectrophotometric methods or in competition experiments with paraoxon. Increases or decreases in the steric bulk of the retained groups generally reduced the rate of hydrolysis, while modifications of the leaving group modulated both binding and turnover. Studies on the hydrolysis of phosphoryl azide analogs as well as amino-modified paraoxon analogs, the former being developed as photo-affinity labels, found enhanced tolerance of structural modifications, when compared with O-alkyl substituted molecules. Results from computational modeling predict a predominant active site binding mode for these molecules which is consistent with several proposed catalytic mechanisms in the literature, and from which a molecular-level explanation of the experimental trends is attempted. Overall, the results of this study suggest that while paraoxonase-1 is a promiscuous enzyme, there are substantial constraints in the active site pocket, which may relate to both the leaving group and the retained portion of paraoxon analogs.
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Affiliation(s)
| | - Vivekanand S. Shete
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, U.S.A
| | - Toby. T. Sanan
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, U.S.A
| | - Shubham Vyas
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, U.S.A
| | - Shameema Oottikkal
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, U.S.A
| | - Lauren M. Porter
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, U.S.A
| | - Thomas J. Magliery
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, U.S.A
- Department of Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, U.S.A
| | - Christopher M. Hadad
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, U.S.A
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19
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Sullivan BJ, Nguyen T, Durani V, Mathur D, Rojas S, Thomas M, Syu T, Magliery TJ. Stabilizing proteins from sequence statistics: the interplay of conservation and correlation in triosephosphate isomerase stability. J Mol Biol 2012; 420:384-99. [PMID: 22555051 DOI: 10.1016/j.jmb.2012.04.025] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 04/16/2012] [Accepted: 04/21/2012] [Indexed: 10/28/2022]
Abstract
Understanding the determinants of protein stability remains one of protein science's greatest challenges. There are still no computational solutions that calculate the stability effects of even point mutations with sufficient reliability for practical use. Amino acid substitutions rarely increase the stability of native proteins; hence, large libraries and high-throughput screens or selections are needed to stabilize proteins using directed evolution. Consensus mutations have proven effective for increasing stability, but these mutations are successful only about half the time. We set out to understand why some consensus mutations fail to stabilize, and what criteria might be useful to predict stabilization more accurately. Overall, consensus mutations at more conserved positions were more likely to be stabilizing in our model, triosephosphate isomerase (TIM) from Saccharomyces cerevisiae. However, positions coupled to other sites were more likely not to stabilize upon mutation. Destabilizing mutations could be removed both by removing sites with high statistical correlations to other positions and by removing nearly invariant positions at which "hidden correlations" can occur. Application of these rules resulted in identification of stabilizing mutations in 9 out of 10 positions, and amalgamation of all predicted stabilizing positions resulted in the most stable yeast TIM variant we produced (+8 °C). In contrast, a multimutant with 14 mutations each found to stabilize TIM independently was destabilized by 2 °C. Our results are a practical extension to the consensus concept of protein stabilization, and they further suggest the importance of positional independence in the mechanism of consensus stabilization.
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Affiliation(s)
- Brandon J Sullivan
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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20
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Magliery TJ, Lavinder JJ, Sullivan BJ. Protein stability by number: high-throughput and statistical approaches to one of protein science's most difficult problems. Curr Opin Chem Biol 2011; 15:443-51. [PMID: 21498105 DOI: 10.1016/j.cbpa.2011.03.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 03/18/2011] [Accepted: 03/18/2011] [Indexed: 01/24/2023]
Abstract
Most proteins are only barely stable, which impedes research, complicates therapeutic applications, and makes proteins susceptible to pathologically destabilizing mutations. Our ability to predict the thermodynamic consequences of even single point mutations is still surprisingly limited, and established methods of measuring stability are slow. Recent advances are bringing protein stability studies into the high-throughput realm. Some methods are based on inferential read-outs such as activity, proteolytic resistance or split-protein fragment reassembly. Other methods use miniaturization of direct measurements, such as intrinsic fluorescence, H/D exchange, cysteine reactivity, aggregation and hydrophobic dye binding (DSF). Protein engineering based on statistical analysis (consensus and correlated occurrences of amino acids) is promising, but much work remains to understand and implement these methods.
