Publications
2024
Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids
Protein Engineering, Design and Selection2024-01-29 | Journal articleDOI: 10.1093/protein/gzae003CONTRIBUTORS: Nandan Haloi; Shan Huang; Aaron L Nichols; Eve J Fine; Nicholas J Friesenhahn; Christopher B Marotta; Dennis A Dougherty; Erik Lindahl; Rebecca J Howard; Stephen L Mayo et al.
2023
CDRxAbs: Antibody Small-Molecule Conjugates with Computationally Designed Target-Binding Synergy
2023-12-20 | PreprintDOI: 10.1101/2023.12.19.572259CONTRIBUTORS: Jingzhou Wang; Aiden J. Aceves; Stephen L. Mayo
Huang, Shan and Wang, Kaihang and Mayo, Stephen L. (2023) Genome manipulation by guide-directed Argonaute cleavage. Nucleic Acids Research, 51 (8). pp. 4078-4085. ISSN 0305-1048. doi:10.1093/nar/gkad188. https://resolver.caltech.edu/CaltechAUTHORS:20230328-708572000.64
Haloi, Nandan and Huang, Shan and Nichols, Aaron N. et al. (2023) Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids. . doi:10.1101/2023.01.16.524298. (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20230316-182493000.35
2021
Huang, Shan and Wang, Kaihang and Mayo, Stephen L. (2021) Guide-directed DNA cleavage by a prokaryotic Argonaute protein induces chromosome recombination in Escherichia coli. . doi:10.1101/2021.11.17.469050. (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20211122-174116390
Breunig, Stephanie and Chapman, Alex and Aceves, Aiden et al. (2021) Modification of Insulin Lispro by Incorporation of Non-canonical Proline Residues. Protein Science, 30 (S1). p. 89. ISSN 0961-8368. doi:10.1002/pro.4191. https://resolver.caltech.edu/CaltechAUTHORS:20211117-181926510
LaPelusa, Michael and Donoviel, Dorit and Branzini, Sergio E. et al. (2021) Microbiome for Mars: surveying microbiome connections to healthcare with implications for long-duration human spaceflight, virtual workshop, July 13, 2020. Microbiome, 9 . Art. No. 2. ISSN 2049-2618. PMCID PMC7781430. https://resolver.caltech.edu/CaltechAUTHORS:20210112-151232385
2019
Oki, Kenji and Lee, Frederick S. and Mayo, Stephen L. (2019) Attempts to develop an enzyme converting DHIV to KIV. Protein Engineering, Design and Selection . ISSN 1741-0126. (In Press) https://resolver.caltech.edu/CaltechAUTHORS:20200102-092224643
Nisthal, Alex and Wang, Connie Y. and Ary, Marie L. et al. (2019) Protein stability engineering insights revealed by domain-wide comprehensive mutagenesis. Proceedings of the National Academy of Sciences of the United States of America, 116 (33). pp. 16367-16377. ISSN 0027-8424.http://resolver.caltech.edu/CaltechAUTHORS:20181207-083716880
Ross, Matthew O. and MacMillan, Fraser and Wang, Jingzhou et al. (2019) Particulate methane monooxygenase contains only mononuclear copper centers. Science, 364 (6440). pp. 566-570. ISSN 0036-8075. http://resolver.caltech.edu/CaltechAUTHORS:20190509-152916236
2018
Wannier, Timothy M. and Gillespie, Sarah K. and Hutchins, Nicholas et al. (2018) Monomerization of Far-Red Fluorescent Proteins. Proceedings of the National Academy of Sciences of the United States of America, 115 (48). E11294-E11301. ISSN 0027-8424. http://resolver.caltech.edu/CaltechAUTHORS:20180105-112949227
Wang, Connie Y. and Chang, Paul M. and Ary, Marie L. et al. (2018) ProtaBank: A repository for protein design and engineering data. Protein Science . ISSN 0961-8368. (In Press)http://resolver.caltech.edu/CaltechAUTHORS:20180402-082750705
2017
Cahn, Jackson K. B. and Werlang, Caroline A. and Baumschlager, Armin et al. (2017) A General Tool for Engineering the NAD/NADP Cofactor Preference of Oxidoreductases. ACS Synthetic Biology, 6 (2). pp. 326-333. ISSN 2161-5063. http://resolver.caltech.edu/CaltechAUTHORS:20161012-112258970
2016
de los Santos, Emmanuel L. C. and Meyerowitz, Joseph T. and Mayo, Stephen L. et al. (2016) Engineering Transcriptional Regulator Effector Specificity using Computational Design and In Vitro Rapid Prototyping: Developing a Vanillin Sensor. ACS Synthetic Biology, 5 (4). pp. 287-295. ISSN 2161-5063.http://resolver.caltech.edu/CaltechAUTHORS:20150303-123633257
Li, Jian and Lawton, Thomas J. and Kostecki, Jan S. et al. (2016) Cell-free protein synthesis enables high yielding synthesis of an active multicopper oxidase. Biotechnology Journal, 11 (2). pp. 212-218. ISSN 1860-7314. http://resolver.caltech.edu/CaltechAUTHORS:20150922-111505818
