Contents
- 1 Compilations of Carter lab publications
- 2 Selected publications by topic:
- 2.1 Domain motion and Bioenergetics
- 2.2 Origin of genetic coding in the aminoacyl-tRNA synthetase duality
- 2.3 Aminoacyl-tRNA synthetase (aaRS) Urzymes and the origin of catalysis.
- 2.4 Bidirectional genetic coding of Class I and II aminoacyl-tRNA synthetases.
- 2.5 Cognate synthetase:tRNA pairs, nanosensing, and the self-organization of genetic coding.
- 2.6 Combinatorial analysis of multidimensional allosteric coupling.
- 2.7 Experimental Design.
- 2.8 Mechanistic Enzymology of Cytidine Deaminase.
Compilations of Carter lab publications
Goggle Scholar Citations
Selected publications by topic:
Domain motion and Bioenergetics
Carter CW, Jr., Wills PR. 2021. Reciprocally-coupled Gating: Strange Loops in Bioenergetics, Genetics, and Catalysis. Biomolecules 11:265.
Carter CW, Jr. 2019. Escapement mechanisms: efficient free energy transduction by reciprocally-coupled gating. Proteins: Structure, Function, and Bioinformatics 88:710–717.
Chandrasekaran SN, Carter CW, Jr. 2017. Adding torsional interaction terms to the Anisotropic Network Model improves the PATH performance, enabling detailed comparison with experimental rate data Structural Dynamics 4:032103.
Carter CW, Jr., Chandrasekaran SN, Weinreb V, Li L, Williams T. 2017. Combining multi-mutant and modular thermodynamic cycles to measure energetic coupling networks in enzyme catalysis Structural Dynamics 4:032101.
Carter CW, Jr. 2017. High-Dimensional Mutant and Modular Thermodynamic Cycles, Molecular Switching, and Free Energy Transduction. Annual Review of Biophysics 46:433-453.
Chandrasekaran SN, Das J, Dokholyan NV, Carter CW, Jr. 2016. A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms. Structural Dynamics 3:012101.
Carter J, Charles W., Chandrasekaran SN, Weinreb V, Li L, Williams T editors. Structural Dynamics. 2016 American Crystallographic Association Annual Meeting.
Origin of genetic coding in the aminoacyl-tRNA synthetase duality
Carter CW, Jr., Wills PR. 2021. The Roots of Genetic Coding in Aminoacyl-tRNA Synthetase Duality Annual Review of Biochemistry 90:349-373.
Carter CW, Jr., Wills PR. 2019. Experimental Solutions to Problems Defining the Origin of Codon-Directed Protein Synthesis. Biosystems 183:103979.
Carter CW, Jr, Wills PR. 2019. Class I and II aminoacyl-tRNA synthetase tRNA groove discrimination created the first synthetase•tRNA cognate pairs and was therefore essential to the origin of genetic coding. IUBMB Life 71:1088–1098.
Carter CW, Jr. 2019. The Evolution of Genetic Coding. In. Scientia. online: Science Diffusion, Ltd Bristol, UK.
Carter CW, Jr , Wills PR. 2018. Hierarchical groove discrimination by Class I and II aminoacyl-tRNA synthetases reveals a palimpsest of the operational RNA code in the tRNA acceptor-stem bases. Nucleic Acids Research 46:9667–9683.
Aminoacyl-tRNA synthetase (aaRS) Urzymes and the origin of catalysis.
Carter CW Jr. Urzymology: experimental access to a key transition in the appearance of enzymes.J Biol Chem. 2014 Oct 31;289(44):30213-20. PMID: 25210034; PMCID: PMC4215205.
