Raman microscopy permits structural analysis of protein crystals in situ in hanging drops, allowing for comparison with Raman measurements in solution. Nevertheless, the two methods sometimes reveal subtle differences in structure that are often ascribed to the water layer surrounding the protein. The novel method of drop-coating deposition Raman spectropscopy (DCDR) exploits an intermediate phase that, although nominally "dry," has been shown to preserve protein structural features present in solution. The potential of this new approach to bridge the structural gap between proteins in solution and in crystals is explored here with extrinsic protein PsbP of photosystem II from Spinacia oleracea. In the high-resolution (1.98 Å) x-ray crystal structure of PsbP reported here, several segments of the protein chain are present but unresolved. Analysis of the three kinds of Raman spectra of PsbP suggests that most of the subtle differences can indeed be attributed to the water envelope, which is shown here to have a similar Raman intensity in glassy and crystal states. Using molecular dynamics simulations cross-validated by Raman solution data, two unresolved segments of the PsbP crystal structure were modeled as loops, and the amino terminus was inferred to contain an additional beta segment. The complete PsbP structure was compared with that of the PsbP-like protein CyanoP, which plays a more peripheral role in photosystem II function. The comparison suggests possible interaction surfaces of PsbP with higher-plant photosystem II. This work provides the first complete structural picture of this key protein, and it represents the first systematic comparison of Raman data from solution, glassy, and crystalline states of a protein.

Institute of Physics Faculty of Mathematics and Physics Charles University Prague Prague Czech Republic

Zobrazit více v PubMed

Carey PR (1999) Raman spectroscopy, the sleeping giant in structural biology, awakes. J Biol Chem 274: 26625–26628. PubMed

Kopecký V Jr, Ettrich R, Hofbauerová K, Baumruk V (2004) Vibrational spectroscopy and computer modeling of proteins: solving structure of human α1-acid glycoprotein. Spectrosc–Int J 18: 323–330.

Carey PR, Dong J (2004) Following ligand binding and ligand reactions in proteins via Raman crystallography. Biochemistry 43: 8885–8893. PubMed

Carpentier P, Royant A, Weik M, Bourgeois D (2010) Raman-assisted crystallography suggests a mechanism of X-ray-induced disulfide radical formation and reparation. Structure 18: 1410–1419. PubMed

McGeehan JE, Bourgeois D, Royant A, Carpentier P (2011) Raman-assisted crystallography of biomolecules at the synchrotron: Instrumentation, methods and applications. Biochim Biophys Acta 1814: 750–759. PubMed

Lafaye C, Iwema T, Carpentier P, Jullian-Binard C, Kroll JS, et al. (2009) Biochemical and structural study of the homologues of the thiol-disulfide oxidoreductase DsbA in Neisseria meningitidis . J Mol Biol 392: 952–966. PubMed

Yu N-T (1974) Comparison of protein structure in crystals, in lyophilized state, and in solution by laser Raman scattering. 3. α-Lactalbumin. J Am Chem Soc 96: 4664–4668. PubMed

Li T, Chen Z, Johnson JE, Thomas GJ Jr (1992) Conformations, interactions, and thermostabilities of RNA and proteins in bean pod mottle virus: investigation of solution and crystal structures by laser Raman spectroscopy. Biochemistry 31: 6673–6682. PubMed

Thomas GA, Kubasek WL, Greene P, Grable J, Rosenberg JM (1989) Environmentally induced conformational changes in B-type DNA: comparison of the conformation of the oligonucleotide d(TCGCGAATTCGCG) in solution and in its crystalline complex with the restriction nuclease EcoRI. Biochemistry 28: 2001–2009. PubMed

Altose MD, Zheng Y, Dong J, Palfey BA, Carey PR (2001) Comparing protein–ligand interactions in solution and single crystals by Raman spectroscopy. Proc Natl Acad Sci USA 98: 3006–3011. PubMed PMC

Zhang D, Xie Y, Mrozek MF, Ortiz C, Davisson VJ, et al. (2003) Raman detection of proteomic analytes. Anal Chem 75: 5703–5709. PubMed

Kapitán J, Baumruk V, Kopecký V Jr, Pohl R, Bouř P (2006) Proline zwitterion dynamics in solution, glass, and crystalline state. J Am Chem Soc 128: 13451–13462. PubMed

Kopecký V Jr, Baumruk V (2006) Structure of the ring in drop coating deposited proteins and its implication for Raman spectroscopy of biomolecules. Vib Spectrosc 42: 184–187.

