Publications of William A. Eaton - The Journal of Physical Chemistry B

Publication Date (Web): December 13, 2018. Copyright © 2018 William A. Eaton. This article is part of the William A. Eaton Festschrift special issue...
1 downloads 0 Views 212KB Size
Download PDF
Special Issue Preface pubs.acs.org/JPCB

Cite This: J. Phys. Chem. B 2018, 122, 10983−10988

Publications of William A. Eaton

Downloaded via AUSTRALIAN NATL UNIV on December 17, 2018 at 07:47:57 (UTC). See https://pubs.acs.org/sharingguidelines for options on how to legitimately share published articles.

■

■

MOLECULAR SPECTROSCOPY: JOURNAL ARTICLES Eaton, W. A.; Hochstrasser, R. M., Electronic Spectrum of Single Crystals of Ferricytochrome c. J. Chem. Phys. 1967, 46 (7), 2533−2539. Eaton, W. A.; Hochstrasser, R. M., Single Crystal Spectra of Ferrimyoglobin Complexes in Polarized Light J. Chem. Phys. 1968, 49 (3), 985−995. Eaton, W. A.; Charney, E., Near Infrared Absorption and Circular Dichroism Spectra of ferrocytochrome c: d → d Transitions. J. Chem. Phys. 1969, 51 (10), 4502−4505. Eaton, W. A.; Lewis, T. P., Polarized Single Crystal Absorption Spectra of 1-Methyluracil. J. Chem. Phys. 1970, 53 (6), 2164−2172. Eaton, W. A.; Lovenberg, W., Near Infrared Circular Dichrosim of an Iron Sulfur Protein. d → d Transitions in Rubredoxin. J. Am. Chem. Soc. 1970, 92 (24), 7195−7198. Lewis, T. P.; Eaton, W. A., Polarized Single Crystal Absorption Spectra of Cytosine Monohydrate. J. Am. Chem. Soc. 1971, 93 (8), 2054−2056. Eaton, W. A.; Palmer, G.; Fee, J. A.; Kimura, T.; Lovenberg, W., Tetrahedral Iron in the Active Center of Plant Ferrodoxins and Beef Adrenodoxin. Proc. Natl. Acad. Sci. U. S. A. 1971, 68 (12), 3015−3020. Makinen, M. W.; Eaton, W. A., Polarized Single Crystal Absorption Spectra of Carboxyhemoglobin and Oxyhemoglobin. Ann. N. Y. Acad. Sci. 1973, 206 (OCT22), 210−222. Cheng, J. C.; Osborne, G. A.; Stephens, P. J.; Eaton, W. A., Infrared Magnetic Circular Dichroism of Metalloproteins. Nature 1973, 241 (5386), 193−194. Makinen, M. W.; Eaton, W. A., Optically Detected Conformational Changes in Hemoglobin Single Crystals. Nature 1974, 247 (5435), 62−64. Eaton, W. A.; Hofrichter, J.; Makinen, M. W.; Andersen, R. D.; Ludwig, M. L., Optical Spectra and Electronic Structure of Flavine Mononucleotide in Flavodoxin Crystals. Biochemistry 1975, 14 (10), 2146−2151. Hanson, L. K.; Eaton, W. A.; Sligar, S. G.; Gunsalus, I. C.; Gouterman, M.; Connell, C. R., Origin of Anomalous Soret Spectra of Carboxycytochrome P-450. J. Am. Chem. Soc. 1976, 98 (9), 2672−2674. Hofrichter, J.; Eaton, W. A., Linear Dichroism of Biological Chromophores. Ann. Rev. Biophys. Bioeng. 1976, 5, 511−560. Eaton, W. A.; Hanson, L. K.; Stephens, P. J.; Sutherland, J. C.; Dunn, J. B. R., Optical Spectra of Oxy- and Deoxyhemoglobin. J. Am. Chem. Soc. 1978, 100 (16), 4991− 5003. Eaton, W. A.; Hofrichter, J., Polarized Absorption and Linear Dichroism Spectroscopy of Hemoglobin. Methods Enzymol. 1981, 76, 175−261. Schejter, A.; Eaton, W. A., Charge-Transfer Optical Spectra, Electron Paramagnetic Resonance, and Redox Potentials of Cytochromes. Biochemistry 1984, 23 (6), 1081−1084. © 2018 William A. Eaton

MOLECULAR SPECTROSCOPY: BOOK CHAPTERS Eaton, W. A.; Hochstrasser, R. M., Spectra of Single Crystals of Ferricytochrome c. In Chemistry of Hemes and Hemoproteins, B. Chance, R. W. Estabrook. T. Yonetani, Eds. Academic Press: 1966; pp 581−583. Eaton, W. A.; Charney, E., Near Infrared Circular Dichroism: d → d Transitions in Hemoproteins. In Structure and Function of Macromolecules and Membranes, B. Chance, C.P. Lee, J. K. Blasie, Eds. Academic Press: 1971; Vol. 1, pp 155−164. Eaton, W. A.; Lovenberg, W., The Iron Sulfur Complex in Rubredoxin. In Iron Sulf ur Proteins, W. Lovenberg, Ed. Academic Press: 1973; pp 131−162. Eaton, W. A.; Hofrichter, J.; Hanson, L. K.; Makinen, M. W., Single Crystal Optical Spectroscopy of Hemoglobin. In Metalloprotein Studies Utilizing Paramagnetic Ef fects of the Metal Ions as Probes, M. Kotani, A. Tasaki, Eds. Osaka University: 1975; pp 51−88. Stephens, P. J.; Sutherland, J. C.; Cheng, J. C.; Eaton, W. A. The Study of Spin-States of Heme Proteins by Near Infrared Magnetic Circular Dichroism. In Excited States of Biological Molecules, J. B. Birks, Ed. Wiley-Interscience: New York, 1976; pp 434−442.

