Partial least-squares functional mode analysis: Application to the membrane proteins AQP1, Aqy1, and CLC-ec1

Biophysical Journal

Volumn 103, Issue 4, 2012, Pages 786-796

  Krivobokova, Tatyana ^a   Briones, Rodolfo ^b   Hub, Jochen S ^a   Munk, Axel ^a   De Groot, Bert L ^b  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

^b MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIPORTER; AQUAPORIN 1; CLC EC1 PROTEIN, E COLI; CLC-EC1 PROTEIN, E COLI; ESCHERICHIA COLI PROTEIN; FUNGAL PROTEIN; LYSOZYME;

ALGORITHM; ARTICLE; BACTERIOPHAGE T4; CHEMISTRY; ENZYMOLOGY; HUMAN; METABOLISM; METHODOLOGY; MOLECULAR DYNAMICS; PRINCIPAL COMPONENT ANALYSIS; PROTEIN CONFORMATION; REGRESSION ANALYSIS; STATISTICS;

ALGORITHMS; ANTIPORTERS; AQUAPORIN 1; BACTERIOPHAGE T4; ESCHERICHIA COLI PROTEINS; FUNGAL PROTEINS; HUMANS; LEAST-SQUARES ANALYSIS; MOLECULAR DYNAMICS SIMULATION; MURAMIDASE; PRINCIPAL COMPONENT ANALYSIS; PROTEIN CONFORMATION; STATISTICS AS TOPIC;

EID: 84865396279     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2012.07.022     Document Type: Article

References (39)

