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Homme W. Hellinga - Publications

Affiliations: 
Duke University, Durham, NC 
Area:
Biochemistry
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80 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Allert MJ, Kumar S, Wang Y, Beese LS, Hellinga HW. Accurate identification of periplasmic urea-binding proteins by structure- and genome context-assisted functional analysis. Journal of Molecular Biology. 168780. PMID 39241982 DOI: 10.1016/j.jmb.2024.168780  0.433
2023 Allert MJ, Kumar S, Wang Y, Beese LS, Hellinga HW. Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching. Communications Chemistry. 6: 168. PMID 37598249 DOI: 10.1038/s42004-023-00982-7  0.424
2022 Allert MJ, Hellinga HW. Discovery of Thermostable, Fluorescently Responsive Glucose Biosensors by Structure-Assisted Function Extrapolation. Biochemistry. 61: 276-293. PMID 35084821 DOI: 10.1021/acs.biochem.1c00738  0.317
2020 Allert MJ, Hellinga HW. Harnessing environmental Ca for extracellular protein thermostabilization. Biochemistry. PMID 32915552 DOI: 10.1021/Acs.Biochem.0C00449  0.385
2020 Allert MJ, Hellinga HW. Describing complex structure-function relationships in biomolecules at equilibrium. Journal of Molecular Biology. PMID 31940471 DOI: 10.1016/J.Jmb.2019.12.039  0.461
2017 Shi Y, Hellinga HW, Beese LS. Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I. Proceedings of the National Academy of Sciences of the United States of America. PMID 28533382 DOI: 10.1073/Pnas.1704845114  0.37
2014 Mabanglo MF, Hast MA, Lubock NB, Hellinga HW, Beese LS. Crystal structures of the fungal pathogen Aspergillus fumigatus protein farnesyltransferase complexed with substrates and inhibitors reveal features for antifungal drug design. Protein Science : a Publication of the Protein Society. 23: 289-301. PMID 24347326 DOI: 10.1002/Pro.2411  0.484
2013 Grimley JS, Li L, Wang W, Wen L, Beese LS, Hellinga HW, Augustine GJ. Visualization of synaptic inhibition with an optogenetic sensor developed by cell-free protein engineering automation. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 33: 16297-309. PMID 24107961 DOI: 10.1523/Jneurosci.4616-11.2013  0.361
2012 Wang W, Wu EY, Hellinga HW, Beese LS. Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides. The Journal of Biological Chemistry. 287: 28215-26. PMID 22648417 DOI: 10.1074/Jbc.M112.366609  0.401
2011 Hast MA, Nichols CB, Armstrong SM, Kelly SM, Hellinga HW, Alspaugh JA, Beese LS. Structures of Cryptococcus neoformans protein farnesyltransferase reveal strategies for developing inhibitors that target fungal pathogens. The Journal of Biological Chemistry. 286: 35149-62. PMID 21816822 DOI: 10.1074/Jbc.M111.250506  0.355
2011 Layton CJ, Hellinga HW. Integration of cell-free protein coexpression with an enzyme-linked immunosorbent assay enables rapid analysis of protein-protein interactions directly from DNA. Protein Science : a Publication of the Protein Society. 20: 1432-8. PMID 21674663 DOI: 10.1002/Pro.675  0.79
2011 Layton CJ, Hellinga HW. Quantitation of protein-protein interactions by thermal stability shift analysis. Protein Science : a Publication of the Protein Society. 20: 1439-50. PMID 21674662 DOI: 10.1002/Pro.674  0.785