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Affiliation(s)
- Thomas J Magliery
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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21
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Abstract
A general combinatorial mutagenesis strategy using common dimethoxytrityl-protected mononucleotide phosphoramidites and a single orthogonally protected trinucleotide phosphoramidite (Fmoc-TAG; Fmoc = 9-fluorenylmethoxycarbonyl) was developed to scan a gene with the TAG amber stop codon with complete synthetic control. In combination with stop-codon suppressors that insert natural (e.g., alanine) or unnatural (e.g., p-benzoylphenylalanine, Bpa) amino acids, a single DNA library can be used to incorporate different amino acids for diverse purposes. Here, we scanned TAG codons through part of the gene for a model four-helix bundle protein, Rop, which regulates the copy number of ColE1 plasmids. Alanine was incorporated into Rop for mapping its binding site using an in vivo activity screen, and subtle but important differences from in vitro gel-shift studies of Rop function are evident. As a test, Bpa was incorporated using a Phe14 amber mutant isolated from the scanning library. Surprisingly, Phe14Bpa-Rop is weakly active, despite the critical role of Phe14 in Rop activity. Bpa is a photoaffinity label unnatural amino acid that can form covalent bonds with adjacent molecules upon UV irradiation. Irradiation of Phe14Bpa-Rop, which is a dimer in solution like wild-type Rop, results in covalent dimers, trimers, and tetramers. This suggests that Phe14Bpa-Rop weakly associates as a tetramer in solution and highlights the use of Bpa cross-linking as a means of trapping weak and transient interactions.
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Affiliation(s)
- Lihua Nie
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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22
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Hari SB, Byeon C, Lavinder JJ, Magliery TJ. Cysteine-free Rop: a four-helix bundle core mutant has wild-type stability and structure but dramatically different unfolding kinetics. Protein Sci 2010; 19:670-9. [PMID: 20095056 DOI: 10.1002/pro.342] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Cysteine residues can complicate the folding and storage of proteins due to improper formation of disulfide bonds or oxidation of residues that are natively reduced. Wild-type Rop is a homodimeric four-helix bundle protein and an important model for protein design in the understanding of protein stability, structure and folding kinetics. In the native state, Rop has two buried, reduced cysteine residues in its core, but these are prone to oxidation in destabilized variants, particularly upon extended storage. To circumvent this problem, we designed and characterized a Cys-free variant of Rop, including solving the 2.3 A X-ray crystal structure. We show that the C38A C52V variant has similar structure, stability and in vivo activity to wild-type Rop, but that it has dramatically faster unfolding kinetics like virtually every other mutant of Rop that has been characterized. This cysteine-free Rop has already proven useful for studies on solution topology and on the relationship of core mutations to stability. It also suggests a general strategy for removal of pairs of Cys residues in proteins, both to make them more experimentally tractable and to improve their storage properties for therapeutic or industrial purposes.
