Numbat: an interactive software tool for fitting Δχ-tensors to molecular coordinates using pseudocontact shifts

Allegrozzi M, Bertini I, Janik MBL, Lee Y-M, Liu G, Luchinat C (2000) Lanthanide-induced pseudocontact shifts for solution structure refinements of macromolecules in shells up to 40 Å from the metal ion. J Am Chem Soc 122:4154–4161

Banci L, Dugad LB, La Mar GN, Keating KA, Luchinat C, Pierattelli R (1992) 1H nuclear magnetic resonance investigation of cobalt(II) substituted carbonic anhydrase. Biophys J 63:530–543

Banci L, Bertini I, Bren KL, Cremonini MA, Gray HB, Luchinat C, Turano P (1996) The use of pseudocontact shifts to refine solution structures of paramagnetic metalloproteins: Met80Ala cyano-cytochrome c as an example. J Biol Inorg Chem 1:117–126

Banci L, Bertini I, Savellini GG, Romagnoli A, Turano P, Cremonini MA, Luchinat C, Gray HB (1997) Pseudocontact shifts as constraints for energy minimization and molecular dynamics calculations on solution structures of paramagnetic metalloproteins. Proteins Struct Funct Genet 29:68–76

Banci L, Bertini I, Cremonini MA, Savellini GG, Luchinat C, Wüthrich K, Güntert P (1998) PSEUDYANA for NMR structure calculation of paramagnetic metalloproteins using torsion angle molecular dynamics. J Biomol NMR 12:553–557

Banci L, Bertini I, Cavallaro G, Giachetti A, Luchinat C, Parigi G (2004) Paramagnetism-based restraints for Xplor-NIH. J Biomol NMR 28:249–261

Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235–242

Bertini I, Donaire A, Jiménez B, Luchinat C, Parigi G, Piccioli M, Poggi L (2001) Paramagnetism-based versus classical constraints: an analysis of the solution structure of Ca Ln calbindin D9k. J Biomol NMR 21:85–98

Bertini I, Luchinat C, Parigi G (2002) Magnetic susceptibility in paramagnetic NMR. Prog NMR Spectrosc 40:249–273

Bertini I, Del Bianco C, Gelis I, Katsaros N, Luchinat C, Parigi G, Peana M, Provenzani A, Zoroddu MA (2004) Experimentally exploring the conformational space sampled by domain reorientation in calmodulin. Proc Natl Acad Sci U S A 101:6841–6846

Bugayevskiy LM, Snyder JP (1995) Map projections: a reference manual. Taylor & Francis, London

Capozzi F, Cremonini MA, Luchinat C, Sola M (1993) Assignment of pseudo-contact-shifted 1H NMR resonances in the EF site of Yb3+-substituted rabbit parvalbumin through a combination of 2D techniques and magnetic susceptibility tensor determination. Magn Reson Chem 31:S118–S127

Clore GM, Gronenborn AM, Bax A (1998) A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information. J Magn Reson 133:216–221

Cornilescu G, Bax A (2000) Measurement of proton, nitrogen, and carbonyl chemical shielding anisotropies in a protein dissolved in a dilute liquid crystalline phase. J Am Chem Soc 122:10143–10154

DeLano WL (2002) The PyMOL molecular graphics system. Palo Alto, CA, USA

Dosset P, Hus J-C, Blackledge M, Marion D (2000) Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data. J Biomol NMR 16:23–28

Eichmüller C, Skrynnikov NR (2007) Observation of μs time-scale protein dynamics in the presence of Ln3+ ions: application to the N-terminal domain of cardiac troponin C. J Biomol NMR 37:79–95

Emerson SD, La Mar GN (1990) NMR determination of the orientation of the magnetic susceptibility tensor in cyanometmyoglobin: a new probe of steric tilt of bound ligand. Biochemistry 29:1556–1566

Galassi M, Davies J, Theiler J, Gough B, Jungman G, Booth M, Rossi F (2006) GNU scientific library reference manual. Network Theory Ltd, Bristol

Gaponenko V, Sarma SP, Altieri AS, Horita DA, Li J, Byrd RA (2004) Improving the accuracy of NMR structures of large proteins using pseudocontact shifts as long-range restraints. J Biomol NMR 28:205–212

Güntert P, Mumenthaler C, Wüthrich K (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 273:283–298

Hess B, Scheek RM (2003) Orientation restraints in molecular dynamics simulations using time and ensemble averaging. J Magn Reson 164:19–27

Jensen MR, Hansen DF, Ayna U, Dagil R, Hass MAS, Christensen HEM, Led JJ (2006) On the use of pseudocontact shifts in the structure determination of metalloproteins. Magn Reson Chem 44:294–301