2011 Orans J, McSweeney EA, Iyer RR, Hast MA, Hellinga HW, Modrich P, Beese LS. Structures of human exonuclease 1 DNA complexes suggest a unified mechanism for nuclease family. Cell. 145: 212-23. PMID 21496642 DOI: 10.1016/J.Cell.2011.03.005  0.369
2011 Isom DG, Marguet PR, Oas TG, Hellinga HW. A miniaturized technique for assessing protein thermodynamics and function using fast determination of quantitative cysteine reactivity. Proteins. 79: 1034-47. PMID 21387407 DOI: 10.1002/Prot.22932  0.525
2011 Antunes MS, Morey KJ, Smith JJ, Albrecht KD, Bowen TA, Zdunek JK, Troupe JF, Cuneo MJ, Webb CT, Hellinga HW, Medford JI. Programmable ligand detection system in plants through a synthetic signal transduction pathway. Plos One. 6: e16292. PMID 21283542 DOI: 10.1371/Journal.Pone.0016292  0.7
2010 Layton CJ, Hellinga HW. Thermodynamic analysis of ligand-induced changes in protein thermal unfolding applied to high-throughput determination of ligand affinities with extrinsic fluorescent dyes. Biochemistry. 49: 10831-41. PMID 21050007 DOI: 10.1021/Bi101414Z  0.788
2010 Allert M, Cox JC, Hellinga HW. Multifactorial determinants of protein expression in prokaryotic open reading frames. Journal of Molecular Biology. 402: 905-18. PMID 20727358 DOI: 10.1016/J.Jmb.2010.08.010  0.346
2010 Isom DG, Vardy E, Oas TG, Hellinga HW. Picomole-scale characterization of protein stability and function by quantitative cysteine reactivity. Proceedings of the National Academy of Sciences of the United States of America. 107: 4908-13. PMID 20194783 DOI: 10.1073/Pnas.0910421107  0.53
2009 Cuneo MJ, Beese LS, Hellinga HW. Structural analysis of semi-specific oligosaccharide recognition by a cellulose-binding protein of thermotoga maritima reveals adaptations for functional diversification of the oligopeptide periplasmic binding protein fold. The Journal of Biological Chemistry. 284: 33217-23. PMID 19801540 DOI: 10.1074/Jbc.M109.041624  0.768
2009 Cuneo MJ, Changela A, Beese LS, Hellinga HW. Structural adaptations that modulate monosaccharide, disaccharide, and trisaccharide specificities in periplasmic maltose-binding proteins. Journal of Molecular Biology. 389: 157-66. PMID 19361522 DOI: 10.1016/J.Jmb.2009.04.008  0.767
2008 Cuneo MJ, Beese LS, Hellinga HW. Ligand-induced conformational changes in a thermophilic ribose-binding protein. Bmc Structural Biology. 8: 50. PMID 19019243 DOI: 10.1186/1472-6807-8-50  0.757
2008 Smith AJ, Müller R, Toscano MD, Kast P, Hellinga HW, Hilvert D, Houk KN. Structural reorganization and preorganization in enzyme active sites: comparisons of experimental and theoretically ideal active site geometries in the multistep serine esterase reaction cycle. Journal of the American Chemical Society. 130: 15361-73. PMID 18939839 DOI: 10.1021/Ja803213P  0.349
2008 Cuneo MJ, Changela A, Miklos AE, Beese LS, Krueger JK, Hellinga HW. Structural analysis of a periplasmic binding protein in the tripartite ATP-independent transporter family reveals a tetrameric assembly that may have a role in ligand transport. The Journal of Biological Chemistry. 283: 32812-20. PMID 18723845 DOI: 10.1074/Jbc.M803595200  0.785
2008 Cuneo MJ, Tian Y, Allert M, Hellinga HW. The backbone structure of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein is essentially identical to its mesophilic E. coli homolog. Bmc Structural Biology. 8: 20. PMID 18373848 DOI: 10.1186/1472-6807-8-20  0.702
