Charles Carter, Jr.
Professor of Biochemistry and Biophysics
(PhD - University of California, San Diego)
Carter Lab Website
HONORS & AWARDS
- Fellow of the American Association for the Advancement of Science, 2012
Protein Crystallography, Structural Polymorphism and Function
The Carter lab uses structural, bioinformatic, molecular genetic, and biophysical techniques to strengthen and deepen understanding of the mechanistic basis and historical origins of enzyme catalysis. One challenge we have undertaken is to study how chemical free energy released by nucleotide triphosphate hydrolysis is converted into protein conformational changes. Combinatorial mutagenesis has shown that a broadly-conserved packing motif remote from the active site of Tryptophanyl-tRNA synthetases senses the domain configuration and communicates it to the active-site Mg2+ ion, converting it from an inactive to an active position, relative to the triphosphate. This allosteric mechanism accounts for the entire rate acceleration by Mg2+, thus tightly coupling catalysis of ATP utilization to domain motion. We are now studying how differential conformational energetic changes along the structural reaction profile actually mediate this coupling.
Our second focus is the question of how polypeptide catalysts arose. Superposition of crystal structures for all 10 Class I aminoacyl-tRNA synthetases onto the structures of the B. stearothermophilus TrpRS allowed us to identify a 130 residue, disjoint subset containing the intact active site. When we constructed and expressed this "minimal catalytic domain" we found it had 65% of the transition state stabilization free energy of the intact dimeric enzyme, which is five times more massive. We call this and similar constructs "Urzymes" from Ur, the German prefix meaning "primitive, original" plus enzyme. Urzymes afford legitimate experimental models to study how the accumulation of modular genetic information enhanced the catalytic activity, specificity, and intramolecular communication in contemporary enzymes.
Class I and Class II aminoacyl-tRNA synthetases are deeply puzzling because they exhibit no obvious sequence, structural or mechanistic homologies. We have developed strong evidence that the enzymatic activities of Urzymes derived from Class I TrpRS and Class II HisRS are authentic. The explicit location of the original catalytic fragments and their experimental activities together validate predictions derived from the hypothesis advanced by Rodin and Ohno that the two classes were originally encoded by opposite strands of the same gene. The possibility that the earliest genes actually coded for two different polypeptides would substantially change our ideas of how life began and have important implications for the understanding of the contemporary proteome. For this reason, we continue to seek additional evidence regarding the Rodin-Ohno hypothesis
- Weinreb, Violetta, Li, Li, Chandrasekaran, Srinivas Niranj, Koehl, Patrice, Delarue, Marc and Carter, Charles W. 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, 289:4367-4376.
- Li, Li, Francklyn, Christopher and Carter, Charles W. Jr. Protein Synthesis and Degradation: Aminoacylating Urzymes Challenge theRNA World Hypothesis J. Biol. Chem. 2013, 288:26856-26863.
- Li, Li, and Carter, Charles W. Jr. Protein Synthesis and Degradation: Full Implementation of the Genetic Code by Tryptophanyl-tRNA Synthetase Requires Intermodular Coupling J. Biol. Chem. 2013, 288:34736-34745
- Chandrasekaran, Srinivas Niranj , Yardimciz, Galip Gurkan, Erdogan, Ozgun, Roach, Jeffrey and Carter, Charles W. Jr. Statistical Evaluation of the Rodin–Ohno Hypothesis: Sense/Antisense Coding of Ancestral Class I and II Aminoacyl-tRNA Synthetases Mol. Biol. Evol. 30(7):1588–1604
- Weinreb V, Li L, Carter CW Jr. A Master Switch Couples Mg(2+)-Assisted Catalysis to Domain Motion in B. stearothermophilus Tryptophanyl-tRNA Synthetase. Structure. 2012 Jan 11;20(1):128-38. PubMed PMID: 22244762; PubMed Central PMCID: PMC3259537.
- Li L, Weinreb V, Francklyn C, Carter CW Jr. 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 Mar 25;286(12):10387-95. Epub 2011 Jan 26. PubMed PMID: 21270472; PubMed Central PMCID: PMC3060492.
