1. L. Pauling, R. B. Corey, H. R. Branson, The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain. Proc. Natl. Acad. Sci. 37, 205–211 (1951).
2. R. M. Smith, D. E. Hansen, The pH-rate profile for the hydrolysis of a peptide bond. J. Am. Chem. Soc. 120, 8910–8913 (1998).
3. L. Pauling, R. B. Corey, Configurations of polypeptide chains with favored orientations around single bonds. Proc. Natl. Acad. Sci. 37, 729–740 (1951).
4. D. Bordo, P. Argos, The role ofside-chain hydrogen bonds in the formation and stabilization ofsecondary structure in soluble proteins. J. Mol. Biol. 243, 504–519 (1994).
5. N. Eswar, C. Ramakrishnan, Secondary structures without backbone: An analysis of backbone mimicry by polar side chains in protein structures. Protein Eng. 12, 447–455 (1999).
6. A. E. Mirsky, L. Pauling, On the structure of native, denatured, and coagulated proteins. Proc. Natl. Acad. Sci. 22, 439–447 (1936).
7. C. N. Pace, H. Fu, K. L. Fryar, J. Landua, S. R. Trevino, D. Schell, R. L. Thurlkill, S. Imura, J. M. Scholtz, K. Gajiwala, J. Sevcik, L. Urbanikova, J. K. Myers, K. Takano, E. J. Hebert, B. A. Shirley, G. R. Grimsley, Contribution of hydrogen bonds to protein stability. Protein Sci. 23, 652–661 (2014).
8. S. Y. Sheu, D. Y. Yang, H. L. Selzle, E. W. Schlag, Energetics of hydrogen bonds in peptides. Proc. Natl. Acad. Sci. U.S.A. 100, 12683–12687 (2003).
9. J. U. Bowie, Membrane protein folding: How important are hydrogen bonds? Curr. Opin. Struct. Biol. 21, 42–49 (2011).
10. S. Rajagopal, S. Vishveshwara, Short hydrogen bonds in proteins. FEBS J. 272, 1819–1832 (2005).
11. B. S. Avvaru, C. U. Kim, K. H. Sippel, S. M. Gruner, M. Agbandje-McKenna, D. N. Silverman, R. McKenna, A short, strong hydrogen bond in the active site of human carbonic anhydrase II. Biochemistry 49, 249–251 (2010).
12. C. N. Pace, Energetics of protein hydrogen bonds. Nat. Struct. Mol. Biol. 16, 681–682 (2009).
13. L. Nisius, S. Grzesiek, Key stabilizing elements of protein structure identified through pressure and temperature perturbation of its hydrogen bond network. Nat. Chem. 4, 711–717 (2012).
14. C. L. Worth, T. L. Blundell, Satisfaction of hydrogen-bonding potential influences the conservation of polar sidechains. Proteins 75, 413–429 (2009).
15. D. S. Berkholz, C. M. Driggers, M. V. Shapovalov, R. L. Dunbrack Jr., P. A. Karplus, Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites. Proc. Natl. Acad. Sci. U.S.A. 109, 449–453 (2012).
16. A. E. Brereton, P. A. Karplus, On the reliability of peptide nonplanarity seen in ultra-high resolution crystal structures. Protein Sci. 25, 926–932 (2016).
17. R. Improta, L. Vitagliano, L. Esposito, Peptide bond distortions from planarity: New insights from quantum mechanical calculations and peptide/protein crystal structures. PLOS ONE 6, e24533 (2011).
18. L. Esposito, A. De Simone, A. Zagari, L. Vitagliano, Correlation between and dihedral angles in protein structures. J. Mol. Biol. 347, 483–487 (2005).
19. Y. Fukuda, Y. Hirano, K. Kusaka, T. Inoue, T. Tamada, High-resolution neutron crystallography visualizes anOH-bound resting state of a copper-containing nitrite reductase. Proc. Natl. Acad. Sci. U.S.A. 117, 4071–4077 (2020).
20. T. S. Ulmer, B. E. Ramirez, F. Delaglio, A. Bax, Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy. J. Am. Chem. Soc. 125, 9179–9191 (2003).
21. B. Vögeli, How uniform is the peptide plane geometry? A high-accuracy NMR study of dipolar C–C′/HN–N cross-correlated relaxation. J. Biomol. NMR 50, 315–329 (2011).