2008 Dwyer MA, Looger LL, Hellinga HW. Retraction. Science (New York, N.Y.). 319: 569. PMID 18239106 DOI: 10.1126/science.319.5863.569b  0.473
2008 Allert M, Dwyer MA, Hellinga HW. Retraction of “Local Encoding of Computationally Designed Enzyme Activity” [J. Mol. Biol. 366 (2007) 945–953] Journal of Molecular Biology. 378: 759. DOI: 10.1016/J.Jmb.2008.02.048  0.579
2007 Tian Y, Cuneo MJ, Changela A, Höcker B, Beese LS, Hellinga HW. Structure-based design of robust glucose biosensors using a Thermotoga maritima periplasmic glucose-binding protein. Protein Science : a Publication of the Protein Society. 16: 2240-50. PMID 17766373 DOI: 10.1110/Ps.072969407  0.691
2007 Cox JC, Lape J, Sayed MA, Hellinga HW. Protein fabrication automation. Protein Science : a Publication of the Protein Society. 16: 379-90. PMID 17242375 DOI: 10.1110/Ps.062591607  0.398
2007 Allert M, Dwyer MA, Hellinga HW. Local encoding of computationally designed enzyme activity. Journal of Molecular Biology. 366: 945-53. PMID 17196220 DOI: 10.1016/J.Jmb.2006.12.002  0.702
2006 Cuneo MJ, Changela A, Warren JJ, Beese LS, Hellinga HW. The crystal structure of a thermophilic glucose binding protein reveals adaptations that interconvert mono and di-saccharide binding sites. Journal of Molecular Biology. 362: 259-70. PMID 16904687 DOI: 10.1016/J.Jmb.2006.06.084  0.759
2006 de Lorimier RM, Tian Y, Hellinga HW. Binding and signaling of surface-immobilized reagentless fluorescent biosensors derived from periplasmic binding proteins. Protein Science : a Publication of the Protein Society. 15: 1936-44. PMID 16823040 DOI: 10.1110/Ps.062261606  0.56
2006 Rizk SS, Cuneo MJ, Hellinga HW. Identification of cognate ligands for the Escherichia coli phnD protein product and engineering of a reagentless fluorescent biosensor for phosphonates. Protein Science : a Publication of the Protein Society. 15: 1745-51. PMID 16751609 DOI: 10.1110/Ps.062135206  0.812
2005 Yang W, Wilkins AL, Ye Y, Liu ZR, Li SY, Urbauer JL, Hellinga HW, Kearney A, van der Merwe PA, Yang JJ. Design of a calcium-binding protein with desired structure in a cell adhesion molecule. Journal of the American Chemical Society. 127: 2085-93. PMID 15713084 DOI: 10.1021/Ja0431307  0.423
2005 Dattelbaum JD, Looger LL, Benson DE, Sali KM, Thompson RB, Hellinga HW. Analysis of allosteric signal transduction mechanisms in an engineered fluorescent maltose biosensor. Protein Science : a Publication of the Protein Society. 14: 284-91. PMID 15659363 DOI: 10.1110/Ps.041146005  0.456
2005 Smith JJ, Conrad DW, Cuneo MJ, Hellinga HW. Orthogonal site-specific protein modification by engineering reversible thiol protection mechanisms. Protein Science : a Publication of the Protein Society. 14: 64-73. PMID 15576565 DOI: 10.1110/Ps.04965405  0.728
2004 Dwyer MA, Hellinga HW. Periplasmic binding proteins: a versatile superfamily for protein engineering. Current Opinion in Structural Biology. 14: 495-504. PMID 15313245 DOI: 10.1016/J.Sbi.2004.07.004  0.748
2004 Dwyer MA, Looger LL, Hellinga HW. Computational design of a biologically active enzyme. Science (New York, N.Y.). 304: 1967-71. PMID 15218149 DOI: 10.1126/Science.1098432  0.657