- Pham Y, Kuhlman B, Butterfoss GL, Hu H, Weinreb V, Carter CW Jr. Tryptophanyl-tRNA synthetase Urzyme: a model to recapitulate molecular evolution and investigate intramolecular complementation. J Biol Chem. 2010 Dec 3;285(49):38590-601. Epub 2010 Sep 23. PubMed PMID: 20864539; PubMed Central PMCID: PMC2992291.
- 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. 2010 Mar 15;26(6):709-14. Epub 2010 Feb 3. PubMed PMID: 20130031; PubMed Central PMCID: PMC2852213.
- Carter CW Jr. E pluribus tres: the 2009 nobel prize in chemistry. Structure. 2009 Dec 9;17(12):1558-61. PubMed PMID: 20004159; PubMed Central PMCID: PMC2821081.
- Rodin AS, Rodin SN, Carter CW Jr. On primordial sense-antisense coding. J Mol Evol. 2009 Nov;69(5):555-67. Epub 2009 Dec 3. PubMed PMID: 19956936; PubMed Central PMCID: PMC2853367.
- Weinreb V, Li L, Campbell CL, Kaguni LS, Carter CW Jr. Mg2+-assisted catalysis by B. stearothermophilus TrpRS is promoted by allosteric effects. Structure. 2009 Jul 15;17(7):952-64. PubMed PMID: 19604475; PubMed Central PMCID: PMC2821082.
- Laowanapiban P, Kapustina M, Vonrhein C, Delarue M, Koehl P, Carter CW Jr. Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations. Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1790-5. Epub 2009 Jan 27. PubMed PMID: 19174517; PubMed Central PMCID: PMC2644116.
- Pandya K, Cowhig J, Brackhan J, Kim HS, Hagaman J, Rojas M, Carter CW Jr, Mao L, Rockman HA, Maeda N, Smithies O. Discordant on/off switching of gene expression in myocytes during cardiac hypertrophy in vivo. Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):13063-8. Epub 2008 Aug 28. PubMed PMID: 18755891; PubMed Central PMCID: PMC2526551.
- Carter CW Jr. Whence the genetic code? Thawing the 'frozen accident'. Heredity (Edinb). 2008 Apr;100(4):339-40. Epub 2008 Feb 13. PubMed PMID: 18270531; PubMed Central PMCID: PMC2824342.
- Weinreb V, Carter CW Jr. Mg2+-free Bacillus stearothermophilus tryptophanyl-tRNA synthetase retains a major fraction of the overall rate enhancement for tryptophan activation. J Am Chem Soc. 2008 Jan 30;130(4):1488-94. Epub 2008 Jan 4. PubMed PMID: 18173270; PubMed Central PMCID: PMC2826132.
- Kapustina M, Weinreb V, Li L, Kuhlman B, Carter CW Jr. A conformational transition state accompanies tryptophan activation by B. stearothermophilus tryptophanyl-tRNA synthetase. Structure. 2007 Oct;15(10):1272-84. PubMed PMID: 17937916; PubMed Central PMCID: PMC2693061.
- Retailleau P, Weinreb V, Hu M, Carter CW Jr. Crystal structure of tryptophanyl-tRNA synthetase complexed with adenosine-5' tetraphosphate: evidence for distributed use of catalytic binding energy in amino acid activation by class I aminoacyl-tRNA synthetases. J Mol Biol. 2007 May 25;369(1):108-28. Epub 2007 Mar 12. PubMed PMID: 17428498; PubMed Central PMCID: PMC2715954.
- Pham Y, Li L, Kim A, Erdogan O, Weinreb V, Butterfoss GL, Kuhlman B, Carter CW Jr. A minimal TrpRS catalytic domain supports sense/antisense ancestry of class I and II aminoacyl-tRNA synthetases. Mol Cell. 2007 Mar 23;25(6):851-62. PubMed PMID: 17386262.
- Carter CW Jr, Riès-Kautt M. Improving marginal crystals. Methods Mol Biol. 2007;363:153-74. PubMed PMID: 17272841.