Gary K. Ackers

Research

Physical basis of biological control; protein-nucleic acid interacting systems.

The role of Dr. Ackers’ research was to understand physical mechanisms of biological function and regulation in macromolecular assemblies. He wanted to know how their structural and chemical features gave rise to the actual biology of multi-subunit allosteric proteins such as human hemoglobin. The hemoglobin molecule is both a carrier of oxygen and a macromolecular switch that might help him understand how other protein assemblies self-regulate in response to environmental signals. Dr. Ackers’ lab achieved a major breakthrough by determining the molecular rules and energetics of molecular switching for all 10 ligation species of tetramer. This new insight opened up the possibility of deciphering a more detailed molecular basis of switching in the hemoglobin system. He was exploring the hemoglobin switching code using a combination of mutant and chemically modified hemoglobins in newly-designed anaerobic environments.
 

His strategy was two parts: (1) experimental dissection of the molecular interactions in terms of the energetic and kinetic roles played by the various structural components (i.e., the binding sites, intersubunit contacts and pairwise chemical group interactions) using a variety of thermodynamic and kinetic techniques along with site-specific alterations in structure; and (2) quantitative synthesis of the behavior of the whole system in terms of properties of the local parts as deduced from the “dissection” studies. He used the tools of statistical mechanics and kinetic theory, along with structural information, to model the biological behavior of the system. The resulting physico-chemical models were tested for their ability to correctly predict biological function.
 

The fundamental discoveries arising from Dr. Ackers’ laboratory work with hemoglobin intermediates has been cited in the major Biochemistry textbooks: Matthews & Van Holde Biochemistry 3rd Ed. (1993), Horton et al. Principles of Biochemistry (1996), Creighton, Proteins (1993), Van Holde et al Principles of Physical Biochemistry (1998), Voet et al Fundamentals of Biochemistry (1998), Berg et al Biochemistry (2001), Dill & Bromberg Molecular Driving Forces (2003), and Nelson & Cox Principles of Biochemistry (2005).
 

For more on Dr. Ackers’ life and career.

Publications

For a complete list of publications (link to PubMed Central)