2004 Allert M, Rizk SS, Looger LL, Hellinga HW. Computational design of receptors for an organophosphate surrogate of the nerve agent soman. Proceedings of the National Academy of Sciences of the United States of America. 101: 7907-12. PMID 15148405 DOI: 10.1073/Pnas.0401309101  0.786
2003 Dwyer MA, Looger LL, Hellinga HW. Computational design of a Zn2+ receptor that controls bacterial gene expression. Proceedings of the National Academy of Sciences of the United States of America. 100: 11255-60. PMID 14500902 DOI: 10.1073/Pnas.2032284100  0.711
2003 Yang W, Jones LM, Isley L, Ye Y, Lee HW, Wilkins A, Liu ZR, Hellinga HW, Malchow R, Ghazi M, Yang JJ. Rational design of a calcium-binding protein. Journal of the American Chemical Society. 125: 6165-71. PMID 12785848 DOI: 10.1021/Ja034724X  0.464
2003 Looger LL, Dwyer MA, Smith JJ, Hellinga HW. Computational design of receptor and sensor proteins with novel functions. Nature. 423: 185-90. PMID 12736688 DOI: 10.1038/Nature01556  0.73
2003 Wisz MS, Hellinga HW. An empirical model for electrostatic interactions in proteins incorporating multiple geometry-dependent dielectric constants. Proteins. 51: 360-77. PMID 12696048 DOI: 10.1002/Prot.10332  0.719
2002 Liu H, Schmidt JJ, Bachand GD, Rizk SS, Looger LL, Hellinga HW, Montemagno CD. Control of a biomolecular motor-powered nanodevice with an engineered chemical switch. Nature Materials. 1: 173-7. PMID 12618806 DOI: 10.1038/Nmat761  0.689
2002 de Lorimier RM, Smith JJ, Dwyer MA, Looger LL, Sali KM, Paavola CD, Rizk SS, Sadigov S, Conrad DW, Loew L, Hellinga HW. Construction of a fluorescent biosensor family. Protein Science : a Publication of the Protein Society. 11: 2655-75. PMID 12381848 DOI: 10.1110/Ps.021860  0.808
2002 Yang W, Lee HW, Hellinga H, Yang JJ. Structural analysis, identification, and design of calcium-binding sites in proteins. Proteins. 47: 344-56. PMID 11948788 DOI: 10.1002/Prot.10093  0.508
2002 Benson DE, Haddy AE, Hellinga HW. Converting a maltose receptor into a nascent binuclear copper oxygenase by computational design. Biochemistry. 41: 3262-9. PMID 11863465 DOI: 10.1021/Bi011359I  0.44
2001 Long SB, Hancock PJ, Kral AM, Hellinga HW, Beese LS. The crystal structure of human protein farnesyltransferase reveals the basis for inhibition by CaaX tetrapeptides and their mimetics. Proceedings of the National Academy of Sciences of the United States of America. 98: 12948-53. PMID 11687658 DOI: 10.1073/Pnas.241407898  0.423
2001 Benson DE, Conrad DW, De Lorimier RM, Trammell SA, Hellinga HW. Design of bioelectronic interfaces by exploiting hinge-bending motions in proteins Science. 293: 1641-1644. PMID 11533486 DOI: 10.1126/Science.1062461  0.547
2001 Marvin JS, Hellinga HW. Manipulation of ligand binding affinity by exploitation of conformational coupling. Nature Structural Biology. 8: 795-8. PMID 11524684 DOI: 10.1038/Nsb0901-795  0.767
2001 Trammell SA, Goldston HM, Tran PT, Tender LM, Conrad DW, Benson DE, Hellinga HW. Synthesis and characterization of a ruthenium(II)-based redox conjugate for reagentless biosensing. Bioconjugate Chemistry. 12: 643-7. PMID 11459471 DOI: 10.1021/Bc010022Q  0.461
2001 Marvin JS, Hellinga HW. Conversion of a maltose receptor into a zinc biosensor by computational design. Proceedings of the National Academy of Sciences of the United States of America. 98: 4955-60. PMID 11320244 DOI: 10.1073/Pnas.091083898  0.764