1. A.E. García Large-amplitude nonlinear motions in proteins Phys. Rev. Lett. 68 1992 2696 2699
2. A. Amadei, A.B.M. Linssen, and H.J.C. Berendsen Essential dynamics of proteins Proteins 17 1993 412 425 (Pubitemid 23358549)
3. J.S. Hub, and B.L. de Groot Detection of functional modes in protein dynamics PLoS Comput. Biol. 5 2009 e1000480
4. Hold, H. O. A. 1966. Nonlinear estimation by iterative least squares procedures. In Research Papers in Statistics: Festschrift for J. Neyman. F. N. David, editor. Wiley, New York. 411-444.
5. H.O.A. Hold Nonlinear iterative partial least squares (NIPALS) modeling: some current developments P. Krishnaiah, Multivariate analysis III 1973 Academic Press New York 383 407
6. H.O.A. Hold Soft modeling: the basic design and some extensions K.G. Jöreskog, H.O.A. Wold, Systems Under Indirect Observation: Causality, Structure, Prediction 1982 North-Holland Amsterdam, The Netherlands
7. M.C. Denham Implementing partial least squares Stat. Comput. 5 1995 191 202
8. I.S. Helland On the structure of partial least squares regression Commun. Stat. Simulat. 17 1988 581 607
9. D. van der Spoel, and E. Lindahl H.J. Berendsen GROMACS: fast, flexible, and free J. Comput. Chem. 26 2005 1701 1718 (Pubitemid 43076182)
10. D.C. Phillips The hen egg-white lysozyme molecule Proc. Natl. Acad. Sci. USA 57 1967 483 495
11. J.W. Neidigh, R.M. Fesinmeyer, and N.H. Andersen Designing a 20-residue protein Nat. Struct. Biol. 9 2002 425 430 (Pubitemid 34568786)
12. G. Fischer, and U. Kosinska-Eriksson K. Lindkvist-Petersson Crystal structure of a yeast aquaporin at 1.15 ngstrom reveals a novel gating mechanism PLoS Biol. 7 2009 e1000130
13. H. Sui, and B.G. Han B.K. Jap Structural basis of water-specific transport through the AQP1 water channel Nature 414 2001 872 878 (Pubitemid 34024731)
14. J.S. Hub, and C. Aponte-Santamaría B.L. de Groot Voltage-regulated water flux through aquaporin channels in silico Biophys. J. 99 2010 L97 L99
15. F. Zhu, E. Tajkhorshid, and K. Schulten Collective diffusion model for water permeation through microscopic channels Phys. Rev. Lett. 93 2004 224501
16. E. Beitz, and B. Wu T. Zeuthen Point mutations in the aromatic/arginine region in aquaporin 1 allow passage of urea, glycerol, ammonia, and protons Proc. Natl. Acad. Sci. USA 103 2006 269 274 (Pubitemid 43122390)
17. H. Li, and H. Chen G.A. Voth Enhancement of proton conductance by mutations of the selectivity filter of aquaporin-1 J. Mol. Biol. 407 2011 607 620
18. T.-Y. Chen Structure and function of CLC channels Annu. Rev. Physiol. 67 2005 809 839 (Pubitemid 40404511)
19. R. Dutzler, and E.B. Campbell R. MacKinnon X-ray structure of a CLC chloride channel at 3.0 reveals the molecular basis of anion selectivity Nature 415 2002 287 294 (Pubitemid 34087544)
20. L. Feng, and E.B. Campbell R. MacKinnon Structure of a eukaryotic CLC transporter defines an intermediate state in the transport cycle Science 330 2010 635 641
21. R. Dutzler, E.B. Campbell, and R. MacKinnon Gating the selectivity filter in CLC chloride channels Science 300 2003 108 112 (Pubitemid 36423038)
22. R. Estévez, and B.C. Schroeder M. Pusch Conservation of chloride channel structure revealed by an inhibitor binding site in CLC-1 Neuron 38 2003 47 59 (Pubitemid 36423352)
23. Y.R. Yusef, and L. Zúñiga F.V. Sepúlveda Removal of gating in voltage-dependent CLC-2 chloride channel by point mutations affecting the pore and C-terminus CBS-2 domain J. Physiol. 572 2006 173 181
24. A.A. Zdebik, and G. Zifarelli M. Pusch Determinants of anion-proton coupling in mammalian endosomal CLC proteins J. Biol. Chem. 283 2008 4219 4227
25. D.L. Bostick, and M.L. Berkowitz Exterior site occupancy infers chloride-induced proton gating in a prokaryotic homolog of the CLC chloride channel Biophys. J. 87 2004 1686 1696 (Pubitemid 39167025)
26. F.L. Gervasio, and M. Parrinello M.L. Klein Exploring the gating mechanism in the CLC chloride channel via metadynamics J. Mol. Biol. 361 2006 390 398 (Pubitemid 44092788)
27. M. Petek, and P. Kosinová M. Otyepka MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels Structure 15 2007 1357 1363
28. N.A. Baker, and D. Sept J.A. McCammon Electrostatics of nanosystems: application to microtubules and the ribosome Proc. Natl. Acad. Sci. USA 98 2001 10037 10041 (Pubitemid 32802969)
29. + exchanger J. Gen. Physiol. 126 2005 563 570 (Pubitemid 41713737)
30. + exchanger Proc. Natl. Acad. Sci. USA 105 2008 11194 11199
31. + antiporter Biophys. J. 101 2011 L47 L49
32. B.L. de Groot, and D.M.F. van Aalten H.J. Berendsen The consistency of large concerted motions in proteins in molecular dynamics simulations Biophys. J. 71 1996 1707 1713 (Pubitemid 26325953)
33. A. Amadei, and A.B.M. Linssen H.J. Berendsen An efficient method for sampling the essential subspace of proteins J. Biomol. Struct. Dyn. 13 1996 615 625 (Pubitemid 26081108)
34. H. Grubmüller Predicting slow structural transitions in macromolecular systems: conformational flooding Phys. Rev. E 52 1995 2893 2906
35. N. Krämer, A.-L. Boulesteix, and G. Tutz Penalized partial least squares with applications to B-spline transformations and functional data Chemometr. Intell. Lab. 94 2008 60 69
36. R. Manne Analysis of two partial least squares algorithms for multivariate calibration Chemometr. Intell. Lab. 2 1987 187 197
37. P. Bühlmann, and B. Yu Boosting with the L2 loss: regression and classification J. Am. Stat. Assoc. 98 2003 324 339
38. N. Bissantz, and T. Hohage F. Ruymgaart Convergence rates of general regularization methods for statistical inverse problems and applications SIAM J. Numer. Anal. 45 2007 2610 2636
39. G. Blanchard, and N. Krämer Optimal learning rates for kernel conjugate gradient regression Adv. Neur. 23 2010 226 234