The following programs were developed by our group. Click each link for
more information and references. If you would like to use them, please
contact Junji Iwahara. Download instructions will be sent via email.
1. NMR pulse programs to study dynamics of lysine side-chain NH3+ groups
This package includes NMR pulse programs to measure:
[1a] Esadze A, Li DW, Wang T, Brüschweiler R, Iwahara J (2011) J Am Chem Soc 133, 909-19.
[1b] Zandashvili L, Li DW, Wang T, Brüschweiler R, Iwahara J (2011) J Am Chem Soc 133, 9192-5.
[1c] Anderson KM, Esadze A, Manoharan M, Brüschweiler R, Gorenstein DG, Iwahara J (2013) J Am Chem Soc 135, 3613-9.
[1d] Zandarashvili L, Esadze A, Iwahara J (2013) Adv Protein Chem Struct Biol 93, 37-80.
[1e] Nguyen, D., Lokesh, G.L.R., Volk, D.E., Iwahara, J. (2017) Molecules 22, 1355.
2. NMR pulse programs for triple resonance experiments to assign lysine NH3+ groups
This package includes NMR pulse programs for:
[2a] Iwahara J, Jung YS, Clore GM (2007) J Am Chem Soc 129, 2971-80.
[2b] Takayama Y, Castaneda CA, Chimenti M, Garcia-Moreno B, Iwahara J (2008) J Am Chem Soc 130, 6714-5.
[2c] Zandarashvili L, Esadze A, Iwahara J (2013) Adv Protein Chem Struct Biol 93, 37-80.
[2d] Esadze A, Zandarashvili L, Iwahara J (2014) J Biomol NMR 60, 23-7.
3. NMR pulse programs for 1H PRE rates Γ1 and Γ2 measurements
These pulse programs are for measuring 1H paramagnetic relaxation enhancement (PRE) rates Γ1 and Γ2 for proteins.
[3a] Iwahara J, Schwieters CD, Clore GM. (2004) J Am Chem Soc 126, 5879-96.
[3b] Iwahara J, Tang C, Clore GM (2007) J Magn Reson 184, 185-93.
[3c] Clore GM, Iwahara J (2009) Chem Rev 109, 4108-39.
[3d] Iwahara J, Clore GM (2010) J Am Chem Soc 132, 13346-56.
4. TDSK: Programs for kinetic analyses of protein translocation on DNA
This is a package of the MATLAB scripts for simulations and data fitting to study kinetics of target search processes of protein in the presence of specific and nonspecific DNA. One-dimensional diffusion coefficient for sliding, effective sliding length, second-order rate constant for intersegment transfer, dissociation from nonspecific sites can be determined from stopped-flow fluorescence kinetic data.
[4a] Esadze A, and Iwahara J (2014) J Mol Biol 426, 230-40.
[4b] Esadze A, Kemme CA, Kolomeisky AB, Iwahara J (2014) Nucleic Acids Res 42, 7039-46.