Pham, Y.et al. A Minimal TrpRS Catalytic Domain Supports Sense/Antisense Ancestry of Class I and II Aminoacyl-tRNA Synthetases. Mol Cell25, 851-862 (2007) PMID: 20864539; PMCID: PMC2992291
Li L, et. al,Histidyl-tRNA synthetase urzymes: Class I and II aminoacyl tRNA synthetase urzymes have comparable catalytic activities for cognate amino acid activation.J. Biol. Chem. 2011; 286(12):10387-95. PMID: 21270472 PMCID: PMC3060492
Li L, Francklyn C, Carter CW Jr. Aminoacylating urzymes challenge the RNA world hypothesis.J Biol Chem. (2013);288(37):26856-63. PMID: 23867455; PMCID: PMC3772232.
Cammer S, Carter CW Jr.Six Rossmannoid folds, including the Class I aminoacyl-tRNA synthetases, share a partial core with the anti-codon-binding domain of a Class II aminoacyl-tRNA synthetase.Bioinformatics(Oxford, England). 2010; 26(6):709-14. PMID: 20130031 PMCID: PMC2852213
Sapienza PJ, Li L, Williams T, Lee AL, Carter CW Jr. An Ancestral Tryptophanyl-tRNA Synthetase Precursor Achieves High Catalytic Rate Enhancement without Ordered Ground-State Tertiary Structures.ACS Chem Biol. 2016 Jun 17;11(6):1661-8. doi: 10.1021/acschembio.5b01011. PMCID: PMC5461432.
Bidirectional genetic coding of Class I and II aminoacyl-tRNA synthetases.
Carter, C. W., Jr., & Kraut, J. (1974) A Proposed Model for Interaction of Polypeptides with RNAProceedings of the National Academy of Sciences, USA 71, 283-287.
Chandrasekaran S, Yardimci GG, Erdogan O, Roach JM, Carter, Jr, CW. Statistical Evaluation of the Rodin-Ohno Hypothesis: Sense/Antisense Coding of Ancestral Class I and II Aminoacyl-tRNA Synthetases. Molecular biology and evolution. 2013 July; 30:1588-1604; PMC3684856.
Carter CW Jr, Li L, Weinreb V, Collier M, Gonzalez-Rivera K, Jimenez-Rodriguez M, Erdogan O, Kuhlman B, Ambroggio X, Williams T, Chandrasekharan SN. The Rodin-Ohno hypothesis that two enzyme superfamilies descended from one ancestral gene: an unlikely scenario for the origins of translation that will not be dismissed.Biol Direct. 2014 Jun 14;9:11. doi: 10.1186/1745-6150-9-11. PubMed PMID: 24927791; PubMed Central PMCID: PMC4082485.
Martinez, L., Jimenez-Rodriguez, M., Gonzalez-Rivera, K., Williams, T., Li, L., Weinreb, V., Niranj Chandrasekaran, S., Collier, M., Ambroggio, X., Kuhlman, B., Erdogan, O. & Carter, C. W. J. (2015) Functional Class I and II Amino Acid Activating Enzymes Can Be Coded by Opposite Strands of the Same GeneJ. Biol. Chem. 290(32): 19710–19725; PMC4528134
Carter, CW Jr. What RNA World? Why a Peptide/RNA Partnership MeritsRenewed Experimental AttentionLife 2015, 5, 294-320; doi:10.3390/life5010294. PMC4390853
Cognate synthetase:tRNA pairs, nanosensing, and the self-organization of genetic coding.
Carter CW Jr, Wills PR. Hierarchical groove discrimination by Class I and II aminoacyl-tRNA synthetases reveals a palimpsest of the operational RNA code in the tRNA acceptor-stem bases.Nucleic Acids Res. 2018 Jul 17. doi: 10.1093/nar/gky600. PubMed PMID: 30016476
Wolfenden, R., Lewis, C. A., Yuan, Y. & Carter, C. W. J. (2015) Temperature dependence of amino acid hydrophobicitiesProc. Nat. Acad. Sci. USA 112:7484–7488; PMC4475965
Carter, C. W., Jr. & Wolfenden, R. (2015) tRNA Acceptor-Stem and Anticodon Bases Form Independent Codes Related to Protein FoldingProc. Nat. Acad. Sci. USA 112:7489–7494; PMC4475997.