2015
Mou, Yun and Yu, Jiun-Yann and Wannier, Timothy M. et al. (2015) Computational design of co-assembling protein–DNA nanowires. Nature, 525 (7568). pp. 230-233. ISSN 0028-0836.http://resolver.caltech.edu/CaltechAUTHORS:20150528-195712684
Mou, Yun and Huang, Po-Ssu and Hsu, Fang-Ciao et al. (2015) Computational design and experimental verification of a symmetric protein homodimer. Proceedings of the National Academy of Sciences, 112 (34). pp. 10714-10719. ISSN 0027-8424. PMCID PMC4553821. http://resolver.caltech.edu/CaltechAUTHORS:20150819-123344330
Mou, Yun and Huang, Po-Ssu and Thomas, Leonard M. et al. (2015) Using molecular dynamics simulations as an aid in the prediction of domain swapping of computationally designed protein variants. Journal of Molecular Biology, 427 (16). pp. 2697-2706. ISSN 0022-2836. http://resolver.caltech.edu/CaltechAUTHORS:20150625-151326038
Wannier, Timothy M. and Moore, Matthew M. and Mou, Yun et al. (2015) Computational Design of the β-Sheet Surface of a Red Fluorescent Protein Allows Control of Protein Oligomerization. PLoS ONE, 10 (6). Art. No. e0130582. ISSN 1932-6203. http://resolver.caltech.edu/CaltechAUTHORS:20150623-115009160
2014
Wannier, Timothy M. and Mayo, Stephen L. (2014) The structure of a far-red fluorescent protein, AQ143, shows evidence in support of reported red-shifting chromophore interactions. Protein Science, 23 (8). pp. 1148-1153. ISSN 0961-8368. PMCID PMC4116662. http://resolver.caltech.edu/CaltechAUTHORS:20140610-104728713
2013
Blomberg, Rebecca and Kries, Hajo and Pinkas, Daniel M. et al. (2013) Precision is essential for efficient catalysis in an evolved Kemp eliminase. Nature, 503 (7476). pp. 418-421. ISSN 0028-0836.http://resolver.caltech.edu/CaltechAUTHORS:20131220-135748515
Jaru-Ampornpan, Peera and Liang, Fu-Cheng and Nisthal, Alex et al. (2013) Mechanism of an ATP-independent Protein Disaggregase. II. Distinct Molecular Interactions Drive Multiple Steps During Aggregate Disassembly. Journal of Biological Chemistry, 288 (19). pp. 13431-13445. ISSN 0021-9258. PMCID PMC3650381. http://resolver.caltech.edu/CaltechAUTHORS:20130621-133910862
Chitsaz, Mohsen and Mayo, Stephen L. (2013) GRID: A high-resolution protein structure refinement algorithm.Journal of Computational Chemistry, 34 (6). pp. 445-450. ISSN 0192-8651.http://resolver.caltech.edu/CaltechAUTHORS:20130321-144912093
2012
Moore, Matthew M. and Oteng-Pabi, Samuel K. and Pandelieva, Antonia T. et al. (2012) Recovery of Red Fluorescent Protein Chromophore Maturation Deficiency through Rational Design. PLoS ONE, 7 (12). Art. No. e52463 . ISSN 1932-6203. http://resolver.caltech.edu/CaltechAUTHORS:20130124-083857529
Alvizo, Oscar and Mittal, Seema and Mayo, Stephen L. et al. (2012) Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease. Protein Science, 21 (7). pp. 1029-1041. ISSN 0961-8368.http://resolver.caltech.edu/CaltechAUTHORS:20120712-085217104
Chen, Mike M. Y. and Snow, Christopher D. and Vizcarra, Christina L. et al. (2012) Comparison of random mutagenesis and semi-rational designed libraries for improved cytochrome P450 BM3-catalyzed hydroxylation of small alkanes. Protein Engineering, Design and Selection, 25 (4). pp. 171-178. ISSN 1741-0126.http://resolver.caltech.edu/CaltechAUTHORS:20120420-110357141
Privett, Heidi K. and Kiss, Gert and Lee, Toni M. et al. (2012) Iterative approach to computational enzyme design. Proceedings of the National Academy of Sciences of the United States of America, 109 (10). pp. 3790-3795. ISSN 0027-8424. PMCID PMC3309769. http://resolver.caltech.edu/CaltechAUTHORS:20120326-153311623
2011
Lee, Toni M. and Farrow, Mary F. and Arnold, Frances H. et al. (2011) A structural study of Hypocrea jecorina Cel5A. Protein Science, 20 (11). pp. 1935-1940. ISSN 0961-8368.http://resolver.caltech.edu/CaltechAUTHORS:20111111-135716977
Keeffe, Jennifer R. and Gnanapragasam, Priyanthi N. P. and Gillespie, Sarah K. et al. (2011) Designed oligomers of cyanovirin-N show enhanced HIV neutralization. Proceedings of the National Academy of Sciences of the United States of America, 108 (34). pp. 14079-14084. ISSN 0027-8424. PMCID PMC3161612.http://resolver.caltech.edu/CaltechAUTHORS:20110913-132623950
