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Carter CW, Wills PR. Reciprocally-Coupled Gating: Strange Loops in Bioenergetics, Genetics, and Catalysis. Biomolecules 2021; 11:265. [PMID: 33670192 PMCID: PMC7916928 DOI: 10.3390/biom11020265] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/04/2021] [Accepted: 02/06/2021] [Indexed: 12/12/2022] Open
Abstract
Bioenergetics, genetic coding, and catalysis are all difficult to imagine emerging without pre-existing historical context. That context is often posed as a "Chicken and Egg" problem; its resolution is concisely described by de Grasse Tyson: "The egg was laid by a bird that was not a chicken". The concision and generality of that answer furnish no details-only an appropriate framework from which to examine detailed paradigms that might illuminate paradoxes underlying these three life-defining biomolecular processes. We examine experimental aspects here of five examples that all conform to the same paradigm. In each example, a paradox is resolved by coupling "if, and only if" conditions for reciprocal transitions between levels, such that the consequent of the first test is the antecedent for the second. Each condition thus restricts fluxes through, or "gates" the other. Reciprocally-coupled gating, in which two gated processes constrain one another, is self-referential, hence maps onto the formal structure of "strange loops". That mapping uncovers two different kinds of forces that may help unite the axioms underlying three phenomena that distinguish biology from chemistry. As a physical analog for Gödel's logic, biomolecular strange-loops provide a natural metaphor around which to organize a large body of experimental data, linking biology to information, free energy, and the second law of thermodynamics.
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Affiliation(s)
- Charles W. Carter
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7260, USA
| | - Peter R. Wills
- Department of Physics and Te Ao Marama Centre for Fundamental Inquiry, University of Auckland, PB 92019, Auckland 1142, New Zealand;
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Xie L, Yang M, Chen ZN. Understanding the entropic effect in chorismate mutase reaction catalyzed by isochorismate-pyruvate lyase fromPseudomonas aeruginosa(PchB). Catal Sci Technol 2019. [DOI: 10.1039/c8cy02123f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The substrate preorganization process in the entropically driven PchB-catalyzed chorismate mutase reaction leads to a remarkable apparent entropic effect.
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Affiliation(s)
- Liangxu Xie
- State Key Laboratory of Structural Chemistry
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences
- Fuzhou 350002
- China
- Department of Chemistry
| | - Mingjun Yang
- XtalPi Inc. (Shenzhen Jingtai Technology Co., Ltd.)
- Times Science & Tech Mansion E. 20F
- Shenzhen
- China
| | - Zhe-Ning Chen
- State Key Laboratory of Structural Chemistry
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences
- Fuzhou 350002
- China
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Carter CW. Coding of Class I and II Aminoacyl-tRNA Synthetases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 966:103-148. [PMID: 28828732 PMCID: PMC5927602 DOI: 10.1007/5584_2017_93] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The aminoacyl-tRNA synthetases and their cognate transfer RNAs translate the universal genetic code. The twenty canonical amino acids are sufficiently diverse to create a selective advantage for dividing amino acid activation between two distinct, apparently unrelated superfamilies of synthetases, Class I amino acids being generally larger and less polar, Class II amino acids smaller and more polar. Biochemical, bioinformatic, and protein engineering experiments support the hypothesis that the two Classes descended from opposite strands of the same ancestral gene. Parallel experimental deconstructions of Class I and II synthetases reveal parallel losses in catalytic proficiency at two novel modular levels-protozymes and Urzymes-associated with the evolution of catalytic activity. Bi-directional coding supports an important unification of the proteome; affords a genetic relatedness metric-middle base-pairing frequencies in sense/antisense alignments-that probes more deeply into the evolutionary history of translation than do single multiple sequence alignments; and has facilitated the analysis of hitherto unknown coding relationships in tRNA sequences. Reconstruction of native synthetases by modular thermodynamic cycles facilitated by domain engineering emphasizes the subtlety associated with achieving high specificity, shedding new light on allosteric relationships in contemporary synthetases. Synthetase Urzyme structural biology suggests that they are catalytically-active molten globules, broadening the potential manifold of polypeptide catalysts accessible to primitive genetic coding and motivating revisions of the origins of catalysis. Finally, bi-directional genetic coding of some of the oldest genes in the proteome places major limitations on the likelihood that any RNA World preceded the origins of coded proteins.
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Affiliation(s)
- Charles W Carter
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7260, USA.