■

SICKLE CELL DISEASE: JOURNAL ARTICLES Hofrichter, J.; Hendricker, D. G.; Eaton, W. A., Structure of Hemoglobin S Fibers: Optical Determination of Molecular Orientation in Sickled Erythrocytes. Proc. Natl. Acad. Sci. U. S. A. 1973, 70 (12), 3604−3608. Hofrichter, J.; Ross, P. D.; Eaton, W. A., Kinetics and Mechanism of Deoxyhemoglobin-S Gelation: A New Approach to Understanding Sickle-Cell Disease. Proc. Natl. Acad. Sci. U. S. A. 1974, 71 (12), 4864−4868. Ross, P. D.; Hofrichter, J.; Eaton, W. A., Calorimetric and Optical Characterization of Sickle Cell Hemoglobin Gelation. J. Mol. Biol. 1975, 96 (2), 239−253. Eaton, W. A.; Hofrichter, J.; Ross, P. D.; Tschudin, R. G.; Becker, E. D., Comparison of Sickle Cell Hemoglobin Gelation Kinetics Measured by NMR and Optical Methods. Biochem. Biophys. Res. Commun. 1976, 69 (2), 538−547. Hofrichter, J.; Ross, P. D.; Eaton, W. A., Supersaturation in Sickle Cell Hemoglobin Solutions. Proc. Natl. Acad. Sci. U. S. A. 1976, 73, 3034−3039. Eaton, W. A.; Hofrichter, J.; Ross, P. D., Delay Time of Gelation: A Possible Determinant of Clinical Severity in Sickle Cell Disease. Blood 1976, 47 (4), 621−627. Ross, P. D.; Hofrichter, J.; Eaton, W. A., Thermodynamics of Gelation of Sickle Cell Hemoglobin. J. Mol. Biol. 1977, 115 (2), 111−134. Special Issue: William A. Eaton Festschrift Published: December 13, 2018 10983

DOI: 10.1021/acs.jpcb.8b06735 J. Phys. Chem. B 2018, 122, 10983−10988

The Journal of Physical Chemistry B

Special Issue Preface

Sunshine, H. R.; Hofrichter, J.; Eaton, W. A., Requirements for Therapeutic Inhibition of Sickle Hemoglobin Gelation. Nature 1978, 275 (5677), 238−240. Sunshine, H. R.; Hofrichter, J.; Eaton, W. A., Gelation of Sickle Cell Hemoglobin in Mixtures with Normal Adult and Fetal Hemoglobins. J. Mol. Biol. 1979, 133 (4), 435−467. Ferrone, F. A.; Hofrichter, J.; Sunshine, H. R.; Eaton, W. A., Kinetic Studies on Photolysis Induced Gelation of Sickle Cell Hemoglobin Suggest a New Mechanism. Biophys. J. 1980, 32, 361−377. Sunshine, H. R.; Hofrichter, J.; Ferrone, F. A.; Eaton, W. A., Oxygen Binding by Sickle Cell Hemoglobin Polymers. J. Mol. Biol. 1982, 158 (2), 251−273. Coletta, M.; Hofrichter, J.; Ferrone, F. A.; Eaton, W. A., Kinetics of Sickle Hemoglobin Polymerization in Single Red Cells. Nature 1982, 300 (5888), 194−197. Bunn, H. F.; Noguchi, C. T.; Hofrichter, J.; Schechter, G. P.; Schechter, A. N.; Eaton, W. A., Molecular and Cellular Pathogenesis of Hemoglobin SC Disease. Proc. Natl. Acad. Sci. U. S. A. 1982, 79 (23), 7527−7531. Antonini, E.; Benedetti, P. A.; Brunori, M.; Coletta, M.; Eaton, W. A.; Giardina, B.; Hofrichter, J., The Use of Microspectrophotometry in the Study of Physiological and Pathological Occurrences in Hemoglobin. Ric. Clin. Lab. 1983, 13, 127−139. Ferrone, F. A.; Hofrichter, J.; Eaton, W. A., Kinetics of Sickle Hemoglobin Polymerization. I. Studies Using Temperature Jump and Laser Photolysis Techniques. J. Mol. Biol. 1985, 183, 591−610. Ferrone, F. A.; Hofrichter, J.; Eaton, W. A., Kinetics of Sickle Hemoglobin Polymerization II. A Double Nucleation Mechanism. J. Mol. Biol. 1985, 183 (4), 611−631. Mozzarelli, A.; Hofrichter, J.; Eaton, W. A., Delay Time of Hemoglobin S Polymerization Prevents Most Cells from Sickling in Vivo. Science 1987, 237 (4814), 500−506. Eaton, W. A.; Hofrichter, J., Hemoglobin S Gelation and Sickle Cell Disease. Blood 1987, 70 (5), 1245−1266. Reprinted in Biological Physics; Key Papers in Physics, E. V. Mielczarek, E. Greenbaum, R. S. Knox, Eds. American Institute of Physics: New York, 1993; pp 204−225. San Biagio, P. L.; Hofrichter, J.; Mozzarelli, A.; Henry, E. R.; Eaton, W. A., Current Perspectives on the Kinetics of Hemoglobin S Gelation. Ann. N. Y. Acad. Sci. 1989, 565, 53−62. Eaton, W. A.; Hofrichter, J., Sickle Cell Hemoglobin Polymerization. Adv. Protein Chem. 1990, 40, 63−279. Eaton, W. A.; Hofrichter, J., The Biophysics of Sickle Cell Hydroxyurea Therapy. Science 1995, 268, 1142−1143. Bridges, K. R.; Barabino, G. D.; Brugnara, C.; Cho, M. R.; Christoph, G. W.; Dover, G.; Ewenstein, B. M.; Golan, D. E.; Guttmann, C. R. G.; Hofrichter, J.; Mulkern, R. V.; Zhang, B.; Eaton, W. A., A Multiparameter Analysis of Sickle Erythrocytes in Patients Undergoing Hydroxyurea Therapy. Blood 1996, 88 (12), 4701−4710. Eaton, W. A., Linus Pauling and Sickle Cell Disease. Biophys. Chem. 2003, 100, 109−116. Christoph, G. W.; Hofrichter, J.; Eaton, W. A., Understanding the Shape of Sickled Red Cells. Biophys. J. 2005, 88 (2), 1371−1376. Cellmer, T.; Ferrone, F. A.; Eaton, W. A., Universality of Supersaturation Ratio in Protein Fiber Formation. Nat. Struct. Mol. Biol. 2016, 23, 459−471.