Zhang, Xin and Lam, Vinh Q. and Mou, Yun et al. (2011) Direct visualization reveals dynamics of a transient intermediate during protein assembly. Proceedings of the National Academy of Sciences of the United States of America, 108 (16). pp. 6450-6455. ISSN 0027-8424. PMCID PMC3081034.http://resolver.caltech.edu/CaltechAUTHORS:20110511-090620791
Hemmert, Andrew C. and Otto, Tamara C. and Chica, Roberto A. et al. (2011) Nerve Agent Hydrolysis Activity Designed into a Human Drug Metabolism Enzyme. PLoS ONE, 6 (3). Art. No. e17441. ISSN 1932-6203.http://resolver.caltech.edu/CaltechAUTHORS:20110404-094940641
2010
Chica, Roberto A. and Moore, Matthew M. and Allen, Benjamin D. et al. (2010) Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries. Proceedings of the National Academy of Sciences of the United States of America, 107 (47). pp. 20257-20262. ISSN 0027-8424.http://resolver.caltech.edu/CaltechAUTHORS:20101213-155449831
Allen, Benjamin D. and Nisthal, Alex and Mayo, Stephen L. (2010) Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles. Proceedings of the National Academy of Sciences of the United States of America, 107 (46). pp. 19838-19843. ISSN 0027-8424.http://resolver.caltech.edu/CaltechAUTHORS:20101213-150517069
Allen, Benjamin D. and Mayo, Stephen L. (2010) An efficient algorithm for multistate protein design based on FASTER. Journal of Computational Chemistry, 31 (5). pp. 904-916. ISSN 0192-8651.http://resolver.caltech.edu/CaltechAUTHORS:20100409-095211072
2008
Crowhurst, Karin A. and Mayo, Stephen L. (2008) NMR-detected conformational exchange observed in a computationally designed variant of protein Gβ1. Protein Engineering, Design and Selection, 21 (9). pp. 577-587. ISSN 1741-0126. http://resolver.caltech.edu/CaltechAUTHORS:20090515-095406688
Alvizo, Oscar and Mayo, Stephen L. (2008) Evaluating and optimizing computational protein design force fields using fixed composition-based negative design. Proceedings of the National Academy of Sciences of the United States of America, 105 (34). pp. 12242-12247. ISSN 0027-8424.http://resolver.caltech.edu/CaltechAUTHORS:ALVpnas08
Vizcarra, Christina L. and Zhang, Naigong and Marshall, Shannon A. et al. (2008) An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design. Journal of Computational Chemistry, 29 (7). pp. 1153-1162. ISSN 0192-8651.http://resolver.caltech.edu/CaltechAUTHORS:20110617-165335622
2007
Huang, Po-Ssu and Love, John J and Mayo, Stephen L. (2007) A de novo designed protein-protein interface.Protein Science, 16 (12). pp. 2770-2774. ISSN 0961-8368.http://resolver.caltech.edu/CaltechAUTHORS:20110913-160000725
Shah, Premal S. and Hom, Geoffrey K and Ross, Scott A. et al. (2007) Full-sequence computational design and solution structure of a thermostable protein variant. Journal of Molecular Biology, 372 (1). pp. 1-6. ISSN 0022-2836. http://resolver.caltech.edu/CaltechAUTHORS:20110913-160001277
Plückthun, Andreas and Mayo, Stephen L. (2007) The design of evolution and the evolution of design. Current Opinion in Structural Biology, 17 (4). pp. 451-453. ISSN 0959-440X.http://resolver.caltech.edu/CaltechAUTHORS:20110913-160001099
Lassila, Jonathan Kyle and Keeffe, Jennifer R. and Kast, Peter et al. (2007) Exhaustive mutagenesis of six secondary active-site residues in Escherichia coli chorismate mutase shows the importance of hydrophobic side chains and a helix N-capping position for stability and catalysis. Biochemistry, 46 (23). pp. 6883-6891. ISSN 0006-2960. http://resolver.caltech.edu/CaltechAUTHORS:20110913-160001644
Choi, Eun Jung and Mao, Jessica and Mayo, Stephen L. (2007) Computational design and biochemical characterization of maize nonspecific lipid transfer protein variants for biosensor applications. Protein Science, 16 (4). pp. 582-588. ISSN 0961-8368. http://resolver.caltech.edu/CaltechAUTHORS:20110614-141918849
Zong, Chenghang and Wilson, Corey J. and Shen, Tongye et al. (2007) Establishing the entatic state in folding metallated Pseudomonas aeruginosa azurin. Proceedings of the National Academy of Sciences of the United States of America, 104 (9). pp. 3159-3164. ISSN 0027-8424.http://resolver.caltech.edu/CaltechAUTHORS:ZONpnas07