2001 Looger LL, Hellinga HW. Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics. Journal of Molecular Biology. 307: 429-45. PMID 11243829 DOI: 10.1006/Jmbi.2000.4424  0.414
2000 Benson DE, Wisz MS, Hellinga HW. Rational design of nascent metalloenzymes. Proceedings of the National Academy of Sciences of the United States of America. 97: 6292-7. PMID 10841535 DOI: 10.1073/Pnas.97.12.6292  0.763
1999 Sloan DJ, Hellinga HW. Dissection of the protein G B1 domain binding site for human IgG Fc fragment. Protein Science : a Publication of the Protein Society. 8: 1643-8. PMID 10452608 DOI: 10.1110/Ps.8.8.1643  0.445
1998 Sloan DJ, Hellinga HW. Structure-based engineering of environmentally sensitive fluorophores for monitoring protein-protein interactions. Protein Engineering. 11: 819-23. PMID 9796832 DOI: 10.1093/Protein/11.9.819  0.469
1998 Benson DE, Wisz MS, Hellinga HW. The development of new biotechnologies using metalloprotein design. Current Opinion in Biotechnology. 9: 370-376. PMID 9751639 DOI: 10.1016/S0958-1669(98)80010-4  0.741
1998 Hellinga HW. Computational protein engineering Nature Structural Biology. 5: 525-527. PMID 9665160 DOI: 10.1038/776  0.432
1998 Piervincenzi RT, Reichert WM, Hellinga HW. Genetic engineering of a single-chain antibody fragment for surface immobilization in an optical biosensor. Biosensors & Bioelectronics. 13: 305-12. PMID 9642767 DOI: 10.1016/S0956-5663(97)00130-9  0.485
1998 Wisz MS, Garrett CZ, Hellinga HW. Construction of a family of Cys2His2 zinc binding sites in the hydrophobic core of thioredoxin by structure-based design. Biochemistry. 37: 8269-77. PMID 9622478 DOI: 10.1021/Bi980718F  0.78
1998 Hellinga HW, Marvin JS. Protein engineering and the development of generic biosensors. Trends in Biotechnology. 16: 183-9. PMID 9586241 DOI: 10.1016/S0167-7799(98)01174-3  0.69
1998 Benson DE, Wisz MS, Liu W, Hellinga HW. Construction of a novel redox protein by rational design: conversion of a disulfide bridge into a mononuclear iron-sulfur center. Biochemistry. 37: 7070-6. PMID 9585516 DOI: 10.1021/Bi980583D  0.73
1998 Hellinga HW. The construction of metal centers in proteins by rational design Folding and Design. 3. PMID 9502313 DOI: 10.1016/S1359-0278(98)00001-7  0.437
1998 Hellinga HW. Construction of a blue copper analogue through iterative rational protein design cycles demonstrates principles of molecular recognition in metal center formation Journal of the American Chemical Society. 120: 10055-10066. DOI: 10.1021/Ja980054X  0.505
1998 Marvin JS, Hellinga HW. Engineering biosensors by introducing fluorescent allosteric signal transducers: Construction of a novel glucose sensor Journal of the American Chemical Society. 120: 7-11. DOI: 10.1021/Ja972993F  0.744
1997 Hellinga HW. Rational protein design: Combining theory and experiment Proceedings of the National Academy of Sciences of the United States of America. 94: 10015-10017. PMID 9294154 DOI: 10.1073/Pnas.94.19.10015  0.444
1997 Coldren CD, Hellinga HW, Caradonna JP. The rational design and construction of a cuboidal iron-sulfur protein. Proceedings of the National Academy of Sciences of the United States of America. 94: 6635-40. PMID 9192617 DOI: 10.1073/Pnas.94.13.6635  0.413