Li, Q.; Henry, E. R.; Hofrichter, J.; Smith, J. F.; Cellmer, T.; Dunkelberger, E. B.; Metaferia, B. B.; Jones-Straehle, S.; Boutom, S.; Christoph, G. W.; Wakefield, T. H.; Link, M. E.; Staton, D.; Vass, E. R.; Miller, J. L.; Hsieh, M. M.; Tisdale, J. F.; Eaton, W. A., Kinetic Assay Shows that Increasing Red Cell Volume Could be a Treatment for Sickle Cell Disease. Proc. Natl. Acad. Sci. U. S. A. 2017, 114 (5), E689−E696. Eaton, W. A.; Bunn, H. F., Treatment of Sickle Cell Disease by Targeting Hb S Polymerization. Blood 2017, 129 (20), 2719−2726.

■

SICKLE CELL DISEASE: BOOK CHAPTERS Hofrichter, J.; Ross, P. D.; Eaton, W. A., Kinetic and Thermodynamic Investigation of Deoxyhemoglobin S Gelation. In Proceedings of the First National Symposium on Sickle Cell Disease, J. I. Hercules, A. N. Schechter, W. A. Eaton, R. E. Jackson, Eds. DHEW Publication No. (NIH) 75−723, Bethesda, MD, 1974; pp 43−45. Hofrichter, J.; Ross, P. D.; Eaton, W. A., A Physical Description of the Gelation of Deoxyhemoglobin S. In Molecular and Cellular Aspects of Sickle Cell Disease, J. I. Hercules, G. L. Cottam, M. R. Waterman, A. N. Schechter, Eds., DHEW Publication No. (NIH) 76-1007, Bethesda, MD, 1976; pp 185−222. Eaton, W. A.; Hofrichter, J. Successes and Failures of a Simple Nucleation Theory for Sickle Cell Hemoglobin Gelation. In Clinical and Biochemical Aspects of Hemoglobin Abnormalities, W. S. Caughey, Ed., Academic Press: New York, 1978; pp 443−457. Ferrone, F. A.; Hofrichter, J.; Eaton, W. A. Hemoglobin S Polymerization in the Photostationary State. In Frontiers of Biological Energetics, Vol. 2: Electrons to Tissues, P. L. Dutton, J. S. Leigh, A. Scarpa, Eds., Academic Press: New York, 1978; pp 1085−1092. Sunshine, H. R.; Ferrone, F. A.; Hofrichter, J.; Eaton, W. A. Gelation Assays and the Evaluation of Therapeutic Inhibitors. In Development of Therapeutic Agents for Sickle Cell Diseases, INSERM Symposium No. 9, J. Rosa, Y. Beuzard, J. I. Hercules, Eds., Elsevier/North Holland Biomedical Press: Amsterdam, 1979; pp 31−46. Hofrichter, J.; Sunshine, H. R.; Ferrone, F. A.; Eaton, W. A. Oxygen Binding and the Gelation of Sickle Cell Hemoglobin. In Molecular Basis of Mutant Hemoglobin Dysfunction, P. Sigler, Ed., Elsevier/North-Holland: New York, 1981; pp 225−236. Sunshine, H. R.; Hofrichter, J.; Ferrone, F. A.; Eaton, W. A. Sickle Cell Hemoglobin Polymers Bind Oxygen Noncooperatively. In Hemoglobin and Oxygen Binding, C. Ho, W. A. Eaton, J. P. Collman, Q. H. Gibson, J. S. Leigh, E. Margoliash, J. K. Moffat, W. R. Scheidt, Eds., Elsevier Biomedical: New York, 1982; pp 291−294. Schechter, A. N.; Eaton, W. A., Sickle Cell Disease. In NIH, An Account of Research in its Laboratories and Clinics, D. Stetten, W. T. Carrigan, Eds., Academic Press: New York, 1984; pp 337−348. Mozzarelli, A.; Hofrichter, J.; Eaton, W. A. Sickling, Unsickling, and Intracellular Polymerization of Hemoglobin S. In Approaches to the Therapy of Sickle Cell Anaemia, Y. Beuzard, S. Charache, Eds., Les Editions INSERM, Paris, 1986; pp 39−51. Mozzarelli, A.; Hofrichter, J.; Eaton, W. A. The Problem of Describing Gelation in Vivo. In Pathophysiological Aspects of Sickle Cell Vaso-occlusion, R. L. Nagel, Ed., Alan R. Liss: New York, 1987; pp 237−244. 10984