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Sapienza PJ, Li L, Williams T, Lee AL, Carter CW. An Ancestral Tryptophanyl-tRNA Synthetase Precursor Achieves High Catalytic Rate Enhancement without Ordered Ground-State Tertiary Structures. ACS Chem Biol 2016; 11:1661-8. [PMID: 27008438 PMCID: PMC5461432 DOI: 10.1021/acschembio.5b01011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Urzymes-short, active core modules derived from enzyme superfamilies-prepared from the two aminoacyl-tRNA synthetase (aaRS) classes contain only the modules shared by all related family members. They have been described as models for ancestral forms. Understanding them currently depends on inferences drawn from the crystal structures of the full-length enzymes. As aaRS Urzymes lack much of the mass of modern aaRS's, retaining only a small portion of the hydrophobic cores of the full-length enzymes, it is desirable to characterize their structures. We report preliminary characterization of (15)N tryptophanyl-tRNA synthetase Urzyme by heteronuclear single quantum coherence (HSQC) NMR spectroscopy supplemented by circular dichroism, thermal melting, and induced fluorescence of bound dye. The limited dispersion of (1)H chemical shifts (0.5 ppm) is inconsistent with a narrow ensemble of well-packed structures in either free or substrate-bound forms, although the number of resonances from the bound state increases, indicating a modest, ligand-dependent gain in structure. Circular dichroism spectroscopy shows the presence of helices and evidence of cold denaturation, and all ligation states induce Sypro Orange fluorescence at ambient temperatures. Although the term "molten globule" is difficult to define precisely, these characteristics are consistent with most such definitions. Active-site titration shows that a majority of molecules retain ∼60% of the transition state stabilization free energy observed in modern synthetases. In contrast to the conventional view that enzymes require stable tertiary structures, we conclude that a highly flexible ground-state ensemble can nevertheless bind tightly to the transition state for amino acid activation.
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Affiliation(s)
- Paul J. Sapienza
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy
| | - Li Li
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 25799
| | - Tishan Williams
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 25799
| | - Andrew L. Lee
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy
| | - Charles W. Carter
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 25799
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Martinez-Rodriguez L, Erdogan O, Jimenez-Rodriguez M, Gonzalez-Rivera K, Williams T, Li L, Weinreb V, Collier M, Chandrasekaran SN, Ambroggio X, Kuhlman B, Carter CW. Functional Class I and II Amino Acid-activating Enzymes Can Be Coded by Opposite Strands of the Same Gene. J Biol Chem 2015; 290:19710-25. [PMID: 26088142 DOI: 10.1074/jbc.m115.642876] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Indexed: 01/11/2023] Open
Abstract
Aminoacyl-tRNA synthetases (aaRS) catalyze both chemical steps that translate the universal genetic code. Rodin and Ohno offered an explanation for the existence of two aaRS classes, observing that codons for the most highly conserved Class I active-site residues are anticodons for corresponding Class II active-site residues. They proposed that the two classes arose simultaneously, by translation of opposite strands from the same gene. We have characterized wild-type 46-residue peptides containing ATP-binding sites of Class I and II synthetases and those coded by a gene designed by Rosetta to encode the corresponding peptides on opposite strands. Catalysis by WT and designed peptides is saturable, and the designed peptides are sensitive to active-site residue mutation. All have comparable apparent second-order rate constants 2.9-7.0E-3 M(-1) s(-1) or ∼750,000-1,300,000 times the uncatalyzed rate. The activities of the two complementary peptides demonstrate that the unique information in a gene can have two functional interpretations, one from each complementary strand. The peptides contain phylogenetic signatures of longer, more sophisticated catalysts we call Urzymes and are short enough to bridge the gap between them and simpler uncoded peptides. Thus, they directly substantiate the sense/antisense coding ancestry of Class I and II aaRS. Furthermore, designed 46-mers achieve similar catalytic proficiency to wild-type 46-mers by significant increases in both kcat and Km values, supporting suggestions that the earliest peptide catalysts activated ATP for biosynthetic purposes.
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Affiliation(s)
- Luis Martinez-Rodriguez
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Ozgün Erdogan
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Mariel Jimenez-Rodriguez
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Katiria Gonzalez-Rivera
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Tishan Williams
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Li Li
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Violetta Weinreb
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Martha Collier
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Srinivas Niranj Chandrasekaran
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Xavier Ambroggio
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Brian Kuhlman
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Charles W Carter
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
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Carter CW. Urzymology: experimental access to a key transition in the appearance of enzymes. J Biol Chem 2014; 289:30213-30220. [PMID: 25210034 DOI: 10.1074/jbc.r114.567495] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Urzymes are catalysts derived from invariant cores of protein superfamilies. Urzymes from both aminoacyl-tRNA synthetase classes possess sophisticated catalytic mechanisms: pre-steady state bursts, significant transition-state stabilization of both amino acid activation, and tRNA acylation. However, they have insufficient specificity to ensure a fully developed genetic code, suggesting that they participated in synthesizing statistical proteins. They represent a robust experimental platform from which to articulate and test hypotheses both about their own ancestors and about how they, in turn, evolved into modern enzymes. They help reshape numerous paradigms from the RNA World hypothesis to protein structure databases and allostery.
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Affiliation(s)
- Charles W Carter
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599-7260.
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