Deegan RD, Bakajin O, Dupot TF, Huber G, Gel SR, et al. (1997) Capillary flow as the cause of ring stains from dried liquid drops. Nature 389: 827–829.

Ortiz C, Zhang D, Xie Y, Ribbe AE, Ben-Amotz D (2006) Validation of the drop coating deposition Raman method for protein analysis. Anal Biochem 353: 157–166. PubMed

Barber J (2003) Photosystem II: the engine of life. Q Rev Biophys 36: 71–89. PubMed

Seidler A (1996) The extrinsic polypeptides of photosystem II. Biochim Biophys Acta 1277: 35–60. PubMed

Suorsa M, Sirpio S, Allahverdiyeva Y, Paakkarinen V, Mamedov F, et al. (2006) PsbR, a missing link in the assembly of the oxygen-evolving complex of plant photosystem II. J Biol Chem 281: 145–150. PubMed

Seidler A (1996) The extrinsic polypeptides of Photosystem II. Biochim Biophys Acta 1277: 35–60. PubMed

Ifuku K, Yamamoto Y, Ono TA, Ishihara S, Sato F (2005) PsbP protein, but not PsbQ protein is essential for the regulation and stabilization of photosystem II in higher plants. Plant Physiol 193: 1175–1184. PubMed PMC

Ifuku K, Nakatsu T, Shimamoto R, Yamamoto Y, Ishihara S, et al. (2005) Structure and function of the PsbP protein of photosystem II from higher plants. Photosyn Res 84: 251–255. PubMed

Yi X, Hargett SR, Liu H, Frankel LK, Bricker TM (2007) The PsbP protein is required for photosystem II complex assembly/stability and photoautotrophy in Arabidopsis thaliana . J Biol Chem 282: 24833–24841. PubMed

De Las Rivas J, Heredia P, Roman A (2007) Oxygen-evolving extrinsic proteins (PsbO, P, Q, R): Bioinformatics and functional analysis. Biochim Biophys Acta 1767: 575–582. PubMed

Nield J, Balsera M, De Las Rivas J, Barber J (2002) Three dimensional cryo-EM study of extrinsic domains of the oxygen-evolving complex of spinach: assignment of the PsbO protein. J Biol Chem 277: 15006–15012. PubMed

Bumba L, Vacha FE (2003) Electron microscopy in structural studies of photosystem II. Photosynth Res 77: 1–19. PubMed

Caffarri S, Kouril R, Kereıche S, Boekema EJ, Croce R (2009) Functional architecture of higher plant photosystem II supercomplexes. EMBO J 28: 3052–3063. PubMed PMC

Zouni A, Witt HT, Kern J, Fromme P, Krauss N, et al. (2001) Crystal structure of photosystem II from Synechococcus elongatus at 3.8 Å resolution. Nature 409: 739–43. PubMed

Kamiya N, Shen JR (2003) Crystal structure of oxygen-evolving photosystem II from Thermosynechococcus vulcanus at 3.7-Å resolution. Proc Natl Acad Sci USA 100: 98–102. PubMed PMC

Loll B, Cern J, Saenger W, Zouni A, Biesiadka J (2005) Towards complete cofactor arrangement in the 3.0 Å resolution structure of photosystem II. Nature 438: 1040–1044. PubMed

Guskov A, Kern J, Gabdullkhakov A, Broser M, Zouni A, et al. (2009) Cyanobacterial photosystem II at 2.9 Å resolution and the role of quinones, lipids, channels and chloride. Nature Struc Mol Biol 16: 334–341. PubMed

Ifuku K, Ishihara S, Shimamoto R, Ido K, Sato F (2008) Structure, function and evolution of the PsbP protein family in higher plants. Photosyn Res 98: 427–437. PubMed

Balsera M, Arellano JB, Revuelta JL, De Las Rivas J, Hermoso JA (2005) The 1.49 Å resolution crystal structure of PsbQ from photosystem II of Spinacia oleracea reveals a PPII structure in the N-terminal region. J Mol Biol 350: 1051–1060. PubMed

Ifuku K, Nakatsu T, Kato H, Sato F (2004) Crystal structure of the PsbP protein of photosystem II from Nicotiana tabacum . EMBO Rep 5: 362–367. PubMed PMC

Michoux F, Takasaka K, Boehm M, Nixon P, Murray JW (2010) Structure of CyanoP at 2.8 Å: implications for the evolution and function of the PsbP subunit of photosystem II. Biochemistry 49: 7411–741. PubMed