DOI: 10.1021/acs.jpcb.8b06735 J. Phys. Chem. B 2018, 122, 10983−10988

The Journal of Physical Chemistry B

Special Issue Preface

Ansari, A.; Jones, C. M.; Henry, E. R.; Hofrichter, J.; Eaton, W. A., The Role of Solvent Viscosity in the Dynamics of Protein Conformational Changes. Science 1992, 256 (5065), 1796−1798. Jones, C. M.; Ansari, A.; Henry, E. R.; Christoph, G. W.; Hofrichter, J.; Eaton, W. A., Speed of Intersubunit Communication in Proteins. Biochemistry 1992, 31 (29), 6692−6702. Ansari, A.; Jones, C. M.; Henry, E. R.; Hofrichter, J.; Eaton, W. A., Photoselection in Polarized Photolysis Experiments on Heme Proteins. Biophys. J. 1993, 64 (3), 852−868. Rivetti, C.; Mozzarelli, A.; Rossi, G. L.; Henry, E. R.; Eaton, W. A., Oxygen Binding by Single Crystals of Hemoglobin. Biochemistry 1993, 32 (11), 2888−2906. Schaad, O.; Zhou, H. X.; Szabo, A.; Eaton, W. A.; Henry, E. R., Simulation of the Kinetics of Ligand Binding to a Protein by Molecular Dynamics: Geminate Recombination of Nitric Oxide to Myoglobin. Proc. Natl. Acad. Sci. U. S. A. 1993, 90 (20), 9547−9551. Ansari, A.; Jones, C. M.; Henry, E. R.; Hofrichter, J.; Eaton, W. A., Conformational Relaxation and Ligand Binding in Myoglobin. Biochemistry 1994, 33 (17), 5128−5145. Hagen, S. J.; Hofrichter, J.; Eaton, W. A., Protein Reaction Kinetics in a Room Temperature Glass. Science 1995, 269 (5226), 959−962. Hagen, S. J.; Hofrichter, H. J.; Bunn, H. F.; Eaton, W. A., Comments on the Physics and Chemistry of Trehalose as a Storage Medium for Hemoglobin-Based Blood Substitutes: “From Kramers Theory to the Battlefield”. Trans. Clin. Biol. 1995, 2 (6), 423−426. Hagen, S. J.; Eaton, W. A., Nonexponential Structural Relaxations in Proteins. J. Chem. Phys. 1996, 104 (9), 3395− 3398. Bettati, S.; Mozzarelli, A.; Rossi, G. L.; Tsuneshige, A.; Yonetani, T.; Eaton, W. A.; Henry, E. R., Oxygen Binding by Single Crystals of Hemoglobin: The Problem of Cooperativity and Inequivalence of Alpha and Beta Subunits. Proteins: Struct., Funct., Genet. 1996, 25 (4), 425−437. Hagen, S. J.; Hofrichter, J.; Eaton, W. A., Geminate Rebinding and Conformational Dynamics of Myoglobin Embedded in a Glass at Room Temperature. J. Phys. Chem. 1996, 100 (29), 12008−12021. Eaton, W. A.; Henry, E. R.; Hofrichter, J., Nanosecond Crystallographic Snapshots of Protein Structural Changes. Science 1996, 274 (5293), 1631−1632. Mozzarelli, A.; Rivetti, C.; Rossi, G. L.; Eaton, W. A.; Henry, E. R., Allosteric Effectors Do Not Alter the Oxygen Affinity of Hemoglobin Crystals. Protein Sci. 1997, 6 (2), 484−489. Henry, E. R.; Jones, C. M.; Hofrichter, J.; Eaton, W. A., Can a Two-State MWC Allosteric Model Explain Hemoglobin Kinetics? Biochemistry 1997, 36 (21), 6511−6528. Henry, E. R.; Bettati, S.; Hofrichter, J.; Eaton, W. A., A Tertiary Two-State Allosteric Model for Hemoglobin. Biophys. J. 2002, 98 (1−2), 149−164. Eaton, W. A.; Henry, E. R.; Hofrichter, J.; Mozzarelli, A., Is Cooperative Oxygen Binding by Hemoglobin Really Understood? Nat. Struct. Biol. 1999, 6 (4), 351−358. Reprinted in Proceedings of the International Conference on “Allosteric proteins; 40 years with Monod-Wyman-Changeux”, Accademia Nazionale dei Lincei, Rome, 2006. M. Brunori, G. Careri, J.-P. Changeux, H. K. Schachman, Eds. (Rend. Fis. Acc. Lincei); Vol. 17, pp 147−163.

Eaton, W. A.; Hofrichter, J. Hemoglobin S Polymerization. In The Sickle Hemoglobinopathies: Science and Medicine, S. H. Embury, R. P. Hebbel, M. Narla, M. H. Steinberg, Eds., Raven Press, New York, 1994; pp 53−87.

■

MYOGLOBIN, HEMOGLOBIN DYNAMICS, AND ALLOSTERY: JOURNAL ARTICLES Padlan, E. A.; Eaton, W. A.; Yonetani, T., Crystallographic Study of Deoxy Cobalt(II) Mesoporphyrin IX Myoglobin. J. Biol. Chem. 1975, 250 (17), 7069−7073. Greene, B. I.; Hochstrasser, R. M.; Weisman, R. B.; Eaton, W. A., Spectrocopic Studies of Oxyhemoglobin and Carbonmonoxyhemoglobin after Pulsed Optical Excitation. Proc. Natl. Acad. Sci. U. S. A. 1978, 75 (11), 5255−5259. Eaton, W. A., Relation between Coding Sequences and Function in Hemoglobin. Nature 1980, 284 (5752), 183−185. Henry, E. R.; Sommer, J. H.; Hofrichter, J.; Eaton, W. A., Geminate Recombination of Carbon Monoxide to Myoglobin. J. Mol. Biol. 1983, 166 (3), 443−451. Hofrichter, J.; Sommer, J. H.; Henry, E. R.; Eaton, W. A., Nanosecond Absorption Spectroscopy of Hemoglobin: Elementary Processes in Kinetic Cooperativity. Proc. Natl. Acad. Sci. U. S. A. 1983, 80 (8), 2235−2239. Hofrichter, J.; Henry, E. R.; Sommer, J. H.; Deutsch, R.; Ikeda-Saito, M.; Yonetani, T.; Eaton, W. A., Nanosecond Optical Spectra of Iron Cobalt Hybrid Hemoglobins: Geminate Recombination, Conformational Changes, and Intersubunit Communication. Biochemistry 1985, 24 (11), 2667−2679. Henry, E. R.; Levitt, M.; Eaton, W. A., Molecular Dynamics Simulation of Photodissociation of Carbon Monoxide from Hemoglobin. Proc. Natl. Acad. Sci. U. S. A. 1985, 82 (7), 2034−2038. Henry, E. R.; Eaton, W. A.; Hochstrasser, R. M., Molecular Dynamics Simulations of Cooling in Laser-Excited Heme Proteins. Proc. Natl. Acad. Sci. U. S. A. 1986, 83 (23), 8982− 8986. Murray, L. P.; Hofrichter, J.; Henry, E. R.; Ikeda-Saito, M.; Kitagishi, K.; Yonetani, T.; Eaton, W. A., The Effect of Quaternary Structure on the Kinetics of Conformational Changes and Nanosecond Geminate Recombination of Carbon Monoxide to Hemoglobin. Proc. Natl. Acad. Sci. U. S. A. 1988, 85 (7), 2151−2155. Murray, L. P.; Hofrichter, J.; Henry, E. R.; Eaton, W. A., Time-Resolved Optical Spectroscopy and Structural Dynamics Following Photodissociation of Carbonmonoxyhemoglobin. Biophys. Chem. 1988, 29 (1−2), 63−76. Janes, S. M.; Dalickas, G. A.; Eaton, W. A.; Hochstrasser, R. M., Picosecond Transient Absorption Study of Photodissociation of Carboxy Hemoglobin and Myoglobin. Biophys. J. 1988, 54 (3), 545−549. Hofrichter, J.; Henry, E. R.; Szabo, A.; Murray, L. P.; Ansari, A.; Jones, C. M.; Coletta, M.; Falcioni, G.; Brunori, M.; Eaton, W. A., Dynamics of the Quaternary Conformational Change in Trout Hemoglobin. Biochemistry 1991, 30 (26), 6583−6598. Eaton, W. A.; Henry, E. R.; Hofrichter, J., Application of Linear Free Energy Relations to Protein Conformational Changes: The Quaternary Structural Change of Hemoglobin. Proc. Natl. Acad. Sci. U. S. A. 1991, 88 (10), 4472−4475. Mozzarelli, A.; Rivetti, C.; Rossi, G. L.; Henry, E. R.; Eaton, W. A., Crystals of Hemoglobin with the T Quaternary Structure Bind Oxygen Cooperatively with no Bohr Effect. Nature 1991, 351 (6325), 416−419. 10985