John M, Park AY, Pintacuda G, Dixon NE, Otting G (2005) Weak alignment of paramagnetic proteins warrants correction for residual CSA effects in measurements of pseudocontact shifts. J Am Chem Soc 127:17190–17191

John M, Pintacuda G, Park AY, Dixon NE, Otting G (2006) Structure determination of protein–ligand complexes by transferred paramagnetic shifts. J Am Chem Soc 128:12910–12916

Keniry MA, Park AY, Owen EA, Hamdan SM, Pintacuda G, Otting G, Dixon NE (2006) Structure of the θ subunit of Escherichia coli DNA polymerase III in complex with the ε subunit. J Bacteriol 188:4464–4473

Kirby TW, Harvey S, DeRose EF, Chalov S, Chikova AK, Perrino FW, Schaaper RM, London RE, Pedersen LC (2006) Structure of the Escherichia coli DNA polymerase III ε-HOT proofreading complex. J Biol Chem 281:38466–38471

Koradi R, Billeter M, Wüthrich K (1996) MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graphics 14:51–55

Krause A (2007) Foundations of GTK + development. Apress. Berkeley, CA, USA

Lee L, Sykes BD (1983) Use of lanthanide-induced nuclear magnetic resonance shifts for determination of protein structure in solution: EF calcium binding site of carp parvalbumin. Biochemistry 22:4366–4373

Marquardt DW (1963) An algorithm for least-squares estimation of nonlinear parameters. J Soc Ind Appl Math 11:431–441

Nelder JA, Mead R (1965) A simplex method for function minimization. Comput J 7:308–313

Pintacuda G, John M, Su X-C, Otting G (2007) NMR structure determination of protein–ligand complexes by lanthanide labeling. Acc Chem Res 40:206–212

Pintacuda G, Keniry MA, Huber T, Park AY, Dixon NE, Otting G (2004) Fast structure-based assignment of 15N HSQC spectra of selectively 15N-labeled paramagnetic proteins. J Am Chem Soc 126:2963–2970

Pintacuda G, Park AY, Keniry MA, Dixon NE, Otting G (2006) Lanthanide labeling offers fast NMR approach to 3D structure determinations of protein–protein complexes. J Am Chem Soc 128:3696–3702

Schmitz C, John M, Park AY, Dixon NE, Otting G, Pintacuda G, Huber T (2006) Efficient χ-tensor determination and NH assignment of paramagnetic proteins. J Biomol NMR 35:79–87

Schwieters CD, Kuszewski JJ, Tjandra N, Clore GM (2003) The Xplor-NIH NMR molecular structure determination package. J Magn Reson 160:65–73

Schwieters CD, Kuszewski JJ, Clore GM (2006) Using Xplor-NIH for NMR molecular structure determination. Prog NMR Spectrosc 48:47–62

Sherry AD, Pascual E (1977) Proton and carbon lanthanide-induced shifts in aqueous alanine. Evidence for structural changes along the lanthanide series. J Am Chem Soc 99:5871–5876

Su X-C, McAndrew K, Huber T, Otting G (2008) Lanthanide-binding peptides for NMR measurements of residual dipolar couplings and paramagnetic effects from multiple angles. J Am Chem Soc 130:1681–1687

Tolman JR, Flanagan JM, Kennedy MA, Prestegard JH (1995) Nuclear magnetic dipole interactions in field-oriented proteins: Information for structure determination in solution. Proc Natl Acad Sci U S A 92:9279–9283

Valafar H, Prestegard JH (2004) REDCAT: a residual dipolar coupling analysis tool. J Magn Reson 167:228–241

Van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC (2005) GROMACS: fast, flexible, and free. J Comput Chem 26:1701–1718

Veitch NC, Whitford D, Williams RJP (1990) An analysis of pseudocontact shifts and their relationship to structural features of the redox states of cytochrome b5. FEBS Lett 269:297–304

Wang X, Srisailam S, Yee AA, Lemak A, Arrowsmith C, Prestegard JH, Tian F (2007) Domain-domain motions in proteins from time-modulated pseudocontact shifts. J Biomol NMR 39:53–61

Wei Y, Werner MH (2006) iDC: a comprehensive toolkit for the analysis of residual dipolar couplings for macromolecular structure determination. J Biomol NMR 35:17–25

Zweckstetter M, Bax A (2000) Prediction of sterically induced alignment in a dilute liquid crystalline phase: aid to protein structure determination by NMR. J Am Chem Soc 122:3791–3792