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Affiliation(s)
- Sanjay B Hari
- Department of Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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23
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Magliery TJ, Lavinder JJ, Hari SB, Nguyen C, Sen S. Combinatorial design of a four‐helix bundle protein using high‐throughput thermal scanning. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.908.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | - Chau Nguyen
- ChemistryThe Ohio State UniversityColumbusOH
| | - Shila Sen
- ChemistryThe Ohio State UniversityColumbusOH
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24
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Otto TC, Harsch CK, Yeung DT, Magliery TJ, Cerasoli DM, Lenz DE. Dramatic differences in organophosphorus hydrolase activity between human and chimeric recombinant mammalian paraoxonase-1 enzymes. Biochemistry 2009; 48:10416-22. [PMID: 19764813 DOI: 10.1021/bi901161b] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human serum paraoxonase-1 (HuPON1) has the capacity to hydrolyze aryl esters, lactones, oxidized phospholipids, and organophosphorus (OP) compounds. HuPON1 and bacterially expressed chimeric recombinant PON1s (G2E6 and G3C9) differ by multiple amino acids, none of which are in the putative enzyme active site. To address the importance of these amino acid differences, the abilities of HuPON1, G2E6, G3C9, and several variants to hydrolyze phenyl acetate, paraoxon, and V-type OP nerve agents were examined. HuPON1 and G2E6 have a 10-fold greater catalytic efficiency toward phenyl acetate than G3C9. In contrast, bacterial PON1s are better able to promote hydrolysis of paraoxon, whereas HuPON1 is considerably better at catalyzing the hydrolysis of nerve agents VX and VR. These studies demonstrate that mutations distant from the active site of PON1 have large and unpredictable effects on the substrate specificities and possibly the hydrolytic mechanisms of HuPON1, G2E6, and G3C9. The replacement of residue H115 in the putative active site with tryptophan (H115W) has highly disparate effects on HuPON1 and G2E6. In HuPON1, variant H115W loses the ability to hydrolyze VR but has improved activity toward paraoxon and VX. The H115W variant of G2E6 has paraoxonase activity similar to that of wild-type G2E6, modest activity with phenyl acetate and VR, and enhanced VX hydrolysis. VR inhibits H115W HuPON1 competitively when paraoxon is the substrate and noncompetitively when VX is the substrate. We have identified the first variant of HuPON1, H115W, that displays significantly enhanced catalytic activity against an authentic V-type nerve agent.
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Affiliation(s)
- Tamara C Otto
- Physiology and Immunology Branch, Research Division, U.S. Army Medical Research Institute of Chemical Defense, 3100 Ricketts Point Road, Aberdeen Proving Ground, Maryland 21010-5400, USA
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25
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Lavinder JJ, Hari SB, Sullivan BJ, Magliery TJ. High-throughput thermal scanning: a general, rapid dye-binding thermal shift screen for protein engineering. J Am Chem Soc 2009; 131:3794-5. [PMID: 19292479 DOI: 10.1021/ja8049063] [Citation(s) in RCA: 173] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The low stability of natural proteins often limits their use in therapeutic, industrial, and research applications. The scale and throughput of methods such as circular dichroism, fluorescence spectroscopy, and calorimetry severely limit the number of variants that can be examined. Here we demonstrate a high-throughput thermal scanning (HTTS) method for determining the approximate stabilities of protein variants at high throughput and low cost. The method is based on binding to a hydrophobic dye akin to ANS, which fluoresces upon binding to molten globules and thermal denaturation intermediates. No inherent properties of the protein, such as enzymatic activity or presence of an intrinsic fluorophore, are required. Very small sample sizes are analyzed using a real-time PCR machine, enabling the use of high-throughput purification. We show that the apparent T(M) values obtained from HTTS are approximately linearly related to those from CD thermal denaturation for a series of four-helix bundle hydrophobic core variants. We demonstrate similar results for a small set of TIM barrel variants. This inexpensive, general, and scaleable approach enables the search for conservative, stable mutants of biotechnologically important proteins and provides a method for statistical correlation of sequence-stability relationships.
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Affiliation(s)
- Jason J Lavinder
- Ohio State Biochemistry Program, Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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26
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Sarkar M, Magliery TJ. Re-engineering a split-GFP reassembly screen to examine RING-domain interactions between BARD1 and BRCA1 mutants observed in cancer patients. Mol Biosyst 2008; 4:599-605. [PMID: 18493658 DOI: 10.1039/b802481b] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Identification of protein-protein interactions is critical for understanding protein function and regulation. Split protein reassembly is an in vivo probe of protein interactions that circumvents some of the problems with yeast 2-hybrid (indirect interactions, false positives) and co-immunoprecipitation (loss of weak and transient interactions, decompartmentalization). Split GFP reassembly, also called Bimolecular Fluorescence Complementation (BiFC), is especially attractive because the GFP chromophore forms spontaneously on protein folding in virtually every cell type tested. However, cellular fluorescence evolves slowly in bacteria and fails to evolve at all for some interactions. We aimed to use split-GFP reassembly to examine the determinants of association for a heterodimeric four-helix bundle, and we chose the N-terminal RING domains of BARD1 and the tumor suppressor BRCA1 as our test system. The wild-type interaction failed to give fluorescence with the split sg100 GFP variant. We found that split folding-reporter GFP (a hybrid of EGFP and GFPuv) evolves fluorescence much faster (overnight) with associating peptides and also evolves fluorescence for the BRCA1/BARD1 wild-type pair. Six cancer-associated BRCA1 interface mutants were examined with the system, and only two resulted in a significant reduction in complex reassembly. These results are generally in accord with Y2H studies, but the differences highlight the utility of complementary approaches. The split frGFP system may also be generally useful for other proteins and cell types, as the split-Venus system has proven to be in mammalian cells.