DOI: 10.1021/acs.jpcb.8b06735 J. Phys. Chem. B 2018, 122, 10983−10988

The Journal of Physical Chemistry B

■

Viappiani, C.; Bettati, S.; Bruno, S.; Ronda, L.; Abbruzzetti, S.; Mozzarelli, A.; Eaton, W. A., New Insights into Allosteric Mechanisms from Trapping Unstable Protein Conformations in Silica Gels. Proc. Natl. Acad. Sci. U. S. A. 2004, 101 (40), 14414−14419. Eaton, W. A.; Henry, E. R.; Hofrichter, J.; Bettati, S.; Viappiani, C.; Mozzarelli A., Evolution of Allosteric Models for Hemoglobin. IUBMB Life 2007, 58, 586−599. Viappiani, C.; Abbruzzetti, S.; Ronda, L.; Bettati, S.; Henry, E. R.; Mozzarelli, A.; Eaton, W. A. Experimental Basis for a New Allosteric Model for Multisubunit Proteins. Proc. Natl. Acad. Sci. U. S. A. 2014, 111, 12758−12763. Henry, E. R., Mozzarelli, A.; Viappiani, C.; Abbruzzetti, S.; Bettati, S.; Ronda, L.; Bruno, S.; Eaton, W. A., Experiments on Hemoglobin in Single Crystals and Silica Gels Distinguish Among Theoretical Allosteric Models. Biophys. J. 2015, 109, 1−9.

■

Special Issue Preface

PROTEIN FOLDING: JOURNAL ARTICLES

Jones, C. M.; Henry, E. R.; Hu, Y.; Chan, C.-K.; Luck, S. D.; Bhuyan, A.; Roder, H.; Hofrichter, J.; Eaton, W. A, Fast Events in Protein Folding Initiated by Nanosecond Laser Photolysis. Proc. Natl. Acad. Sci. U. S. A. 1993, 90, 11860−11864. Hagen, S. J.; Hofrichter, J.; Szabo, A.; Eaton, W. A., Diffusion-limited Contact Formation in Unfolded Cytochrome c: Estimating the Maximum Rate of Protein Folding. Proc. Natl. Acad. Sci. U. S. A. 1996, 93, 11615−11617; Commentary on article in same issue (pp 11426−11427), entitled “A Speed Limit for Protein Folding” by J. A. McCammon. Eaton, W. A.; Thompson, P. A.; Chan, C.-K.; Hagen, S. J.; Hofrichter, J., Fast Events in Protein Folding. Structure 1996, 4, 1133−1139. Chan, C.-K.; Hofrichter, J.; Eaton, W. A., Optical Triggers of Protein Folding, Science 1996, 274, 628−629. Hagen, S. J.; Hofrichter, J.; Eaton, W. A., The Rate of Intrachain Diffusion of Unfolded Cytochrome c. J. Phys. Chem. B 1997, 101, 2352−2365. Chan, C.-K.; Hu, Y.; Takahashi, S.; Rousseau, D. L.; Eaton, W. A.; Hofrichter, J., Submillisecond Protein Folding Kinetics Studied by Ultrarapid Mixing. Proc. Natl. Acad. Sci. U. S. A. 1997, 94, 1779−1784. Eaton, W. A.; Muñoz, V.; Thompson, P. A.; Chan, C. K.; Hofrichter, J. Submillisecond Kinetics of Protein Folding. Curr. Opin. Struct. Biol. 1997, 7, 10−14. Thompson, P. A.; Eaton, W. A.; Hofrichter, J., Laser Temperature Jump Studies of the Helix−Coil Kinetics of an Alanine Peptide Interpreted with a “Kinetic Zipper” Model. Biochemistry 1997, 36, 9200−9210. Muñoz, V.; Thompson, P. A.; Hofrichter, J.; Eaton, W. A., Folding Dynamics and Mechanism of β-Hairpin Formation. Nature 1997, 390, 196−199. Muñoz, V.; Henry, E. R.; Hofrichter, J.; Eaton, W. A., A Statistical Mechanical Model for β-Hairpin Kinetics. Proc. Natl. Acad. Sci. U. S. A. 1998, 95, 5872−5879. Eaton, W. A.; Muñoz, V.; Thompson, P. A.; Henry, E. R.; Hofrichter, J., Kinetics and Dynamics of Loops, α-Helices, βHairpins, and “Fast-folding” Proteins, Acc. Chem. Res. 1998, 31, 745−753. Eaton, W. A., Searching for “Downhill Scenarios” in Protein Folding. A Commentary, Proc. Natl. Acad. Sci. U. S. A. 1999, 96, 5897−5899. Pollack, L.; Tate, M. W.; Darnton, N. C.; Knight, J. B.; Gruner, S. M.; Eaton, W. A.; Austin, R. H., Compactness of the Denatured State of a Fast-folding Protein Measured by Submillisecond Small-angle X-ray Scattering. Proc. Natl. Acad. Sci. U. S. A. 1999, 96, 10115−10117. Wolynes, P. G.; Eaton, W. A., The Physics of Protein Folding. Physics World, Sept 1999, pp 39−44. Muñoz, V.; Eaton, W. A., A Simple Model for Calculating the Kinetics of Protein Folding from Three-dimensional Structure. Proc. Natl. Acad. Sci. U. S. A. 1999, 96, 11311− 11316. Thompson, P. A.; Muñoz, V.; Jas, G. S.; Eaton, W. A.; Hofrichter, J. The Helix−coil Kinetics of an Heteropeptide. J. Phys. Chem. 2000, 104, 378−389. Hagen, S. J.; Eaton, W. A., Two-state Expansion and Collapse of a Polypeptide. J. Mol. Biol. 2000, 301, 1019−1027. Eaton, W. A.; Muñoz, V.; Hagen, S. J.; Jas, G. S.; Lapidus, L. J.; Henry, E. R.; Hofrichter, J., Fast Kinetics and Mechanisms

