Quantum chemical estimates chemical shifts in proteins and nucleic acids

The afnmr suite allows one to estimate chemical shifts in biomoleucles, based on a fragmentation approach, and quantum chemical calculations. This functionality is self-contained and does not require AmberTools.

The basic ideas are presented in the following papers:

1. X. He, B. Wang, and K.M. Merz, Jr. Protein NMR Chemical Shift Calculations Based on the Automated Fragmentation QM/MM Approach. J. Phys. Chem. B 113, 10380-10388 (2009).

2. T. Zhu, X. He, and J.Z.H. Zhang. Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation. Phys. Chem. Chem. Phys. 14, 7837-7845 (2012)

3. T. Zhu, J.Z.H. Zhang, and X. He. Automated Fragmentation QM/MM Calculation of Amide Proton Chemical Shifts in Proteins with Explicit Solvent Model. J. Chem. Theory Comput. 9, 2104-2114 (2013)

4. S. Tang and D.A. Case. Calculation of chemical shift anisotropy in proteins. J. Biomol. NMR 51, 303-312 (2011).

5. D.A. Case. Chemical shifts in biomolecules. Curr. Opin. Struct. Biol. 23, 172-176 (2013).

6. J. Swails, T. Zhu, X. He and David A. Case. AFNMR: Automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules. J. Biomol. NMR 63, 125-139 (2015).

7. D.A. Case. Using quantum chemistry to estimate chemical shifts in biomolecules. Biophys. Chem. 267, 106476 (2020).

Here are some recent applications:

• H. Zhang, G. Hou, M. Lu, J. Ahn, I.-J. Byeon, C.J. Langmead, J.R. Perilla, I. Hung, P.L. Gor'kov, Z. Gan, W. Brey, D.A. Case, K. Schulten, A.M. Gronenborn, and T. Polenova. HIV-1 Capsid Function is Regulated by Dynamics: Quantitative Atomic-Resolution Insights by Integrating Magic-Angle-Spinning NMR, QM/MM, and MD. J. Am. Chem. Soc. 138, 14066-14075 (2016).

• M. Fritz, C.M. Quinn, M. Wang, G. Hou, X. Lu, L.M.I. Koharudin, J. Struppe, D.A. Case, T. Polenova and A.M. Gronenborn. Accurate determination of backbone chemical shift tensors in microcrystalline proteins by integrated MAS NMR and QM/MM. Phys. Chem. Chem. Phys. 20, 9543-9553 (2018).

• H. Shi, M.C. Clay, A. Rangadurai, B. Sathyamoorthy, D.A. Case, and H.M. Al-Hashimi. Atomic Structures of Excited State A-T Hoogsteen Base Pairs in Duplex DNA by Combining NMR Relaxation Dispersion, Mutagenesis, and Chemical Shift Calculations. J. Biomol. NMR 70, 229-244 (2018).

• H. Zhou, B. Sathyamoorthy, A. Stelling, Y. Xu, Y. Xue, Y.Z. Pigli, D.A. Case, P.A. Rice, and H.M. Al-Hashimi. Characterizing Watson–Crick versus Hoogsteen Base Pairing in a DNA–Protein Complex Using Nuclear Magnetic Resonance and Site-Specifically 13C-and 15N-Labeled DNA. Biochemistry 58, 1963-1974 (2019).

• H. Shi, A. Rangadurai, H.A. Assi, R. Roy, D.A. Case, D. Herschlag, J.D. Yesselman, and H.M. Al-Hashimi. Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction. Nature Commun. 11, 5531 (2020).

• B. Liu, H. Shi, A. Rangadurai, C.-C. Chu, F. Nussbaumer, K.A. Erharter, D.A. Case, C. Kreutz, and H.M. Al-Hashimi. m6A delays base-pairing through syn-anti isomerization of the methylamino group. Nature Commun. 12, 5201 (2021).

The latest version (1.9.0, February, 2025) of the afnmr package can be obtained from:

github.com/dacase/afnmr

Installation and usage instructions are in the afnmr.pdf file, in the "doc" folder. As noted above, afnmr is fully self-contained, and does not require AmberTools.