• Holt, J. and Ackers, G.K. Kinetic trapping of a key hemoglobin intermediate. Methods Mol Biol 796:19-29 (2012). [Abstract]
• Johnson, M.L., Holt, J. and Ackers, G.K. Biothermodynamics, Part D. Preface. Methods Enzymol 492:xii-xiv (2011). [Abstract]
• Johnson, M.L., Holt, J. and Ackers, G.K. Biothermodynamics, Part C. Preface. Methods Enzymol 488:xv (2011). [Abstract]
• Holt, J.M. and Ackers, G.K. The Hill coefficient: Inadequate resolution of cooperativity in human hemoglobin. Methods Enzymol 455:193-212 (2009). [Abstract]
• Ackers, G.K. and Holt, J.M. Asymmetric cooperativity in a symmetric tetramer: Human hemoglobin. J Biol Chem 281:11441-11443 (2006). [Abstract]
• Ackers, G.K. and Holt, J.M. Asymmetric distribution of cooperativity in the binding cascade of normal human hemoglobin. 2. Stepwise cooperative free energy Biochem 44:11939-11949 (2005). [Abstract]
• Holt, J.M., Klinger, A.L., Yarian, C.S., Keelara, V. and Ackers, G.K. Asymmetric distribution of cooperativity in the binding cascade of normal human hemoglobin. 1. Cooperative and noncooperative oxygen binding in Zn-substituted hemoglobin. Biochemistry 44:11925-11938 (2005). [Abstract]
• Goldbeck, R.A., Esquerra, R.M., Kliger, D.S., Holt, J.M. and Ackers, G.K. The molecular code for hemoglobin allostery revealed by linking the thermodynamics and kinetics of quaternary structural change. 2. Cooperative free energies of (alphaFeCObetaFe)2 and (alphaFebetaFeCO)2 T-state tetramers. Biochemistry 43:12065-12080 (2004). [Abstract]
• Goldbeck, R.A., Esquerra, R.M., Kliger, D.S., Holt, J.M. and Ackers, G.K. The molecular code for hemoglobin allostery revealed by linking the thermodynamics and kinetics of quaternary structural change. 1. Microstate linear free energy relations. Biochemistry 43:12048-12064 (2004). [Abstract]
• Ackers, G.K., Holt, J.M., Burgie, E.S. and Yarian, C.S. Analyzing intermediate state cooperativity in hemoglobin. Methods Enzymol 379:3-28 (2004). [Abstract]
• Ackers, G.K., Delessio, P.M., Lew, G.H., Daugherty, M.A. and Holt, J.M. Single residue modification of only one dimer within the hemoglobin tetramer reveals autonomous dimer function. PNAS 99:9777-9782 (2002). [Abstract]
• Kaufman, R.M., Lu, Z.H., Behl, R., Holt, J.M., Ackers, G.K., Ley, T.J. Lack of neighborhood effects from a transcriptionally active phosphoglycerate kinase-neo cassette located between the murine beta-major and beta-minor globin genes. Blood 98:65-73 (2001). [Abstract]
• Kaufman, R.M., Lu, Z.H., Behl, R., Holt, J.M., Ackers, G.K., Ley, T.J. Lack of neighborhood effects from a transcriptionally active phosphoglycerate kinase-neo cassette located between the murine beta-major and beta-minor globin genes. Blood 98:65-73 (2001). [Abstract]
• Ackers, G.K., Holt, J.M., Huang, Y., Grinkova, Y., Klinger, A.L. and Denisov, L. Confirmation of a unique intra-dimer cooperativity in the human hemoglobin alpha(1)beta(1)half-oxygenated intermediate supports the symmetry rule model of allosteric regulation. Proteins Suppl 4:23-43 (2000). [Abstract]
• Darling, P.J., Holt, J.M. and Ackers, G.K. Coupled energetics of lambda cro repressor self-assembly and site-specific DNA operator binding II: cooperative interactions of cro dimers. J Mol Biol 302:625-638 (2000). [Abstract]
• Darling, P.J., Holt, J.M. and Ackers, G.K. Coupled energetics of lambda cro repressor self-assembly and site-specific DNA operator binding I: analysis of cro dimerization from nanomolar to micromolar concentrations. Biochemistry 39:11500-11507 (2000). [Abstract]
• Hui, H.L., Kavanaugh, J.S., Doyle, M.L., Wierzba, A., Rogers, P.H., Amone, A., Holt, J.M., Ackers, G.K. and Noble, R.W. Structural and functional properties of human hemoglobins reassembled after synthesis in Escherichia coli. Biochemistry 38:1040-1049 (1999). [Abstract]
• Pray, T.R., Burz, D.S. and Ackers, G.K. Cooperative non-specific DNA binding by octamerizing lambda cI repressors: a site-specific thermodynamic analysis. J Mol Biol 282:947-958 (1998). [Abstract]
• Merabet, E.K., Burz, D.S. and Ackers, G.K. Thermal melting properties of C-terminal domain mutants of bacteriophage lambda cI repressor. Methods Enzymol 295:450-467 (1998). [Abstract]