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Affiliation(s)
- Mohosin Sarkar
- Department of Chemistry, The Ohio State University, 100 W. 18th Ave., Columbus, OH 43210-1185, USA
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27
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Affiliation(s)
- Thomas J Magliery
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA
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28
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Abstract
Background The recent explosion in the availability of complete genome sequences has led to the cataloging of tens of thousands of new proteins and putative proteins. Many of these proteins can be structurally or functionally categorized from sequence conservation alone. In contrast, little attention has been given to the meaning of poorly-conserved sites in families of proteins, which are typically assumed to be of little structural or functional importance. Results Recently, using statistical free energy analysis of tetratricopeptide repeat (TPR) domains, we observed that positions in contact with peptide ligands are more variable than surface positions in general. Here we show that statistical analysis of TPRs, ankyrin repeats, Cys2His2 zinc fingers and PDZ domains accurately identifies specificity-determining positions by their sequence variation. Sequence variation is measured as deviation from a neutral reference state, and we present probabilistic and information theory formalisms that improve upon recently suggested methods such as statistical free energies and sequence entropies. Conclusion Sequence variation has been used to identify functionally-important residues in four selected protein families. With TPRs and ankyrin repeats, protein families that bind highly diverse ligands, the effect is so pronounced that sequence "hypervariation" alone can be used to predict ligand binding sites.
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Affiliation(s)
- Thomas J Magliery
- Department of Molecular Biophysics & Biochemistry, Yale University, P.O. Box 208114, New Haven, CT 06520-8114, USA
- Present address: Department of Chemistry and Department of Biochemistry, The Ohio State University, 100 W. 18Ave., Columbus, OH 43210, USA
| | - Lynne Regan
- Department of Molecular Biophysics & Biochemistry, Yale University, P.O. Box 208114, New Haven, CT 06520-8114, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
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Magliery TJ, Wilson CGM, Pan W, Mishler D, Ghosh I, Hamilton AD, Regan L. Detecting protein-protein interactions with a green fluorescent protein fragment reassembly trap: scope and mechanism. J Am Chem Soc 2005; 127:146-57. [PMID: 15631464 DOI: 10.1021/ja046699g] [Citation(s) in RCA: 333] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Identification of protein binding partners is one of the key challenges of proteomics. We recently introduced a screen for detecting protein-protein interactions based on reassembly of dissected fragments of green fluorescent protein fused to interacting peptides. Here, we present a set of comaintained Escherichia coli plasmids for the facile subcloning of fusions to the green fluorescent protein fragments. Using a library of antiparallel leucine zippers, we have shown that the screen can detect very weak interactions (K(D) approximately 1 mM). In vitro kinetics show that the reassembly reaction is essentially irreversible, suggesting that the screen may be useful for detecting transient interactions. Finally, we used the screen to discriminate cognate from noncognate protein-ligand interactions for tetratricopeptide repeat domains. These experiments demonstrate the general utility of the screen for larger proteins and elucidate mechanistic details to guide the further use of this screen in proteomic analysis. Additionally, this work gives insight into the positional inequivalence of stabilizing interactions in antiparallel coiled coils.