22. M. P. Blakeley, S. S. Hasnain, S. V. Antonyuk, Sub-atomic resolution X-ray crystallography and neutron crystallography: Promise, challenges and potential. IUCrJ. 2, 464–474 (2015).
23. B. Schoepp, P. Parot, L. Menin, J. Gaillard, P. Richaud, A. Verméglio, In vivo participation of a high potential iron-sulfur protein as electron donor to the photochemical reaction center of Rubrivivax gelatinosus. Biochemistry 34, 11736–11742 (1995).
24. H. A. Heering, Y. B. M. Bulsink, W. R. Hagen, T. E. Meyer, Influence of charge and polarity on the redox potentials of high-potential iron-sulfur proteins: Evidence for the existence of two groups. Biochemistry 34, 14675–14686 (1995).
25. T. Glaser, I. Bertini, J. J. G. Moura, B. Hedman, K. O. Hodgson, E. I. Solomon, Protein effects on the electronic structure ofthe [Fe4S4] 2+ cluster in ferredoxin andHiPIP. J. Am. Chem. Soc. 123, 4859–4860 (2001).
26. S. Niu, T. Ichiye, Insight into environmental effects on bonding and redox properties of [4Fe-4S] clusters in proteins. J. Am. Chem. Soc. 131, 5724–5725 (2009).
27. A. Dey, F. E. J. Jenney Jr., M. W. W. Adams, E. Babini, Y. Takahashi, K. Fukuyama, K. O. Hodgson, B. Hedman, E. I. Solomon, Solvent tuning of electrochemical potentials in the active sites of HiPIP versus ferredoxin. Science 318, 1464–1468 (2007).
28. Y. Hirano, K. Takeda, K. Miki, Charge-density analysis of an iron-sulfur protein at an ultra-high resolution of 0.48 Å. Nature 534, 281–284 (2016).
29. T. Nogi, I. Fathir, M. Kobayashi, T. Nozawa, K. Miki, Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: Thermostability and electron transfer. Proc. Natl. Acad. Sci. U.S.A. 97, 13561–13566 (2000).
30. L. Liu, T. Nogi, M. Kobayashi, T. Nozawa, K. Miki, Ultrahigh-resolution structure of high-potential iron-sulfur protein from Thermochromatium tepidum. Acta Crystallogr. D Biol. Crystallogr. 58, 1085–1091 (2002).
31. K. Takeda, K. Kusumoto, Y. Hirano, K. Miki, Detailed assessment of X-ray induced structural perturbation in a crystalline state protein. J. Struct. Biol. 169, 135–144 (2010).
32. H. Ohno, K. Takeda, S. Niwa, T. Tsujinaka, Y. Hanazono, Y. Hirano, K. Miki, Crystallographic characterization of the high-potential iron-sulfur protein in the oxidized state at 0.8 Å resolution. PLOS ONE 12, e0178183 (2017).
33. Y. Hanazono, K. Takeda, K. Miki, Characterization of perdeuterated high-potential iron-sulfur protein with high-resolution X-ray crystallography. Proteins 88, 251–259 (2020).
34. L. Esposito, L. Vitagliano, A. Zagari, L. Mazzarella, Experimental evidence for the correlation of bond distances in peptide groups detected in ultrahigh-resolution protein structures. Protein Eng. 13, 825–828 (2000).
35. A. Kvick, A. R. Al-Karaghouli, T. F. Koetzle, Deformation electron density of -glycylglycine at 82 K. I. The neutron diffraction study. Acta Crystallogr. B. B33, 3796–3801 (1977).
36. L. Yao, B. Vögeli, J. Ying, A. Bax, NMR determination of amide N-H equilibrium bond length from concerted dipolar coupling measurements. J. Am. Chem. Soc. 130, 16518–16520 (2008).
37. T. Steiner, Lengthening of the covalent X-H bond in heteronuclear hydrogen bonds quantified from organic and organometallic neutron crystal structures. J. Phys. Chem. A 102, 7041–7052 (1998).
38. E. S. Feldblum, I. T. Arkin, Strength of a bifurcated H bond. Proc. Natl. Acad. Sci. U.S.A. 111, 4085–4090 (2014).
39. N. W. Moriarty, D. Liebschner, D. E. Tronrud, P. D. Adams, Arginine off-kilter: Guanidinium is not as planar asrestraints denote. Acta Crystallogr. Sect. D Struct. Biol. 76, 1159–1166 (2020).