• Klinger, A.L. and Ackers, G.K. Analysis of spectra from multiwavelength oxygen-binding studies of mixed metal hybrid hemoglobins. Methods Enzymol 295:190-207 (1998). [Abstract]
• Ackers, G.K. Deciphering the molecular code of hemoglobin allostery. Adv Protein Chem 51:185-253 (1998). [Abstract]
• Bain, D.L. and Ackers, G.K. A quantitative cryogenic gel-shift technique for analysis of protein-DNA binding. Anal Biochem 258:240-245 (1998). [Abstract]
• Kiger, L., Klinger, A.L., Kwiatkowski, L.D., De Young, A., Doyle, M.L., Holt, J.M., Noble, R.W. and Ackers, G.K. Thermodynamic studies on the equilibrium properties of a series of recombinant betaW37 hemoglobin mutants. Biochemistry 37:4336-4345 (1998). [Abstract]
• Abraham, D.J., Kellogg, G.E., Holt, J.M. and Ackers, G.K. Hydropathic analysis of the non-covalent interactions between molecular subunits of structurally characterized hemoglobins. J Mol Biol 272:613-632 (1997). [Abstract]
• Ackers, G.K., Perrella, M., Holt, J.M., Denisov, I. and Huang, Y. Thermodynamic stability of the asymmetric doubly-ligated hemoglobin tetramer (alpha+CNbeta+CN)(alphabeta): methodological and mechanistic issues. Biochemistry 36:10822-10829 (1997). [Abstract]
• Ackers, G.K. and Bolen, D.W. The Gibbs conference on biothermodynamics: origins and evolution. Biophys Chem 64:3-5 (1997). [Abstract]
• Doyle, M.L., Holt, J.M. and Ackers, G.K. Effects of NaCl on the linkages between O2 binding and subunit assembly in human hemoglobin: titration of the quaternary enhancement effect. Biophys Chem 64:271-287 (1997). [Abstract]
• Huang, Y., Koestler, M.L. and Ackers, G.K. Tertiary and quaternary chloride effects of the partially ligated (CN-met) hemoglobin intermediates. Biophys Chem 64:157-173 (1997). [Abstract]
• Huang, Y., Koestler, M.L. and Ackers, G.K. Heterotropic effects of chloride on the ligation microstates of hemoglobin at constant water activity. Biophys J 71:2106-2116 (1996). [Abstract]
• Huang, Y., Doyle, M.L. and Ackers, G.K. The oxygen-binding intermediates of human hemoglobin: evaluation of their contributions to cooperativity using zinc-containing hybrids. Biophys J 71:2094-2105 (1996). [Abstract]
• Huang, Y., Yonetani, T., Tsuneshige, A., Hoffman, B.M. and Ackers, G.K. Heterometallic hybrids of homometallic human hemoglobins. PNAS 93:4425-4430 (1996). [Abstract]
• Burz, D.S. and Ackers, G.K. Cooperativity mutants of bacteriophage lambda cI repressor: temperature dependence of self-assembly. Biochemistry 35:3341-3350 (1996). [Abstract]
• Huang, Y. and Ackers, G.K. Transformation of cooperative free energies between ligation systems of hemoglobin: resolution of the carbon monoxide binding intermediates. Biochemistry 35:704-718 (1996). [Abstract]
• Merabet, E. and Ackers, G.K. Calorimetric analysis of lambda cI repressor binding to DNA operator sites. Biochemistry 34:8554-8563 (1995). [Abstract]
• Huang, Y. and Ackers, G.K. Enthalpic and entropic components of cooperativity for the partially ligated intermediates of hemoglobin support a “symmetry rule” mechanism. Biochemistry 34:6316-6327 (1995). [Abstract]
• LiCata, V.J. and Ackers, G.K. Long-range, small magnitude nonadditivity of mutational effects in proteins. Biochemistry 34:3133-3139 (1995). [Abstract]
• Holt, J.M. and Ackers, G.K. The pathway of allosteric control as revealed by hemoglobin intermediate states. FASEB J 9:210-218 (1995). [Abstract]
• Bain, D.L. and Ackers, G.K. Self-association and DNA binding of lambda cI repressor N-terminal domains reveal linkage between sequence-specific binding and the C-terminal cooperativity domain. Biochemistry 33:14679-14689 (1994). [Abstract]
• Daugherty, M.A., Shea, M.A. and Ackers, G.K. Bohr effects of the partially-ligated (CN-met) intermediates of hemoglobin as probed by quaternary assembly. Biochemistry 33:10345-10357 (1994). [Abstract]
• Burz, D.S. and Ackers, G.K. Single-site mutations in the C-terminal domain of bacteriophage lambda cI repressor alter cooperative interactions between dimers adjacently bound to OR. Biochemistry 33:8406-8416 (1994). [Abstract]
• Burz, D.S., Beckett, D., Benson, N. and Ackers, G.K. Self-assembly of bacteriophage lambda cI repressor: effects of single-site mutations on the monomer-dimer equilibrium. Biochemistry 33:8399-8405 (1994). [Abstract]