Treynor, Thomas P. and Vizcarra, Christina L. and Nedelcu, Daniel et al. (2007) Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function. Proceedings of the National Academy of Sciences of the United States of America, 104 (1). pp. 48-53. ISSN 0027-8424.http://resolver.caltech.edu/CaltechAUTHORS:TREpnas07
Alvizo, Oscar and Allen, Benjamin D. and Mayo, Stephen L. (2007) Computational protein design promises to revolutionize protein engineering. BioTechniques, 42 (1). pp. 31-39. ISSN 0736-6205.http://resolver.caltech.edu/CaltechAUTHORS:20110913-152351498
2006
Mena, Marco A. and Treynor, Thomas P. and Mayo, Stephen L. et al. (2006) Blue fluorescent proteins with enhanced brightness and photostability from a structurally targeted library. Nature Biotechnology, 24 (12). pp. 1569-1571. ISSN 1087-0156. http://resolver.caltech.edu/CaltechAUTHORS:20110620-160435158
Lassila, Jonathan Kyle and Privett, Heidi K. and Allen, Benjamin D. et al. (2006) Combinatorial methods for small-molecule placement in computational enzyme design. Proceedings of the National Academy of Sciences of the United States of America, 103 (45). pp. 16710-16715. ISSN 0027-8424.http://resolver.caltech.edu/CaltechAUTHORS:LASpnas06
Shifman, Julia M. and Choi, Mee H. and Mihalas, Stefan et al. (2006) Ca2+/calmodulin-dependent protein kinase II (CaMKII) is activated by calmodulin with two bound calciums. Proceedings of the National Academy of Sciences of the United States of America, 103 (38). pp. 13968-13973. ISSN 0027-8424. PMCID PMC1599897.http://resolver.caltech.edu/CaltechAUTHORS:SHIpnas06b
Zollars, Eric S. and Marshall, Shannon A. and Mayo, Stephen L. (2006) Simple electrostatic model improves designed protein sequences. Protein Science, 15 (8). pp. 2014-2018. ISSN 0961-8368.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160436627
Allen, Benjamin D. and Mayo, Stephen L. (2006) Dramatic performance enhancements for the FASTER optimization algorithm. Journal of Computational Chemistry, 27 (10). pp. 1071-1075. ISSN 0192-8651.http://resolver.caltech.edu/CaltechAUTHORS:20110913-165232651
Choi, Eun Jung and Mayo, Stephen L (2006) Generation and analysis of proline mutants in protein G. Protein Engineering, Design and Selection, 19 (6). pp. 285-289. ISSN 1741-0126.http://peds.oxfordjournals.org/content/19/6/285.long
Hom, Geoffrey K. and Mayo, Stephen L. (2006) A search algorithm for fixed-composition protein design. Journal of Computational Chemistry, 27 (3). pp. 375-378. ISSN 0192-8651.http://resolver.caltech.edu/CaltechAUTHORS:20110913-173427297
2005
Vizcarra, Christina L. and Mayo, Stephen L. (2005) Electrostatics in computational protein design. Current Opinion in Chemical Biology, 9 (6). pp. 622-626. ISSN 1367-5931.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160432503
Huang, Po-Ssu and Love, John J. and Mayo, Stephen L. (2005) Adaptation of a fast Fourier transform-based docking algorithm for protein design. Journal of Computational Chemistry, 26 (12). pp. 1222-1232. ISSN 0192-8651. http://resolver.caltech.edu/CaltechAUTHORS:20111004-074354772
Oelschlaeger, Peter and Mayo, Stephen L. (2005) Hydroxyl groups in the ββ sandwich of metallo-β-lactamases favor enzyme activity: a computational protein design study. Journal of Molecular Biology, 350 (3). pp. 395-401. ISSN 0022-2836. http://resolver.caltech.edu/CaltechAUTHORS:20110620-160427419
Marshall, Shannon A. and Vizcarra, Christina L. and Mayo, Stephen L. (2005) One- and two-body decomposable Poisson-Boltzmann methods for protein design calculations. Protein Science, 14 (5). pp. 1293-1304. ISSN 0961-8368. http://resolver.caltech.edu/CaltechAUTHORS:20110620-160427069
Lassila, Jonathan Kyle and Keeffe, Jennifer R. and Oelschlaeger, Peter et al. (2005) Computationally designed variants of Escherichia coli chorismate mutase show altered catalytic activity. Protein Engineering, Design and Selection, 18 (4). pp. 161-163. ISSN 1741-0126. http://resolver.caltech.edu/CaltechAUTHORS:LASpeds05
Hom, Geoffrey K. and Lassila, J. Kyle and Thomas, Leonard M. et al. (2005) Dioxane contributes to the altered conformation and oligomerization state of a designed engrailed homeodomain variant. Protein Science, 14 (4). pp. 1115-1119. ISSN 0961-8368. http://resolver.caltech.edu/CaltechAUTHORS:20110620-160432981