40. K. Yonezawa, N. Shimizu, K. Kurihara, Y. Yamazaki, H. Kamikubo, M. Kataoka, Neutron crystallography of photoactive yellow protein reveals unusual protonation state of Arg52 in the crystal. Sci. Rep. 7, 9361 (2017).
41. Y. Zu, M. M. J. Couture, D. R. J. Kolling, A. R. Crofts, L. D. Eltis, J. A. Fee, J. Hirst, Reduction potentials of rieske clusters: Importance of the coupling between oxidation state and histidine protonation state. Biochemistry 42, 12400–12408 (2003).
42. I. J. Lin, E. B. Gebel, T. E. Machonkin, W. M. Westler, J. L. Markley, Changes in hydrogenbond strengths explain reduction potentials in 10 rubredoxin variants. Proc. Natl. Acad. Sci. U.S.A. 102, 14581–14586 (2005).
43. J. Wang, L. Yao, Dissecting C−H∙∙∙ and N−H∙∙∙ interactions in two proteins using a combined experimental and computational approach. Sci. Rep. 9, 20149 (2019).
44. T. Kawakami, L. J. Yu, T. Liang, K. Okazaki, M. T. Madigan, Y. Kimura, Z. Y. Wang-Otomo, Crystal structure of a photosynthetic LH1-RC in complex with its electron donor HiPIP. Nat. Commun. 12, 1104 (2021).
45. F. Drepper, T. Saito, M. Kobayashi, T. Nozawa, P. Mathis, Electron transfer reactions of high-potential cytochromes in the reaction centre of Chromatium tepidum. Photosynth. Res. 55, 325–330 (1998).
46. I. Tanaka, K. Kusaka, T. Hosoya, N. Niimura, T. Ohhara, K. Kurihara, T. Yamada, Y. Ohnishi, K. Tomoyori, T. Yokoyama, Neutron structure analysis using the IBARAKI biological crystal diffractometer (iBIX) at J-PARC. Acta Crystallogr. D Biol. Crystallogr. 66, 1194–1197 (2010).
47. K. Kusaka, T. Hosoya, T. Yamada, K. Tomoyori, T. Ohhara, M. Katagiri, K. Kurihara, I. Tanaka, N. Niimura, Evaluation of performance for IBARAKI biological crystal diffractometer iBIX with new detectors. J. Synchrotron Radiat. 20, 994–998 (2013).
48. T. Ohhara, K. Kusaka, T. Hosoya, K. Kurihara, K. Tomoyori, N. Niimura, I. Tanaka, J. Suzuki, T. Nakatani, T. Otomo, S. Matsuoka, K. Tomita, Y. Nishimaki, T. Ajima, S. Ryufuku, Development of data processing software for a new TOF single crystal neutron diffractometer at J-PARC. Nucl. Instrum. Methods Phys. Res. A 600, 195–197 (2009).
49. N. Yano, T. Yamada, T. Hosoya, T. Ohhara, I. Tanaka, N. Niimura, K. Kusaka, Status of the neutron time-of-flight single-crystal diffraction data-processing software STARGazer. Acta Crystallogr. D Struct. Biol. 74, 1041–1052 (2018).
50. Z. Otwinowski, W. Minor, Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).
51. A. Vagin, A. Teplyakov, MOLREP: An automated program for molecular replacement. J. Appl. Cryst. 30, 1022–1025 (1997).
52. P. Emsley, B. Lohkamp, W. G. Scott, K. Cowtan, Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).
53. D. Liebschner, P. V. Afonine, M. L. Baker, G. Bunkoczi, V. B. Chen, T. I. Croll, B. Hintze, L. W. Hung, S. Jain, A. J. McCoy, N. W. Moriarty, R. D. Oeffner, B. K. Poon, M. G. Prisant, R. J. Read, J. S. Richardson, D. C. Richardson, M. D. Sammito, O. V. Sobolev, D. H. Stockwell, T. C. Terwilliger, A. G. Urzhumtsev, L. L. Videau, C. J. Williams, P. D. Adams, Macromolecular structure determination using X-rays, neutrons and electrons: Recent developments in Phenix. Acta Crystallogr. D Struct. Biol. 75, 861–877 (2019).
54. G. M. Sheldrick, Crystal structure refinement with SHELXL. Acta Crystallogr. C Struct. Chem. 71, 3–8 (2015).
論文の公開元へ
