Software

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.

NMR pulse programs to study dynamics of lysine side-chain NH3+ groups

Software Available from the Iwahara Lab

1. NMR pulse programs to study dynamics of lysine side-chain NH₃⁺ groups

This package includes NMR pulse programs to measure:

¹⁵N longitudinal relaxation rates R₁ for lysine NH₃⁺ groups
¹⁵N transverse relaxation rates R₂ for lysine NH₃⁺ groups
{¹H-} ¹⁵N NOE for lysine NH₃⁺ groups
Relaxation rates R(4N_zH_zH_z) for lysine NH₃⁺ groups
Scalar couplings ³J_NC between lysine side-chain ¹⁵Nζ and ¹³Cγ
Hydrogen-bond scalar couplings ^h3J_NC involving lysine side-chain NH₃⁺ groups
Hydrogen-bond scalar couplings ^h3J_NP between protein lysine ¹⁵Nζ and DNA ³¹P nuclei
Hydrogen exchange rates k_ex^water

References:
[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.

NMR pulse programs for triple resonance experiments to assign lysine NH3+ groups

Software Available from the Iwahara Lab

2. NMR pulse programs for triple resonance experiments to assign lysine NH₃⁺ groups

This package includes NMR pulse programs for:

2D ¹H-¹⁵N HISQC experiment for lysine NH₃⁺ groups
3D H3NCECD for lysine side chains
3D HDHECDCENH3 for lysine side chains
3D (H)CCNH3 for lysine side chains
3D H3NCG for lysine side chains
3D H2CN for lysine side chains
2D (H2C)N(CC)H-TOCSY

References:
[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.

NMR pulse programs for 1H PRE rates Γ1 and Γ2 measurements

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.

References:
[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.

TDSK for kinetic analyses of protein translocation on DNA

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.

References:
[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.