Carter, C.W., Jr and Wills, P.R. (2018) Interdependence, Reflexivity, Fidelity, and Impedance Matching, and the Evolution of Genetic Coding. Molecular Biology and Evolution, 35, 269-286. PMID: 29077934
Wills PR, Carter CW Jr. (2018) Insuperable problems of the genetic code initially emerging in an RNA world.Bio Systems.; 164:155-166.PMID: 28903058, PMCID:PMC5895081
Combinatorial analysis of multidimensional allosteric coupling.
Weinreb V, Li L, Chandrasekaran SN, Koehl P, Delarue M, Carter CW Jr. Enhanced amino acid selection in fully evolved tryptophanyl-tRNA synthetase, relative to its urzyme, requires domain motion sensed by the D1 switch, a remote dynamic packing motif.J Biol Chem. (2014)289(7):4367-76. PMC3924299.
Li L, Carter CW Jr. Full implementation of the genetic code by tryptophanyl-tRNA synthetase requires intermodular coupling.J Biol Chem. (2013);288:34736-45. PMCID: PMC3843085.
Chandrasekaran SN, Das J, Dokholyan NV, Carter CW Jr. A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms.Struct Dyn. (2016) 3:012101. PMCID4769271
Chandrasekaran, S.N. and Carter, C.W.J. (2017) Adding torsional interaction terms to the Anisotropic Network Model improves the PATH performance, enabling detailed comparison with experimental rate dataStructural Dynamics, 4, 032103. PMCID PMC5315668
Carter, C.W., Jr., Chandrasekaran, S.N., Weinreb, V., Li, L. and Williams, T. (2017) Combining multi-mutant and modular thermodynamic cycles to measure energetic coupling networks in enzyme catalysis Structural Dynamics,4, 032101. PMCID PMC5272822
Experimental Design.
Carter CW Jr, Carter CW. Protein crystallization using incomplete factorial experiments.J Biol Chem. 1979 Dec 10;254(23):12219-23. PubMed PMID: 500706.
Yin Y, Carter CW Jr. Incomplete factorial and response surface methods in experimental design: yield optimization of tRNA(Trp) from in vitro T7 RNA polymerase transcription.Nucleic Acids Res. 1996 Apr 1;24(7):1279-86. PubMed PMID: 8614631; PubMed Central PMCID: PMC145796.
Chester A, Weinreb V, Carter CW Jr, Navaratnam N. Optimization of apolipoprotein B mRNA editing by APOBEC1 apoenzyme and the role of its auxiliary factor, ACF.RNA. 2004 Sep;10(9):1399-411. Epub 2004 Jul 23. PubMed PMID: 15273326; PubMed Central PMCID: PMC3225921.
Carter CW Jr, Riès-Kautt M. Improving marginal crystals.Methods Mol Biol. 2007;363:153-74. PubMed PMID: 17272841.
Mechanistic Enzymology of Cytidine Deaminase.
Betts L, Xiang S, Short SA, Wolfenden R, Carter CW Jr. Cytidine deaminase. The 2.3 A crystal structure of an enzyme: transition-state analog complex.(1994) J Mol Biol. 235:635-656. PubMed PMID: 8289286.
Xiang S, Short SA, Wolfenden R, Carter CW Jr. Transition-state selectivity for a single hydroxyl group during catalysis by cytidine deaminase.Biochemistry. 1995 Apr 11;34(14):4516-23. PubMed PMID: 7718553.
Xiang S, Short SA, Wolfenden R, Carter CW Jr. Cytidine deaminase complexed to 3-deazacytidine: a “valence buffer” in zinc enzyme catalysis.Biochemistry. 1996 Feb 6;35(5):1335-41. PubMed PMID: 8634261.
Xiang S, Short SA, Wolfenden R, Carter CW Jr. The structure of the cytidine deaminase-product complex provides evidence for efficient proton transfer and ground-state destabilization.Biochemistry. 1997 Apr 22;36(16):4768-74. PubMed PMID: 9125497.