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Affiliation(s)
- Thomas J Magliery
- Department of Molecular Biophysics & Biochemistry, Yale University, P.O. Box 208114, New Haven, Connecticut 06520-8114, USA
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30
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Magliery TJ, Regan L. Beyond consensus: statistical free energies reveal hidden interactions in the design of a TPR motif. J Mol Biol 2004; 343:731-45. [PMID: 15465058 DOI: 10.1016/j.jmb.2004.08.026] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2004] [Revised: 07/20/2004] [Accepted: 08/10/2004] [Indexed: 11/20/2022]
Abstract
Consensus design methods have been used successfully to engineer proteins with a particular fold, and moreover to engineer thermostable exemplars of particular folds. Here, we consider how a statistical free energy approach can expand upon current methods of phylogenetic design. As an example, we have analyzed the tetratricopeptide repeat (TPR) motif, using multiple sequence alignment to identify the significance of each position in the TPR. The results provide information above and beyond that revealed by consensus design alone, especially at poorly conserved positions. A particularly striking finding is that certain residues, which TPR-peptide co-crystal structures show are in direct contact with the ligand, display a marked hypervariability. This suggests a novel means of identifying ligand-binding sites, and also implies that TPRs generally function as ligand-binding domains. Using perturbation analysis (or statistical coupling analysis), we examined site-site interactions within the TPR motif. Correlated occurrences of amino acid residues at poorly conserved positions explain how TPRs achieve their near-neutral surface charge distributions, and why a TPR designed from straight consensus has an unusually high net charge. Networks of interacting sites revealed that TPRs fall into two unrecognized families with distinct sets of interactions related to the identity of position 7 (Leu or Lys/Arg). Statistical free energy analysis provides a more complete description of "What makes a TPR a TPR?" than consensus alone, and it suggests general approaches to extend and improve the phylogenetic design of proteins.
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Affiliation(s)
- Thomas J Magliery
- Department of Molecular Biophysics and Biochemistry, Yale University, P.O. Box 208114, New Haven, CT 06520-8114, USA.
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31
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Affiliation(s)
- Christopher G M Wilson
- Department of Molecular Biophysics and Biochemistry, Yale University, P.O. Box 208114, New Haven, Connecticut 06520-8114, USA
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32
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Magliery TJ, Regan L. A cell-based screen for function of the four-helix bundle protein Rop: a new tool for combinatorial experiments in biophysics. Protein Eng Des Sel 2004; 17:77-83. [PMID: 14985540 DOI: 10.1093/protein/gzh010] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Combinatorial methodologies have revolutionized studies in biomolecular function, but they have so far proven less useful for understanding macromolecular structure and stability. This is largely because of the difficulty of screening libraries of molecules for biophysical properties, and the difficulty of interpreting structural effects in complicated molecules. Here, we report a novel, robust, cell-based screen for function of the four-helix bundle protein, Rop. By expression of green fluorescent protein from a ColE1 plasmid, the screen reports the copy number of the plasmid, which is modulated in Escherichia coli by Rop. We have engineered the screen so that the fluorescent phenotype can correspond to either Rop activity or lack thereof. We have used the screen to demonstrate with systematically constructed Rop core variants that not all molecules that bind small stem-loop RNAs in vitro are active in vivo. Rop is well understood from structural work and systematic mutations, which makes it possible to construct rational, targeted libraries. This screen makes it possible to rapidly interrogate such libraries effectively for proper protein folding and stability. In addition to its intended utility for combinatorial experiments in biophysics, the screen will allow further dissection of the mechanism of Rop-mediated plasmid copy number regulation in vivo.
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Affiliation(s)
- Thomas J Magliery
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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33
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Affiliation(s)
- Thomas J Magliery
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
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34
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Abstract
Why do proteins adopt the conformations that they do, and what determines their stabilities? While we have come to some understanding of the forces that underlie protein architecture, a precise, predictive, physicochemical explanation is still elusive. Two obstacles to addressing these questions are the unfathomable vastness of protein sequence space, and the difficulty in making direct physical measurements on large numbers of protein variants. Here, we review combinatorial methods that have been applied to problems in protein biophysics over the last 15 years. The effects of hydrophobic core composition, the most important determinant of structure and stability, are still poorly understood. Particular attention is given to core composition as addressed by library methods. Increasingly useful screens and selections, in combination with modern high-throughput approaches borrowed from genomics and proteomics efforts, are making the empirical, statistical correlation between sequence and structure a tractable problem for the coming years.
