Sealy Center for Structural Biology and Molecular Biophysics

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.

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.

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.