Oelschlaeger, Peter and Mayo, Stephen L. and Pleiss, Juergen (2005) Impact of remote mutations on metallo-β-lactamase substrate specificity: implications for the evolution of antibiotic resistance. Protein Science, 14 (3). pp. 765-774. ISSN 0961-8368. http://resolver.caltech.edu/CaltechAUTHORS:20110913-173427641
2004
Shah, Premal S. and Hom, Geoffrey K. and Mayo, Stephen L. (2004) Preprocessing of rotamers for protein design calculations. Journal of Computational Chemistry, 25 (14). pp. 1797-1800. ISSN 0192-8651.http://resolver.caltech.edu/CaltechAUTHORS:20110913-173425840
Shukla, Ushma J. and Marino, Heather and Huang, Po-Ssu et al. (2004) A designed protein interface that blocks fibril formation. Journal of the American Chemical Society, 126 (43). pp. 13914-13915. ISSN 0002-7863.http://resolver.caltech.edu/CaltechAUTHORS:20110913-173424834
2003
Shifman, Julia M. and Mayo, Stephen L. (2003) Exploring the origins of binding specificity through the computational redesign of calmodulin. Proceedings of the National Academy of Sciences of the United States of America, 100 (23). pp. 13274-13279. ISSN 0027-8424.http://resolver.caltech.edu/CaltechAUTHORS:SHIpnas03
Mooers, Blaine H. M. and Datta, Deepshikha and Baase, Walter A. et al. (2003) Repacking the Core of T4 lysozyme by automated design. Journal of Molecular Biology, 332 (3). pp. 741-756. ISSN 0022-2836.http://resolver.caltech.edu/CaltechAUTHORS:20110913-173426073
Lazar, Greg A. and Marshall, Shannon A. and Plecs, Joseph J. et al. (2003) Designing proteins for therapeutic applications. Current Opinion in Structural Biology, 13 (4). pp. 513-518. ISSN 0959-440X.http://resolver.caltech.edu/CaltechAUTHORS:20110913-173425194
Meyer, Michelle M. and Silberg, Jonathan J. and Voigt, Christopher A. et al. (2003) Library analysis of SCHEMA-guided protein recombination. Protein Science, 12 (8). pp. 1686-1693. ISSN 0961-8368.http://resolver.caltech.edu/CaltechAUTHORS:20110913-173426256
Gillespie, Blake and Vu, Dung M. and Shah, Premal S. et al. (2003) NMR and temperature-jump measurements of de novo designed proteins demonstrate rapid folding in the absence of explicit selection for kinetics. Journal of Molecular Biology, 330 (4). pp. 813-819. ISSN 0022-2836.http://resolver.caltech.edu/CaltechAUTHORS:20110913-173426521
Bolon, Daniel N. and Marcus, Joshua S. and Ross, Scott A. et al. (2003) Prudent modeling of core polar residues in computational protein design. Journal of Molecular Biology, 329 (3). pp. 611-622. ISSN 0022-2836.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160434663
Gordon, D. Benjamin and Hom, Geoffrey K. and Mayo, Stephen L. et al. (2003) Exact rotamer optimization for protein design. Journal of Computational Chemistry, 24 (2). pp. 232-243. ISSN 0192-8651.http://resolver.caltech.edu/CaltechAUTHORS:20110913-173425474
Offredi, F. and Dubail, F. and Kischel, P. et al. (2003) De novo backbone and sequence design of an idealized α/β-barrel protein: evidence of stable tertiary structure. Journal of Molecular Biology, 325 (1). pp. 163-174. ISSN 0022-2836. http://resolver.caltech.edu/CaltechAUTHORS:20110913-173426926
2002
Shifman, Julia M. and Mayo, Stephen L. (2002) Modulating calmodulin binding specificity through computational protein design. Journal of Molecular Biology, 323 (3). pp. 417-423. ISSN 0022-2836.http://resolver.caltech.edu/CaltechAUTHORS:20110928-154513858
Datta, Deepshikha and Mayo, Stephen L. (2002) A designed apoplastocyanin variant that shows reversible folding. Biochemical and Biophysical Research Communications, 296 (4). pp. 988-990. ISSN 0006-291X.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160423337
Desjarlais, John R. and Mayo, Stephen L. (2002) Engineering and design computational protein design - Editorial overview. Current Opinion in Structural Biology, 12 (4). pp. 429-430. ISSN 0959-440X.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160422247
Voigt, Christopher A. and Martinez, Carlos and Wang, Zhen-Gang et al. (2002) Protein building blocks preserved by recombination. Nature Structural Biology, 9 (7). pp. 553-558. ISSN 1072-8368 .http://resolver.caltech.edu/CaltechAUTHORS:20110927-143229047