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Affiliation(s)
- Thomas J Magliery
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
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35
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Abstract
This review considers chemical and genetic approaches to the modification of protein structure. The historical interest in chemical and site-directed modifications will be briefly covered. Current chemical modification strategies will be presented. Biosynthetic mutagenesis with unnatural aminoacyl-tRNAs and current synthetic peptide ligation technologies will be covered in greater detail. The application of combinatorial genetic methods (e.g. phage display, DNA shuffling) to protein engineering with unnatural amino acids will be briefly discussed, with emphasis on the in vitro evolution of new enzymatic function (i.e. aminoacyl-tRNA synthetases). Throughout the review, the powerful insights gained from the combined use of these technologies will be illustrated by examples that focus on the elucidation of protein-ligand interactions.
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36
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Abstract
We previously employed a combinatorial approach to identify the most efficient suppressors of four-base codons in E. coli. We have now examined the suppression of two-, three-, four-, five-, and six-base codons with tRNAs containing 6-10 nt in their anticodon loops. We found that the E. coli translational machinery tolerates codons of 3-5 bases and that tRNAs with 6-10 nt anticodon loops can suppress these codons. However, N-length codons were found to prefer N + 4-length anticodon loops. Additionally, sequence preferences, including the requirement of Watson-Crick complementarity to the codon, were evident in the loops. These selections have yielded efficient suppressors of four-base and five-base codons for our ongoing efforts to expand the genetic code. They also highlight some of the parameters that underlie the fidelity of frame maintenance.
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Affiliation(s)
- J Christopher Anderson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Magliery TJ, Anderson J, Schultz PG. Expanding the genetic code: selection of efficient suppressors of four-base codons and identification of "shifty" four-base codons with a library approach in Escherichia coli. J Mol Biol 2001; 307:755-69. [PMID: 11273699 PMCID: PMC7125544 DOI: 10.1006/jmbi.2001.4518] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Naturally occurring tRNA mutants are known that suppress +1 frameshift mutations by means of an extended anticodon loop, and a few have been used in protein mutagenesis. In an effort to expand the number of possible ways to uniquely and efficiently encode unnatural amino acids, we have devised a general strategy to select tRNAs with the ability to suppress four-base codons from a library of tRNAs with randomized 8 or 9 nt anticodon loops. Our selectants included both known and novel suppressible four-base codons and resulted in a set of very efficient, non-cross-reactive tRNA/four-base codon pairs for AGGA, UAGA, CCCU and CUAG. The most efficient four-base codon suppressors had Watson-Crick complementary anticodons, and the sequences of the anticodon loops outside of the anticodons varied with the anticodon. Additionally, four-base codon reporter libraries were used to identify "shifty" sites at which +1 frameshifting is most favorable in the absence of suppressor tRNAs in Escherichia coli. We intend to use these tRNAs to explore the limits of unnatural polypeptide biosynthesis, both in vitro and eventually in vivo. In addition, this selection strategy is being extended to identify novel five- and six-base codon suppressors.