BOOK CHAPTERS: MYOGLOBIN, HEMOGLOBIN DYNAMICS, AND ALLOSTERY

Greene, B. I.; Hochstrasser, R. M.; Weisman, R. B.; Eaton, W. A. Picosecond Transient Absorption Spectra of Hemoglobin. In Frontiers of Biological Energetics, Vol. 2: Electrons to Tissues, P. L. Dutton, J. S. Leigh, A. Scarpa, Eds., Academic Press: New York, 1978; pp 1075−1083. Henry, E. R.; Hofrichter, J.; Sommer, J. H.; Eaton, W. A. Photolysis of Hemoglobin and the Cooperativity Problem. In Photochemistry and Photobiology: Proceedings of the International Conference, Alexandria, Egypt, A. H. Zewail, Ed., Harwood Academic Publishers: New York, 1983; pp 791−828. Henry, E. R.; Hofrichter, J.; Sommer, J. H.; Eaton, W. A. Conformational Changes and Ligand Rebinding Following Nanosecond Photodissociation of Carbonmonoxyhemoglobin. In the Proceedings of the Brussels Hemoglobin Symposium: Hemoglobins: Structure and Function, A. G. Schnek, C. Paul, Eds., Brussels University Press: Brussels, 1983; pp 193−203. Henry, E. R.; Hofrichter, J.; Sommer, J. H.; Deutsch, R.; Eaton, W. A. Photodissociation of Hemoglobin and Structural Dynamics. In the Proceedings of the Ninth International Conference on Photobiology, J. Longworth, J. Jagger, W. Shropshire, Eds., Praeger: Philadelphia, 1984. Henry, E. R.; Eaton, W. A.; Hochstrasser, R. M. Molecular Dynamics Study of Vibrational Cooling in Optically Excited Hemeproteins. In Ultrafast Phenomena, G. Fleming, A. E. Siegman, Eds., Springer Verlag: Berlin, 1986; pp 430−432. Henry, E. R.; Hofrichter, J.; Eaton, W. A. Dynamics of Structural Changes in Hemoglobin. In Structure, Dynamics and Function of Biomolecules, A. Ehrenberg, R. Rigler, A. Graslund, L. Nilsson, Eds., Springer Verlag: Heidelberg, 1987; pp 20−24. Eaton, W. A. Hemoglobin and Allostery: is it Understood? In Simplicity and Complexity in Proteins and Nucleic Acids, H. Frauenfelder, J. Deisenhofer, P. G. Wolynes, Eds., Dahlem University Press: Berlin 1999; pp 179−191. Eaton, W. A. (Rapporteur); Austin, R. H.; Halle, B.; Karplus, M.; Orland, H.; Richards, F. M.; Schlichting, I.; Wolynes, P. G. Are There Common Themes in the Function, Energy Landscape, and Dynamics of Proteins? Group 2 Report: In Simplicity and Complexity in Proteins and Nucleic Acids, H. Frauenfelder, J. Deisenhofer, P. G. Wolynes, Eds., Dahlem University Press: Berlin, 1999; pp 117−138. 10986

DOI: 10.1021/acs.jpcb.8b06735 J. Phys. Chem. B 2018, 122, 10983−10988

The Journal of Physical Chemistry B

Special Issue Preface

in Protein Folding. Annu. Rev. Biophys. Biomol. Struct. 2000, 29, 327−359. Lapidus, L. J.; Eaton, W. A.; Hofrichter, J., Measuring the Rate of Intramolecular Contact Formation in Polypeptides. Proc. Natl. Acad. Sci. U. S. A. 2000, 97, 7220−7225. Jas, G. S.; Eaton, W. A.; Hofrichter, J., Effect of Viscosity on the Kinetics of α-Helix and β-Hairpin Formation. J. Phys. Chem. B 2001, 105, 261−272. Lapidus, L. J.; Eaton, W. A.; Hofrichter, J., Dynamics of Intramolecular Contact Formation in Polypeptides: Distance Dependence of Quenching Rates in a Room-temperature Glass. Phys. Rev. Lett. 2001, 87, 258101-1−258101-4. Lapidus, L. J.; Eaton, W. A.; Hofrichter, J., Measuring Dynamic Flexibility of the Coil State of a Helix-forming Peptide. J. Mol. Biol. 2002, 319, 19−25. Lapidus, L. J.; Steinbach, P. J.; Eaton, W. A.; Szabo, A.; Hofrichter, J. Effect of Chain Stiffness on the Dynamics of Loop Formation in Polypeptides. J. Phys. Chem. B 2002, 106, 11628−11640. Schuler, B.; Lipman, E. A.; Eaton, W. A., Probing the Free Energy Surface for Protein Folding with Single Molecule Fluorescence, Nature 2002, 419, 743−747. Kubelka, J.; Eaton, W. A.; Hofrichter, J., Experimental Tests of Villin Subdomain Folding Simulations. J. Mol. Biol. 2003, 329, 625−630. Buscaglia, M.; Schuler, B.; Lapidus, L. J.; Eaton, W. A.; Hofrichter, J., Kinetics of Intramolecular Contact formation in a Denatured Protein. J. Mol. Biol. 2003, 332, 9−12. Lipman, E. A.; Schuler, B.; Bakajin, O.; Eaton, W. A., Singlemolecule Measurement of Protein Folding Kinetics. Science 2003, 301, 1233−1235. Kubelka, J.; Hofrichter, J.; Eaton, W. A., The Protein Folding Speed Limit. Curr. Opin. Struct. Biol. 2004, 14, 76−88. Henry, E. R.; Eaton, W. A., Combinatorial Modeling of Protein Folding Kinetics: Free Energy Profiles and Relative Rates. Chem. Phys. 2004, 307, 163−185 Buscaglia, M.; Kubelka, J.; Eaton, W. A.; Hofrichter, J., Determination of Ultrafast Protein Folding Rates from Loop Formation Dynamics. J. Mol. Biol. 2005, 347, 657−664. Schuler, B.; Lipman, E. A.; Steinbach, P. J.; Kumke, M.; Eaton, W. A., Polyproline and the “Spectroscopic Ruler” Revisited with Single Molecule Fluorescence. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 2754−2759. Chiu, T. K.; Kubelka, J.; Herbst-Irmer, R.; Eaton, W. A.; Hofrichter, J.; Davies, D. R., High-Resolution X-ray Crystal Structures of the Villin Headpiece Subdomain, an Ultrafast Folding Protein. Proc. Natl. Acad. Sci. U. S. A. 2005, 102 (21), 7517−7522. Kubelka, J.; Chiu, T. K.; Davies, D. R.; Eaton, W. A.; Hofrichter, J., Submicrosecond Protein Folding. J. Mol. Biol. 2006, 359, 546−553. Muñoz, V.; Ghirlando, R.; Blanco, F. J.; Jas, G. S.; Hofrichter, J.; Eaton, W. A., Folding and Aggregation Kinetics of a Beta-Hairpin. Biochemistry 2006, 45 (23), 7023−7035. Buscaglia, M.; Lapidus, L. J.; Eaton, W. A.; Hofrichter, J., Effects of Denaturants on the Dynamics of Loop Formation in Polypeptides. Biophys. J. 2006, 91 (1), 276−288. Merchant, K. A.; Best, R. B.; Louis, J. M.; Gopich, I. V.; Eaton, W. A., Characterizing the Unfolded States of Proteins Using Single-molecule FRET Spectroscopy and Molecular Simulations. Proc. Natl. Acad. Sci. U. S. A. 2007, 104 (5), 1528−1533.