1997 Pinto AL, Hellinga HW, Caradonna JP. Construction of a catalytically active iron superoxide dismutase by rational protein design. Proceedings of the National Academy of Sciences of the United States of America. 94: 5562-7. PMID 9159112 DOI: 10.1073/Pnas.94.11.5562  0.457
1997 Marvin JS, Corcoran EE, Hattangadi NA, Zhang JV, Gere SA, Hellinga HW. The rational design of allosteric interactions in a monomeric protein and its applications to the construction of biosensors. Proceedings of the National Academy of Sciences of the United States of America. 94: 4366-71. PMID 9113995 DOI: 10.1073/Pnas.94.9.4366  0.793
1996 De Lorimier R, Hellinga HW, Spicer LD. NMR studies of structure, hydrogen exchange, and main-chain dynamics in a disrupted-core mutant of thioredoxin. Protein Science : a Publication of the Protein Society. 5: 2552-65. PMID 8976564 DOI: 10.1002/Pro.5560051218  0.318
1996 Hellinga HW. Metalloprotein design Current Opinion in Biotechnology. 7: 437-441. PMID 8768904 DOI: 10.1016/S0958-1669(96)80121-2  0.35
1994 Ladbury JE, Kishore N, Hellinga HW, Wynn R, Sturtevant JM. Thermodynamic effects of reduction of the active-site disulfide of Escherichia coli thioredoxin explored by differential scanning calorimetry. Biochemistry. 33: 3688-92. PMID 8142367 DOI: 10.1021/Bi00178A027  0.451
1994 Hellinga HW, Richards FM. Optimal sequence selection in proteins of known structure by simulated evolution. Proceedings of the National Academy of Sciences of the United States of America. 91: 5803-7. PMID 8016069 DOI: 10.1073/Pnas.91.13.5803  0.399
1994 Ermácora MR, Ledman DW, Hellinga HW, Hsu GW, Fox RO. Mapping staphylococcal nuclease conformation using an EDTA-Fe derivative attached to genetically engineered cysteine residues. Biochemistry. 33: 13625-41. PMID 7947771 DOI: 10.1021/Bi00250A013  0.433
1993 Hellinga H, Zhang V, Caradonna J, Richards F. Design, construction and analysis of new metal binding sites in proteins of known structure. Journal of Inorganic Biochemistry. 51: 59. DOI: 10.1016/0162-0134(93)85095-P  0.423
1992 Hellinga HW, Wynn R, Richards FM. The hydrophobic core of Escherichia coli thioredoxin shows a high tolerance to nonconservative single amino acid substitutions. Biochemistry. 31: 11203-9. PMID 1445859 DOI: 10.1021/Bi00160A034  0.368
1991 Hellinga HW, Richards FM. Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with pre-defined geometry. Journal of Molecular Biology. 222: 763-85. PMID 1749000 DOI: 10.1016/0022-2836(91)90510-D  0.535
1991 Hellinga HW, Caradonna JP, Richards FM. Construction of new ligand binding sites in proteins of known structure. II. Grafting of a buried transition metal binding site into Escherichia coli thioredoxin. Journal of Molecular Biology. 222: 787-803. PMID 1660933 DOI: 10.1016/0022-2836(91)90511-4  0.531
1987 Lau FTK, Fersht AR, Hellinga HW, Evans PR. Site-directed mutagenesis in the effector site of Escherichia coli phosphofructokinase Biochemistry. 26: 4143-4148. PMID 2958087 DOI: 10.1021/Bi00387A060  0.401
1987 Hellinga HW, Evans PR. Mutations in the active site of Escherichia coli phosphofructokinase Nature. 327: 437-439. PMID 2953977 DOI: 10.1038/327437A0  0.303
1985 Hellinga HW, Evans PR. Nucleotide sequence and high-level expression of the major Escherichia coli phosphofructokinase European Journal of Biochemistry. 149: 363-373. PMID 3158524 DOI: 10.1111/J.1432-1033.1985.Tb08934.X  0.315
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