Datta, Deepshikha and Wang, Pin and Carrico, Isaac S. et al. (2002) A designed phenylalanyl-tRNA synthetase variant allows efficient in vivo incorporation of aryl ketone functionality into proteins. Journal of the American Chemical Society, 124 (20). pp. 5652-5653. ISSN 0002-7863.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160431532
Bolon, Daniel N. and Voigt, Christopher A. and Mayo, Stephen L. (2002) De novo design of biocatalysts. Current Opinion in Chemical Biology, 6 (2). pp. 125-129. ISSN 1367-5931.http://resolver.caltech.edu/CaltechAUTHORS:20110928-152719152
Lassila, Kirsten S. and Datta, Deepshikha and Mayo, Stephen L. (2002) Evaluation of the energetic contribution of an ionic network to beta-sheet stability. Protein Science, 11 (3). pp. 688-690. ISSN 0961-8368.http://resolver.caltech.edu/CaltechAUTHORS:20110928-153816383
Marshall, Shannon A. and Morgan, Chantal S. and Mayo, Stephen L. (2002) Electrostatics significantly affect the stability of designed homeodomain variants. Journal of Molecular Biology, 316 (1). pp. 189-199. ISSN 0022-2836. http://resolver.caltech.edu/CaltechAUTHORS:20110927-135624170
2001
Bolon, Daniel N. and Mayo, Stephen L. (2001) Enzyme-like proteins by computational design. Proceedings of the National Academy of Sciences of the United States of America, 98 (25). pp. 14274-14279. ISSN 0027-8424.http://resolver.caltech.edu/CaltechAUTHORS:BOLpnas01
Bolon, Daniel N. and Mayo, Stephen L. (2001) Polar residues in the protein core of Escherichia coli thioredoxin are important for fold specificity. Biochemistry, 40 (34). pp. 10047-10053. ISSN 0006-2960.http://resolver.caltech.edu/CaltechAUTHORS:20110928-133003644
Sarisky, Catherine A. and Mayo, Stephen L. (2001) The ββα fold: explorations in sequence space. Journal of Molecular Biology, 307 (5). pp. 1411-1418. ISSN 0022-2836.http://resolver.caltech.edu/CaltechAUTHORS:20111003-155045528
Voigt, Christopher A. and Mayo, Stephen L. and Arnold, Frances H. et al. (2001) Computational method to reduce the search space for directed protein evolution. Proceedings of the National Academy of Sciences of the United States of America, 98 (7). pp. 3778-3783. ISSN 0027-8424.http://resolver.caltech.edu/CaltechAUTHORS:VOIpnas01
Ross, Scott A. and Sarisky, Catherine A. and Su, Alyce et al. (2001) Designed protein G core variants fold to native-like structures: sequence selection by ORBIT tolerates variation in backbone specification. Protein Science, 10 (2). pp. 450-454. ISSN 0961-8368. http://resolver.caltech.edu/CaltechAUTHORS:20110621-075054655
Marshall, Shannon A. and Mayo, Stephen L. (2001) Achieving stability and conformational specificity in designed proteins via binary patterning. Journal of Molecular Biology, 305 (3). pp. 619-631. ISSN 0022-2836.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160433490
Voigt, Christopher A. and Mayo, Stephen L. and Arnold, Frances H. et al. (2001) Computationally Focusing the Directed Evolution of Proteins. Journal of Cellular Biochemistry, 84 (S37). pp. 58-63. ISSN 0730-2312.http://resolver.caltech.edu/CaltechAUTHORS:20110927-154155139
2000
Shimaoka, Motomu and Shifman, Julia M. and Jing, Hua et al. (2000) Computational design of an integrin I domain stabilized in the open high affinity conformation. Nature Structural Biology, 7 (8). pp. 674-678. ISSN 1072-8368 . http://www.nature.com/doifinder/10.1038/77978
Pierce, Niles A. and Spriet, Jan A. and Desmet, Johan et al. (2000) Conformational splitting: a more powerful criterion for dead-end elimination. Journal of Computational Chemistry, 21 (11). pp. 999-1009. ISSN 0192-8651.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160432187
Strop, Pavel and Marinescu, Andrei M. and Mayo, Stephen L. (2000) Structure of a protein G helix variant suggests the importance of helix propensity and helix dipole interactions in protein design. Protein Science, 9 (7). pp. 1391-1394. ISSN 0961-8368. http://resolver.caltech.edu/CaltechAUTHORS:20110620-160435792
Voigt, Christopher A. and Gordon, D. Benjamin and Mayo, Stephen L. (2000) Trading accuracy for speed: a quantitative comparison of search algorithms in protein sequence design. Journal of Molecular Biology, 299 (3). pp. 789-803. ISSN 0022-2836. http://resolver.caltech.edu/CaltechAUTHORS:20110620-160433649