Godoy-Ruiz, R.; Henry, E. R.; Kubelka, J.; Hofrichter, J.; Muñoz, V.; Sanchez-Ruiz, J. M.; Eaton, W. A., Estimating FreeEnergy Barrier Heights for an Ultrafast Folding Protein from Calorimetric and Kinetic Data. J. Phys. Chem. B 2008, 112 (19), 5938−5949. Cellmer, T.; Henry, E. R.; Kubelka, J.; Hofrichter, J.; Eaton, W. A., Relaxation Rate for an Ultrafast Folding Protein is Independent of Chemical Denaturant Concentration. J. Am. Chem. Soc. 2007, 129, 14564−14565. Best, R. B.; Merchant, K. A.; Gopich, I. V.; Schuler, B.; Bax, A.; Eaton, W. A., Effect of Flexibility and Cis Residues in Single-molecule FRET Studies of Polyproline. Proc. Natl. Acad. Sci. U. S. A. 2007, 104 (48), 18964−18969. Schuler, B.; Eaton, W. A., Protein Folding Studied by Singlemolecule FRET. Curr. Opin. Struct. Biol. 2008, 18 (1), 16−26. Cellmer, T.; Henry, E. R.; Hofrichter, J.; Eaton, W. A., Measuring Internal Friction of an Ultrafast Folding Protein. Proc. Natl. Acad. Sci. U. S. A. 2008, 105 (47), 18320−18325. Kubelka, J.; Henry, E. R.; Cellmer, T.; Hofrichter, J.; Eaton, W. A., Chemical, Physical, and Theoretical Kinetics of an Ultrafast Folding Protein. Proc. Natl. Acad. Sci. U. S. A. 2008, 105 (48), 18655−18662. Chung, H. S.; Louis, J. M.; Eaton, W. A., Experimental Determination of Upper Bound for Transition Path Times in Protein Folding from Single Molecule Photon-by-photon Trajectories. Proc. Natl. Acad. Sci. U. S. A. 2009, 106 (29), 11837−11844. Feature Article in Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 11837−11844. Commentary by E. I. Shakhnovich in same issue, pp 11823−11824. Chung, H. S.; Louis, J. M.; Eaton, W. A., Distinguishing Between Protein Dynamics and Dye Photophysics in Single Molecule FRET Experiments. Biophys. J. 2010, 98, 696−706. Chung, H. S.; Gopich, I. V.; McHale, K.; Cellmer, T.; Louis, J. M.; Eaton, W. A., Extracting Rate Coefficients from SingleMolecule Photon Trajectories and FRET Efficiency Histograms for a Fast-Folding Protein. J. Phys. Chem. A 2011, 115 (16), 3642−3656. Cellmer, T.; Buscaglia, M.; Henry, E. R.; Hofrichter, J.; Eaton, W. A., Making Connections Between Ultrafast Protein Folding Kinetics and Molecular Dynamics Simulations. Proc. Natl. Acad. Sci. U. S. A. 2011, 108 (15), 6103−6108. Chung, H. S.; McHale, K.; Louis, J. M.; Eaton, W. A., Single Molecule Fluorescence Experiments Determine Protein Folding Transition Path Times. Science 2012, 335 (6071), 981−984. Chung, H. S.; Cellmer, T.; Louis, J. M.; Eaton, W. A., Measuring Ultrafast Protein Folding Rates from Photon-byphoton Analysis of Single Molecule Fluorescence Trajectories. Chem. Phys. 2013, 422, 229−237. Chung, H. S.; Eaton, W. A., Single Molecule Fluorescence Probes Dynamics of Barrier Crossing. Nature 2013, 502, 685− 688. News and Views, Benjamin Schuler and Jane Clarke, same issue, 632−633. Henry, E. R.; Best, R. B.; Eaton, W. A., Comparing a Simple Theoretical Model for Protein Folding with All-atom Molecular Dynamics Simulations. Proc. Natl. Acad. Sci. U. S. A. 2013, 110 (44), 17880−17885. Best, R. B.; Hummer, G.; Eaton, W. A., Native Contacts Determine Protein Folding Mechanisms in Atomistic Simulations. Proc. Natl. Acad. Sci. U. S. A. 2013, 110 (44), 17874− 17879. Truex, K.; Chung, H. S.; Louis, J. M.; Eaton, W. A., Testing Landscape Theory for Biomolecular Processes with Single 10987

DOI: 10.1021/acs.jpcb.8b06735 J. Phys. Chem. B 2018, 122, 10983−10988

The Journal of Physical Chemistry B

Special Issue Preface

Molecule Fluorescence Spectroscopy. Phys. Rev. Lett. 2015, 115 (1), 018101. Chung, H. S.; Piana-Agostinetti, S.; Shaw, D. E.; Eaton, W. A., Structural Origin of Slow Diffusion in Protein Folding. Science 2015, 349 (6255), 1504−1510. Chung, H. S.; Eaton, W. A., Protein Folding Transition Path Times from Single Molecule FRET. Curr. Opin. Struct. Biol. 2018, 48, 30−39.

