Joseph M. Chalovich, PhD
Distinguished Professor & Emeritus
The Brody School of Medicine at East Carolina University
Greenville, NC 27834
- Pennsylvania State University, Univ. Park, 1974, B.S. Biochemistry
- Virginia Polytechnic Institute & State Univ., Blacksburg, 1976, M.S. Biochemistry & Nutrition
- University of Illinois Medical Center, Chicago, 1978, Ph.D. Biochemistry
This file contains a collection of simple programs that are useful in biophysical studies of contractile proteins. Two mathematical platforms are used: MLAB (Civilized Software) and Mathematica (Wolfram).
Ligand binding to actin: I published a Book Chapter on actin binding studies in Molecular Motors. Methods and Protocols edited by Ann O. Sperry. That chapter describes methods of analysis of binding to actin.
Binding of a large ligand that interacts with several actin protomers cannot be analyzed by the Scatchard analysis. The appropriate model is that of McGhee and von Hippel J. Mol Biol (1974). Two programs are available for exploring that formalism and for fitting that equation to data. Data are most easily fit using the MLAB routine MC.do. A set of data to fit is also given: test2.txt.
Simulating data can be done using the Mathematica program mcgheesimple.nb. Mathematica is not as well suited for fitting although it may be possible.
The cooperative binding of single headed myosin fragments (S1) to actin-tropomyosin-troponin can be fitted with the model of T. Hill using the MLAB program Hill2.do and the test data file test1.txt. The Hill binding equation can also be simulated with two Mathematica programs: hillfunction.nb and hilleqn.nb. They both produce similar results but the former is written as a series of functions that can be useful for some applications.
Actin polymerization: Many proteins bind to actin. Some of these affect actin polymerization in some manner. Some proteins accelerate actin polymerization, others fragment actin filaments and others have other functions. Actin polymerization can be simulated with the Mathematica program polymer4.nb or with the MLAB program polysim.do. A polymerization model can be fit to polymerization data using the MLAB program polyfit.do. A test data set is included: actinpdata.txt. Users of the program KINTEK (Ken Johnson) should note that a polymerization program is included in that package.
Foerster Resonance Energy Transfer: The program “ae” is a collection of programs for fluorescence studies. It is available for free. We use some Mathematica routines for resolving overlapping spectral peaks, calculating Ro and R. These routines are present in the file FRET Suite JMC.nb. I find these small programs to be useful although everything can probably be done in ae.
Baxley, T., Johnson, D., Pinto, J.R. and Chalovich, J.M. (2017) Troponin C mutations partially stabilize the active state of regulated actin and fully stabilize the active state when paired with D14 TnT. Biochemistry, 56: 2928-2973.
Johnson, D., Angus, C.W. and Chalovich, J.M. (2018) Stepwise C-terminal truncation of cardiac troponin T alters function at low and saturating Ca2+. Biophys J 115: 702-712.
Johnson, D., Zhu, L., Landim-Vieira, M., Pinto, J. R. & Chalovich, J. M. (2019) Basic residues within the cardiac troponin T C-terminus are required for full inhibition of muscle contraction and limit activation by calcium. J. Biol. Chem. 294: 19535-45.
Lopez-Davila, A.J., Chalovich, J.M., Zittrich, S., Piep, B., Matinmehr, F., Malnasi-Csizmadia, A., Rauscher, A.A., Kraft, T., Brenner, B., and Stehle, R. (2020) Cycling cross-bridges contribute to thin filament activation in human slow-twitch fibers. Front Physiol 11: 144.
Chalovich, J.M. (2012) Michael Bárány: a recollection. J. Muscle Res. Cell Motil. 33: 373-6. DOI: 10.1007/s10974-012-9295-8
Chalovich, J.M. and Johnson, D. (2016) Commentary: Effect of Skeletal Muscle Native Tropomyosin on the Interaction of Amoeba Actin with Heavy Meromyosin. Front. Physiol. 7: 377.
Chalovich, J.M., Kraft, T. and Yu, L.C. (2017) Obituary Bernhard Brenner. J Muscle Res Cell Motil. 38: 269-270.