Street, Arthur G. and Datta, Deepshikha and Gordon, D. Benjamin et al. (2000) Designing protein β-sheet surfaces by Z-score optimization. Physical Review Letters, 84 (21). pp. 5010-5013. ISSN 0031-9007.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160435469
Strop, Pavel and Mayo, Stephen L. (2000) Contribution of surface salt bridges to protein stability. Biochemistry, 39 (6). pp. 1251-1255. ISSN 0006-2960. http://resolver.caltech.edu/CaltechAUTHORS:20110620-160425030
1999
Gordon, D. Benjamin and Mayo, Stephen L. (1999) Branch-and-terminate: a combinatorial optimization algorithm for protein design. Structure, 7 (9). pp. 1089-1098. ISSN 0969-2126.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160432352
Street, Arthur G. and Mayo, Stephen L. (1999) Intrinsic beta -sheet propensities result from van der Waals interactions between side chains and the local backbone. Proceedings of the National Academy of Sciences of the United States of America, 96 (16). pp. 9074-9076. ISSN 0027-8424.http://resolver.caltech.edu/CaltechAUTHORS:STRpnas99
Gordon, D. Benjamin and Marshall, Shannon A. and Mayo, Stephen L. (1999) Energy functions for protein design. Current Opinion in Structural Biology, 9 (4). pp. 509-513. ISSN 0959-440X.http://resolver.caltech.edu/CaltechAUTHORS:20110621-154505395
Street, Arthur G. and Mayo, Stephen L. (1999) Computational protein design. Structure, 7 (5). R105-R109. ISSN 0969-2126. http://resolver.caltech.edu/CaltechAUTHORS:20110620-160435008
Strop, Pavel and Mayo, Stephen L. (1999) Rubredoxin Variant Folds without Iron. Journal of the American Chemical Society, 121 (11). pp. 2341-2345. ISSN 0002-7863.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160421544
1998
Street, Arthur G. and Mayo, Stephen L. (1998) Pairwise calculation of protein solvent-accessible surface areas.Folding and Design, 3 (4). pp. 253-258. ISSN 1359-0278.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160423998
Malakauskas, Sandra M. and Mayo, Stephen L. (1998) Design, structure and stability of a hyperthermophilic protein variant. Nature Structural Biology, 5 (6). pp. 470-475. ISSN 1072-8368 .http://resolver.caltech.edu/CaltechAUTHORS:20110620-160422818
Bökenkamp, Dirk and Desai, Amish and Yang, Xing et al. (1998) Microfabricated Silicon Mixers for Submillisecond Quench-Flow Analysis. Analytical Chemistry, 70 (2). pp. 232-236. ISSN 0003-2700.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160422644
1997
Dahiyat, Bassil I. and Sarisky, Catherine A. and Mayo, Stephen L. (1997) De novo protein design: towards fully automated sequence selection. Journal of Molecular Biology, 273 (4). pp. 789-796. ISSN 0022-2836.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160423493
Dahiyat, Bassil I. and Mayo, Stephen L. (1997) De novo protein design: fully automated sequence selection.Science, 278 (5335). pp. 82-87. ISSN 0036-8075. http://resolver.caltech.edu/CaltechAUTHORS:20110928-132632399
Dahiyat, Bassil I. and Mayo, Stephen L. (1997) Probing the role of packing specificity in protein design.Proceedings of the National Academy of Sciences of the United States of America, 94 (19). pp. 10172-10177. ISSN 0027-8424. http://resolver.caltech.edu/CaltechAUTHORS:DAHpnas97
Morgan, Chantal S. and Holton, James M. and Olafson, Barry D. et al. (1997) Circular dichroism determination of class I MHC-peptide equilibrium dissociation constants. Protein Science, 6 (8). pp. 1771-1773. ISSN 0961-8368. PMCID PMC2143769. http://resolver.caltech.edu/CaltechAUTHORS:20110620-160424679
Su, Alyce and Mayo, Stephen L. (1997) Coupling backbone flexibility and amino acid sequence selection in protein design. Protein Science, 6 (8). pp. 1701-1707. ISSN 0961-8368.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160424464
Dahiyat, Bassil I. and Gordon, D. Benjamin and Mayo, Stephen L. (1997) Automated design of the surface positions of protein helices. Protein Science, 6 (6). pp. 1333-1337. ISSN 0961-8368.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160427729
Desai, Amish and Bökenkamp, Dirk and Yang, Xing et al. (1997) Microfluidic sub-millisecond mixers for the study of chemical reaction kinetics. In: Transducers '97: Digest of Technical Papers. IEEE , Piscataway, NJ, pp. 167-170. ISBN 0-7803-3829-4 http://resolver.caltech.edu/CaltechAUTHORS:20110620-160422991