• Doyle, M.L., Myers, D.W., Ackers, G.K. and Shrager, R.I. Weighted nonlinear regression analysis of highly cooperative oxygen equilibrium curves. Methods Enzymol 232:576-597 (1994). [Abstract]
• Ackers, G.K. and Hazard, J.H. Single-site modifications of half-ligated hemoglobin reveal autonomous dimer cooperativity within a quaternary T tetramer. Proteins 17:279-296 (1993). [Abstract]
• Licata, V.J., Dalessio, P.M. and Ackers, G.K. Transduction of binding energy into hemoglobin cooperativity. Trends Biochem 18:385-390 (1993). [Abstract]
• Beckett, D., Burz, D.S., Ackers, G.K. and Sauer, R.T. Isolation of lambda repressor mutants with defects in cooperative operator binding. Biochemistry 32:9073-9079 (1993). [Abstract]
• Doyle, M.L. and Ackers, G.K. Cooperative oxygen binding, subunit assembly, and sulfhydryl reaction kinetics of the eight cyanomet intermediate ligation states of human hemoglobin. Biochemistry 31:11182-11195 (1992). [Abstract]
• Doyle, M.L., Lew, G., Turner, G.J., Rucknagel, D. and Ackers, G.K. Regulation of oxygen affinity by quaternary enhancement: does hemoglobin Ypsilanti represent an allosteric intermediate? Proteins 14:351-362 (1992). [Abstract]
• Turner, G.J., Galacteros, F., Doyle, M.L., Hedlund, B., Pettigrew, D.W., Turner, B.W., Smith, F.R., Moo-Penn, W., Rucknagel, D.L. and Ackers, G.K. Mutagenic dissection of hemoglobin cooperativity: effects of amino acid alteration on subunit assembly of oxy and deoxy tetramers. Proteins 14:333-350 (1992). [Abstract]
• Doyle, M.L., Lew, G., De Young, A., Kwiatkowski, L., Wierzba, A., Noble, R.W. and Ackers, G.K. Functional properties of human hemoglobins synthesized from recombinant mutant beta-globins. Biochemistry 31:8629-8639 (1992). [Abstract]
• Englander, S.W., Englander, J.J., McKinnie, R.E., Ackers, G.K., Turner, G.J., Westrick, J.A. and Gill, S.J. Hydrogen exchange measurement of the free energy of structural and allosteric change in hemoglobin. Science 256:1684-1687 (1992). [Abstract]
• Doyle, M.L. and Ackers, G.K. Weighting functions and parameter resolvability for oxygenation data subject to error in the independent variable. Biophys Chem 42:271-281 (1992). [Abstract]
• Koblan, K.S. and Ackers, G.K. Site-specific enthalpic regulation of DNA transcription at bacteriophage lambda OR. Biochemistry 31:57-65 (1992). [Abstract]
• Ackers, G.K., Doyle, M.L., Myers, D. and Daugherty, M.A. Molecular code for cooperativity in hemoglobin. Science 255:54-63 (1992). [Abstract]
• Koblan, K.S., Bain, D.L., Beckett, D., Shea, M.A. and Ackers, G.K. Analysis of site-specific interaction parameters in protein-DNA complexes. Methods Enzymol. 210:405-425 (1992). [Abstract]
• Koblan, K.S. and Ackers, G.K. Cooperative protein-DNA interactions: effects of KCl on lambda cI binding to OR. Biochemistry 30:7822-7827 (1991). [Abstract]
• Koblan, K.S. and Ackers, G.K. Energetics of subunit dimerization in bacteriophage lambda ci repressor: linkage to protons temperature and KCl. Biochemistry 30:7817-7821 (1991). [Abstract]
• Doyle, M.L., Speros, P.C., Licata, V.J., Gingrich, D., Hoffman, B.M. and Ackers, G.K. Linkage between cooperative oxygenation and subunit assembly of cobaltous human hemoglobin. Biochemistry 30:7263-7271 (1991). [Abstract]
• Speros, P.C., Licata, V.J., Yonetani, T. and Ackers, G.K. Experimental resolution of cooperative free energies for the ten ligation species of cobalt(II)/iron(II)-CO hemoglobin. Biochemistry 30:7254-7262 (1991). [Abstract]
• Beckett, D., Koblan, K.S. and Ackers, G.K. Quantitative study of protein association at pico molar concentrations: the lambda phage cl repressor. Anal Biochem 196:69-75 (1991). [Abstract]
• Daugherty, M.A., Shea, M.A., Johnson, J.A., Licata, V.J., Turner, G.J. and Ackers, G.K. Identification of the intermediate allosteric species in human hemoglobin reveals a molecular code for cooperative switching. PNAS 88:1110-1114 (1991). [Abstract]
• Licata, V.J., Speros, P.C., Rovida, E. and Ackers, G.K. Direct and indirect pathways of functional coupling in human hemoglobin are revealed by quantitative low-temperature isoelectric focusing of mutant hybrids. Biochemistry 29:9771-9783 (1990). [Abstract]