Phosphate and Adenosine Triphosphate during Single Contraction of Isolated Muscles. In Biochemistry of Muscle Contraction, Gergely, Ed., Little, Brown and Company: 1964; pp 463−467. George, P; Hanania, G. I. H.; Eaton, W. A., Effect of Electrostatic Environment on Redox Potentials. In Chemistry of Hemes and Hemoproteins. B. Chance, R. E. W. Estabrook, Y. Yonetani, Eds. Academic Press: 1966; pp 267−271.

■

■

OTHER PUBLICATIONS Eaton, W. A.; Szabo, A., Special Issue: Protein Dynmaics. Preface. Chem. Phys. 1991, 158 (2−3), U191−U191. Eaton, W. A.; Trommsdorff, H. P.; Zewail, A. H., Robin M. Hochstrasser - Biography. J. Phys. Chem. 1996, 100 (29), 11789−11790. Eaton, W. A.; Zewail, A. H., Scientific Contributions of Robin M. Hochstrasser. J. Chem. Phys. 1996, 100 (29), 11791−11805. Baker, D.; Eaton, W. A., Folding and Binding - Editorial Overview. Curr. Opin. Struct. Biol. 2004, 14 (1), 67−69. Eaton, W. A.; Hummer, G.; Zwanzig, R. W., A Tribute to Attila Szabo. J. Phys. Chem. B 2008, 112 (19), 5881−5882. Wolynes, P. G.; Eaton, W. A.; Fersht, A. R., Chemical Physics of Protein Folding. Proc. Natl. Acad. Sci. U. S. A. 2012, 109 (44), 17770−17771. Eaton, W. A.; Trommsdorff, H. P., Robin Main Hochstrasser (1931−2013), Giant of Physical Chemistry. Proc. Natl. Acad. Sci. U. S. A. 2013, 110 (23), 9189−9190. Eaton, W. A.; Gruebele, M.; Lubchenko, V.; Onuchic, J. N., Tribute to Peter G. Wolynes. J. Phys. Chem. B 2013, 117 (42), 12669−12671. Biographical Memoirs of Terrell L. Hill (1917−2014) for the National Academy of Sciences by R. Chamberlin with personal recollection by W. A. Eaton. Biographical Memoirs of Robin M. Hochstrasser (1931− 2013) for the National Academy of Sciences by W. A. Eaton, G. R. Fleming, and H. P. Trommsdorff.

PROTEIN FOLDING: BOOK CHAPTERS Hofrichter, J.; Thompson, P. A.; Muñoz, V.; Jas, G. S.; Henry, E. R.; Hagen, S. J.; Lapidus, L. J.; Eaton, W. A., Dynamics of αHelices, β-Hairpins and Loops. In Old and New Views of Protein Folding, K. Kuwajuma, M. Arai, Eds., Elsevier Science B.V.: 1999; pp 53−62. Lapidus, L. J.; Hofrichter, J.; Eaton, W. A., Dynamics of Endto-end Contact Formation in Polypeptides. In Proceedings of the International School of Physics “Enrico Fermi” on Protein Folding, Evolution and Design, R. A. Brohlia, E. I. Shakhnovich, G. Tiana, Eds., 2001, pp 3−12. Kubelka, J.; Buscaglia, M.; Hofrichter, J.; Eaton, W. A., Ultrafast Kinetic Studies and the Protein Folding “Speed Limit”. In Structure, Dynamics and Function of Biological Macromolecules and Assemblies. Volume 364, NATO Science Series: Life and Behavioral Sciences. J. D. Puglisi, Ed., 2005. Henry, E. R.; Eaton, W. A., A Simple Model for Protein Folding. In Biophysics and the Challenges of Emerging Threats. Proceedings of the International School of Structural Biology and Magnetic Resonance. 8th Course, Erice, Sicily, Ettore Majorana Foundation and Centre for Scientific Culture. A NATO Advanced Study Institute, J. D. Puglisi, Ed., Springer: 2009; pp 1−20.

■

MISCELLANEOUS: JOURNAL ARTICLES Eaton, W. A.; George, P.; Hanania, G. I. H., Thermodynamic Aspects of the Potassium Hexacyanoferrate(III)-(II) System. I. Ion Association. J. Phys. Chem. 1967, 71 (7), 2016−2021. Hanania, G. I. H.; Irvine, D. H.; Eaton, W. A.; George, P., Thermodynamic Aspects of Potassium Hexacyanoferrate(III)(II) System. II. Reduction Potential. J. Phys. Chem. 1967, 71 (7), 2022−2030. Vaiana, S. M.; Ghirlando, R.; Yau, W. M.; Eaton, W. A.; Hofrichter, J., Sedimentation Studies on Human Amylin Fail to Detect Low Molecular Weight Oligomers. Biophys. J. 2008, 94 (7), L45−L47. Vaiana, S. M.; Best, R. B.; Yau, W. M.; Eaton, W. A.; Hofrichter, J., Evidence for a Partially Structured State of the Amylin Monomer. Biophys. J. 2009, 97 (11), 2948−2957. Boura, E.; Rozycki, B.; Herrick, D. Z.; Chung, H. S.; Vecer, J.; Eaton, W. A.; Cafiso, D. S.; Hummer, G.; Hurley, J. H., Solution Structure of the ESCRT-I Complex by Small Angle Xray Scattering, EPR, and FRET Spectroscopy. Proc. Natl. Acad. Sci. U. S. A. 2011, 108 (23), 9437−9442. Boura, E.; Rozycki, B.; Chung, H. S.; Herrick, D. Z.; Canagarajah, B.; Cafiso, D. S.; Eaton, W. A.; Hummer, G.; Hurley, J. H., Solution Structure of the ESCRT-I and -II Supercomplex: Implications for Membrane Budding and Scission. Structure 2012, 20 (5), 874−886.

■

MISCELLANEOUS: BOOK CHAPTERS Davies, R. E.; Cain, D. F.; Infante, A. A.; Klaupiks, D.; Eaton, W. A., Changes in Creatine, Phosphocreatine, Inorganic 10988

DOI: 10.1021/acs.jpcb.8b06735 J. Phys. Chem. B 2018, 122, 10983−10988