1996
Dahiyat, Bassil I. and Mayo, Stephen L. (1996) Protein design automation. Protein Science, 5 (5). pp. 895-903. ISSN 0961-8368. http://resolver.caltech.edu/CaltechAUTHORS:20110620-160429268
Dahiyat, Bassil I. and Meade, Thomas J. and Mayo, Stephen L. (1996) Site-specific modification of α-helical peptides with electron donors and acceptors. Inorganica Chimica Acta, 243 (1-2). pp. 207-212. ISSN 0020-1693. http://resolver.caltech.edu/CaltechAUTHORS:20110620-160429999
Su, Alyce and Mager, Sela and Mayo, Stephen L. et al. (1996) A multi-substrate single-file model for ion-coupled transporters. Biophysical Journal, 70 (2). pp. 762-777. ISSN 0006-3495.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160434844
1994
Qian, Hong and Mayo, Stephen L. and Morton, Andrew (1994) Protein hydrogen exchange in denaturant: quantitative analysis by a two-process model. Biochemistry, 33 (27). pp. 8167-8171. ISSN 0006-2960.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160428085
1993
Mayo, Stephen L. and Baldwin, Robert L. (1993) Guanidinium chloride induction of partial unfolding in amide proton exchange in RNase A. Science, 262 (5135). pp. 873-876. ISSN 0036-8075.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160428244
1990
Mayo, Stephen L. and Olafson, Barry D. and Goddard, William A., III (1990) DREIDING: A generic force field for molecular simulations. Journal of Physical Chemistry, 94 (26). pp. 8897-8909. ISSN 0022-3654 .http://resolver.caltech.edu/CaltechAUTHORS:20110620-160435314
1989
Bowler, Bruce E. and Meade, Thomas J. and Mayo, Stephen L. et al. (1989) Long-range electron transfer in structurally engineered pentaammineruthenium (histidine-62) cytochrome c. Journal of the American Chemical Society, 111 (23). pp. 8757-8759. ISSN 0002-7863. http://resolver.caltech.edu/CaltechAUTHORS:20110620-160433811
Maryanoff, Bruce E. and McComsey, David F. and Inners, Ruth R. et al. (1989) Stereochemical studies on protonated bridgehead amines. ^1H NMR determination of cis and trans B-C ring-fused structures for salts of hexahydropyrrolo [2,1-a] isoquinolines and related C ring homologs. Capture of unstable ring-fused structures in the solid state. Journal of the American Chemical Society, 111 (7). pp. 2487-2496. ISSN 0002-7863.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160436278
1988
Haddon, R. C. and Chichester-Hicks, S. V. and Mayo, Stephen L. (1988) Phenalene-phosphazene complexes: effect of exocyclic charge densities on the cyclotriphosphazene ring system. Inorganic Chemistry, 27 (11). pp. 1911-1915. ISSN 0020-1669. http://resolver.caltech.edu/CaltechAUTHORS:20110928-144707183
Axup, Andrew W. and Albin, Michael and Mayo, Stephen L. et al. (1988) Distance dependence of photoinduced long-range electron transfer in zinc/ruthenium-modified myoglobins. Journal of the American Chemical Society, 110 (2). pp. 435-439. ISSN 0002-7863. http://resolver.caltech.edu/CaltechAUTHORS:20110620-160435945
1986
Mayo, Stephen L. and Ellis, Walther R., Jr. and Crutchley, Robert J. et al. (1986) Long-range electron transfer in heme proteins. Science, 233 (4767). pp. 948-952. ISSN 0036-8075.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160434289
1985
Brunschwig, Bruce S. and DeLaive, Patricia J. and English, Ann M. et al. (1985) Kinetics and mechanisms of electron transfer between blue copper proteins and electronically excited chromium and ruthenium polypyridine complexes. Inorganic Chemistry, 24 (23). pp. 3743-3749. ISSN 0020-1669.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160433152
Haddon, R. C. and Chichester, S. V. and Mayo, Stephen L. (1985) Direct Amination of 9-Hydroxy-1-oxophenalene to Produce 9-Amino-1-oxophenalene and Related Compounds. Synthesis-Stuttgart, 1985 (6-7). pp. 639-641. ISSN 0039-7881. http://resolver.caltech.edu/CaltechAUTHORS:20110928-141129059
1984
Bemis, Guy W. and Whittle, Robert R. and Mayo, Stephen L. et al. (1984) 1,3,4,6-Tetramethyl-1,4-dihydro-1,2,4,5-tetrazine, C_6H_(12)N_4. Acta Crystallographica Section C, 40 (12). pp. 2076-2078. ISSN 0108-2701.http://resolver.caltech.edu/CaltechAUTHORS:20110620-160432815