• Ackers, G.K. The energetics of ligand-linked subunit assembly in hemoglobin require a third allosteric structure. Biophys Chem 37:371-382 (1990). [Abstract]
• Ackers, G.K. and Johnson, M.L. Analysis of hemoglobin oxygenation from combined equilibrium and kinetic data. Is quaternary enhancement necessary? Biophys Chem 37:265-279 (1990). [Abstract]
• Senear, D.F. and Ackers, G.K. Proton-linked contributions to site-specific interactions of lambda cI repressor and OR. Biochemistry 29:6568-6577 (1990). [Abstract]
• Perrelli, M., Benazzi, L., Shea, M.A. and Ackers, G.K. Subunit hybridization studies of partially ligated cyanomethemoglobins using a cryogenic method. Evidence for three allosteric states. Biophys Chem 35:97-103 (1990). [Abstract]
• Brenowitz, M., Senear, D.F. and Ackers, G.K. Flanking DNA-sequences contribute to the specific binding of cI-repressor and OR1. Nucleic Acids Res 17:3747-3755 (1989). [Abstract]
• Smith, F.R., Gingrich, D., Hoffman, B.M. and Ackers, G.K. Three-state combinatorial switching in hemoglobin tetramers: comparison between functional energetics and molecular structures. PNAS 84:7089-7093 (1987). [Abstract]
• Ackers, G.K. and Smith, F.R. The hemoglobin tetramer: a three-state molecular switch for control of ligand affinity. Annu Rev Biophys Biophys Chem 16:583-609 (1987). [Abstract]
• Senear, D.F., Brenowitz, M., Shea, M.A. and Ackers, G.K. Energetics of cooperative protein-DNA interactions: comparison between quantitative deoxyribonuclease footprint titration and filter binding. Biochemistry 25:7344-7354 (1986). [Abstract]
• Brenowitz, M., Senear, D.F., Shea, M.A. and Ackers, G.K. “Footprint” titrations yield valid thermodynamic isotherms. PNAS 83:8462-8466 (1986). [Abstract]
• Ackers, G.K. and Smith, F.R. Resolving pathways of functional coupling within protein assemblies by site-specific structural perturbation. Biophys J 49:155-165 (1986). [Abstract]
• Brenowitz, M., Senear, D.F., Shea, M.A. and Ackers, G.K. Quantitative DNase footprint titration: a method for studying protein-DNA interactions. Methods Enzymol. 130:132-181 (1986). [Abstract]
• Smith, F.R. and Ackers, G.K. Experimental resolution of cooperative free energies for the ten ligation state of human hemoglobin. PNAS 82:5347-5351 (1985). [Abstract]
• Frankel, A.D., Ackers, G.K. and Smith, H.O. Measurement of DNA-protein equilibria using gel chromatography: application to the Hinfl restriction endonuclease. Biochemistry 24:3049-3054 (1985). [Abstract]
• Shea, M.A. and Ackers, G.K. The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation. J Mol Biol 181:211-230 (1985). [Abstract]
• Ackers, G.K. and Smith, F.R. Effects of site-specific amino acid modification on protein interactions an biological function. Annu Rev Biochem 54:597-629 (1985). [Abstract]
• Kukuruzinska, M.A., Turner, B.W., Ackers, G.K. and Roseman, S. Subunit association of enzyme I of the Salmonella typhimurium phosphoenolpyruvate: glycose phosphotransferase system. Temperature dependence and thermodynamic properties. J Biol Chem 259:11679-11681 (1984). [Abstract]
• McCarthy, M.P., Steffen, P.K., Allewell, N.M., Benedict, R.C., Moudrianakis, E.N. and Ackers, G.K. Effects of ionic strength and state of assembly on kinetics of hydrogen exchange of calf thymus histones. Biochemistry 23:2227-2230 (1984). [Abstract]
• Johnson, M.L., Turner, B.W. and Ackers, G.K. A quantitative model for the cooperative mechanisms of human hemoglobin. PNAS 81:1093-1097 (1984). [Abstract]
• Ackers, G.K., Shea, M.A. and Smith, F.R. Free energy coupling within macromolecules. The chemical work of ligand binding at the individual sites in co-operative systems. J Mol Biol 170:223-242 (1983). [Abstract]
• Thillet, J., Chu, A.H., Romeo, P., Tsapis, A. and Ackers, G.K. Effects of anions on the ligand-linked subunit assembly of human hemoglobin: the mutual effects of Cl- and EDTA. Hemoglobin 7:141-157 (1983). [Abstract]
• Ackers, G.K., Benesch, R.E. and Edalji, R. Effects of inositol hexasulfate on the oxygen affinity of hemoglobin: verification of the integral function theory of thermodynamic linkage. Biochemistry 21:875-879 (1982). [Abstract]