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MESH Headings
- Amino Acid Sequence
- Ampicillin/pharmacology
- Anticodon/chemistry
- Anticodon/genetics
- Anticodon/metabolism
- Base Pairing
- Base Sequence
- Cephalosporins/metabolism
- Codon/chemistry
- Codon/genetics
- Codon/metabolism
- Escherichia coli/drug effects
- Escherichia coli/genetics
- Frameshift Mutation/genetics
- Gene Expression Regulation, Bacterial/drug effects
- Gene Library
- Genes, Reporter/genetics
- Genetic Code/genetics
- Molecular Sequence Data
- Mutagenesis
- Protein Biosynthesis/drug effects
- Protein Biosynthesis/genetics
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Transfer, Ser/chemistry
- RNA, Transfer, Ser/genetics
- RNA, Transfer, Ser/metabolism
- Serine/genetics
- Serine/metabolism
- Substrate Specificity
- Suppression, Genetic/genetics
- beta-Lactamases/biosynthesis
- beta-Lactamases/chemistry
- beta-Lactamases/genetics
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Affiliation(s)
- Thomas J Magliery
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - J.Christopher Anderson
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Peter G Schultz
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA
- Corresponding author
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38
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Wang L, Magliery TJ, Liu DR, Schultz PG. A New Functional Suppressor tRNA/Aminoacyl−tRNA Synthetase Pair for the in Vivo Incorporation of Unnatural Amino Acids into Proteins. J Am Chem Soc 2000. [DOI: 10.1021/ja000595y] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lei Wang
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Thomas J. Magliery
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, California 92037
| | - David R. Liu
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Peter G. Schultz
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, California 92037
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Liu DR, Magliery TJ, Pastrnak M, Schultz PG. Engineering a tRNA and aminoacyl-tRNA synthetase for the site-specific incorporation of unnatural amino acids into proteins in vivo. Proc Natl Acad Sci U S A 1997; 94:10092-7. [PMID: 9294168 PMCID: PMC23315 DOI: 10.1073/pnas.94.19.10092] [Citation(s) in RCA: 125] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In an effort to expand the scope of protein mutagenesis, we have completed the first steps toward a general method to allow the site-specific incorporation of unnatural amino acids into proteins in vivo. Our approach involves the generation of an "orthogonal" suppressor tRNA that is uniquely acylated in Escherichia coli by an engineered aminoacyl-tRNA synthetase with the desired unnatural amino acid. To this end, eight mutations were introduced into tRNA2Gln based on an analysis of the x-ray crystal structure of the glutaminyl-tRNA aminoacyl synthetase (GlnRS)-tRNA2Gln complex and on previous biochemical data. The resulting tRNA satisfies the minimal requirements for the delivery of an unnatural amino acid: it is not acylated by any endogenous E. coli aminoacyl-tRNA synthetase including GlnRS, and it functions efficiently in protein translation. Repeated rounds of DNA shuffling and oligonucleotide-directed mutagenesis followed by genetic selection resulted in mutant GlnRS enzymes that efficiently acylate the engineered tRNA with glutamine in vitro. The mutant GlnRS and engineered tRNA also constitute a functional synthetase-tRNA pair in vivo. The nature of the GlnRS mutations, which occur both at the protein-tRNA interface and at sites further away, is discussed.
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Affiliation(s)
- D R Liu
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, CA 94720, USA
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40
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Abstract
BACKGROUND In an effort to expand further our ability to manipulate protein structure, we have completed the first step towards a general method that allows the site-specific incorporation of unnatural amino acids into proteins in vivo. Our approach involves the construction of an 'orthogonal' suppressor tRNA that is uniquely acylated in vivo, by an engineered aminoacyl-tRNA synthetase, with the desired unnatural amino acid. The Escherichia coli tRNA2(Gln)-glutaminyl-tRNA synthetase (GlnRS) pair provides a biochemically and structurally well-characterized starting point for developing this methodology. To generate the orthogonal tRNA, mutations were introduced into the acceptor stem, D-loop/stem, and anticodon loop of tRNA2(Gln). We report here the characterization of the properties of the resulting tRNAs and their suitability to severe as an orthogonal suppressor. Our efforts to generate an engineered synthetase are described elsewhere. RESULTS Mutant tRNAs were generated by runoff transcription and assayed for their ability to be aminoacylated by purified E. coli GlnRS and to suppress an amber codon in an in vitro transcription/translation reaction. One tRNA bearing eight mutations satisfies the minimal requirements for the delivery of an unnatural amino acid: it is not acylated by any endogenous E. coli aminoacyl-tRNA synthetase, including GlnRS, yet functions efficiently during protein translation. Mutations in the acceptor stem and D-loop/stem, when introduced in combination, had very different effects on the properties of the resulting tRNAs compared with the effects of the individual mutations. CONCLUSIONS Mutations at sites within tRNA2(Gln) separated by 23-31 A interact strongly with each other, often in a nonadditive fashion, to modulate both aminoacylation activities and translational efficiencies. The observed correlation between the effects of mutations at very distinct regions of the GlnRS-tRNA and possibly the ribosomal/tRNA complexes may contribute in part to the fidelity of protein biosynthesis.
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Affiliation(s)
- D R Liu
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley 94720, USA.
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