Kohoutová J, Kuta Smatanová I, Brynda J, Lapkouski M, Revuelta JL, et al. (2009) Crystallization and preliminary crystallographic characterization of the extrinsic PsbP protein of photosystem II from Spinacia olerace . Acta Cryst F65: 111–115. PubMed PMC

Ifuku K, Ido K, Sato F (2011) Molecular functions of PsbP and PsbQ proteins in the photosystem II supercomplex. J Photochem Photobiol 104: 158–164. PubMed

Miura T, Takeuchi H, Harada I (1989) Tryptophan Raman bands sensitive to hydrogen bonding and side-chain conformation. J Raman Spectrosc 20: 667–671.

Overman SA, Thomas GJ Jr (1999) Raman markers of nonaromatic side chains in an α-helix assembly: Ala, Asp, Glu, Gly, Ile, Leu, Lys, Ser, and Val residues of phage fd subunits. Biochemistry 38: 4018–4027. PubMed

Tuma R (2005) Raman spectroscopy of proteins: from peptides to large assemblies. J Raman Spectrosc 36: 307–319.

Tensmeyer LG, Kauffman II EW (1996) Protein structure as revealed by nonresonance Raman spectroscopy. In: Havel HA, editor. Spectroscopic Methods for Determining Protein Structure in Solution. New York: VCH Publishers, pp. 69–95.

Miura T, Thomas GJ Jr (1995) Raman spectroscopy of proteins and their assemblies. In: Biswas BB, Roy S, editors. Subcellular Biochemistry, Vol. 24, Proteins: Structure, Function, and Engineering. New York: Plenum Press, pp. 55–99. PubMed

Williams RW (1986) The secondary structure analysis using Raman amide I and amide III spectra. Methods Enzymol 130: 311–331. PubMed

Berjot M, Marx J, Alix AJP (1987) Determination of the secondary structure of proteins from the Raman amide I band: the reference intensity profiles method. J Raman Spectrosc 18: 289–300.

Thomas GJ Jr, Prescott B, Urry DW (1987) Raman amide bands of type-II β-turns in cyclo-(VPGVG)3 and poly-(VPGVG), and implications for protein secondary-structure analysis. Biopolymers 26: 921–934. PubMed

Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876–4882. PubMed PMC

Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 26: 283–291.

Munoz V, Serrano L (1994) Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comaprison with experimental scales. Proteins 20: 301–311. PubMed

Leslie AGW (1992) Recent changes to the MOSFLM package for processing film and image plate data. Jnt CCP4/ESF-EACBM Newsl Protein Crystallogr 26.

Collaborative Computational Project, Number 4 (1994) Acta Cryst D50: 760–763. PubMed

Matthews BW (1968) Solvent content of protein crystals. J Mol Biol 33: 491–497. PubMed

Murshudov GN, Vagin AA, Lebedev A, Wilson KS, Dodson EJ (1999) Efficient anisotropic refinement of macromolecular structures using FFT. Acta Cryst D55: 247–255. PubMed

Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Cryst D60: 2126–2132. PubMed

Vagin A, Teplyakov A (1997) MOLREP: an Automated Program for Molecular Replacement. J Appl Cryst 30: 1022–1025.

Sali A, Overington JH (1994) Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Sci 3: 1582–1596. PubMed PMC

Berendsen HJC, Van der Spoel D, Van Drunen R (1995) GROMACS: a message-passing parallel molecular dynamics implementation. Comput Phys Commun 91: 43–56.

Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. JCTC 4: 435–447. PubMed

Berendsen HJC, Postma JPM, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81: 3684–3690.

Jorgensen WL, Tirado-Rives J (1988) The OPLS force field for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc 110: 1657–1666. PubMed

Essman U, Perela L, Berkowitz ML, Darden T, Lee H, et al. (1995) A smooth particle mesh Ewald method. J Chem Phys 103: 8577–8592.

Feenstra KA, Hess B, Berendsen HJC (1999) Improving efficiency of large time-scale molecular dynamics of hydrogen-rich systems. J Comput Chem 20: 786–798. PubMed

Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: A LInear Constraint Solver for molecular simulations. J Comput Chem 18: 1463–1472.

Resonance assignment of PsbP: an extrinsic protein from photosystem II of Spinacia oleracea

Solution NMR and molecular dynamics reveal a persistent alpha helix within the dynamic region of PsbQ from photosystem II of higher plants

Zobrazit více v PubMed

PDB
2VU4