@article {2264,
	title = {The hand of the filamentous bacteriophage helix},
	journal = {European Biophysics Journal with Biophysics Letters},
	volume = {37},
	number = {6},
	year = {2008},
	note = {ISI Document Delivery No.: 314QDTimes Cited: 1Cited Reference Count: 30Straus, S. K. Scott, W. R. P. Marvin, D. A.},
	month = {Jul},
	pages = {1077-1082},
	type = {Article},
	abstract = {Filamentous bacteriophage (Inovirus) is a widely studied model system in molecular biophysics. The structure of the virion has been analysed by various methods, but the methods have seldom questioned the hand of the virion helix. The hand of the helix relating the protein subunits in the class II virus strain Pf1 was chosen by calculating an electron-density distribution from X-ray fibre diffraction data, using a maximum-entropy method, but to our knowledge this method has not been used for a similar purpose in any other system. Moreover, this same hand was extended only by analogy, with no direct analysis of the corresponding data, to the class I virus strain Ff (fd, f1, M13), which has a different helix symmetry. Here we use published solid-state NMR data to confirm the validity of the hand of Pf1 chosen by the maximum-entropy method, and to confirm the extension to Ff.},
	keywords = {ALPHA-HELIX, COAT PROTEIN, ELECTRON-DENSITY, FIBER DIFFRACTION DATA, fibre diffraction, MEMBRANE-PROTEIN, models, MOLECULAR-STRUCTURE DETERMINATION, NMR-SPECTROSCOPY, PF1, RESOLUTION, SOLID-STATE NMR, STATE, XPLOR-NIH},
	isbn = {0175-7571},
	url = {<Go to ISI>://000256823000038},
	author = {Straus, S. K. and Scott, W. R. P. and Marvin, D. A.}
}
@article {1484,
	title = {Molecular structure of fd (f1, M13) filamentous bacteriophage refined with respect to X-ray fibre diffraction and solid-state NMR data supports specific models of phage assembly at the bacterial membrane},
	journal = {Journal of Molecular Biology},
	volume = {355},
	number = {2},
	year = {2006},
	note = {ISI Document Delivery No.: 999EPTimes Cited: 30Cited Reference Count: 84},
	month = {Jan},
	pages = {294-309},
	type = {Article},
	abstract = {Filamentous bacteriophage (Inovirus) is a simple and well-characterized model system. The phage particle, or virion, is about 60 A in diameter and several thousand angstrom units long. The virions are assembled at the bacterial membrane as they extrude out of the host without killing it, an example of specific transport of nucleoprotein assemblages across membranes. The Ff group (fd, f1. and M13) has been especially widely studied. Models of virion assembly have been proposed based on a molecular model of the fd virion derived by X-ray fibre diffraction. A somewhat different model of the fd virion using solid-state NMR data has been proposed, not consistent with these models of assembly nor with the X-ray diffraction data. Here we show that reinterpreted NMR data are also consistent with the model derived from X-ray fibre diffraction studies, and discuss models of virion assembly. (c) 2005 Elsevier Ltd. All rights reserved.},
	keywords = {ALPHA-HELICES, ALPHA-HELIX, ATOMIC REFINEMENT, fibre diffraction, filamentous bacteriophage, INOVIRUS, MAJOR COAT PROTEIN, MEMBRANE, ORIENTATIONAL RESTRAINTS, PF1 BACTERIOPHAGE, PISEMA, PROTEINS, RESOLUTION, SINGLE-STRANDED-DNA, VIRION, VIRUS},
	isbn = {0022-2836},
	url = {<Go to ISI>://000234371900012},
	author = {Marvin, D. A. and Welsh, L. C. and Symmons, M. F. and Scott, W. R. P. and Straus, S. K.}
}
@article {541,
	title = {Inhibitory module of Ets-1 allosterically regulates DNA binding through a dipole-facilitated phosphate contact},
	journal = {Journal of Biological Chemistry},
	volume = {277},
	number = {3},
	year = {2002},
	note = {ISI Document Delivery No.: 514CWTimes Cited: 21Cited Reference Count: 50},
	month = {Jan},
	pages = {2225-2233},
	type = {Article},
	abstract = {DNA binding of the transcription factor Ets-1 is negatively regulated by three inhibitory helices that lie near the ETS domain. The current model suggests that this negative regulation, termed autoinhibition, is caused by the energetic expense of a DNA-induced structural transition that includes the unfolding of one inhibitory helix. This report investigates the role of helix H1 of the ETS domain in the autoinhibition mechanism. Previous structural studies modeled the inhibitory helices packing together and connecting with helix H1, suggesting a role of this helix in the configuration of an inhibitory module. Recently, high-resolution structures of the ETS domain-DNA interface indicate that the N terminus of helix H1 directly contacts DNA. The contact, which is augmented by the macrodipole of helix H1, consists of a hydrogen bond between the amide NH of leucine 337 in helix HI and the oxygen of a corresponding phosphate. We propose that this hydrogen bond positions helix H1 to be a link between autoinhibition and DNA binding. Four independent approaches tested this hypothesis. First, the hydrogen bond was disrupted by removal of the phosphate in a missing phosphate analysis. Second, base pairs that surround the helix HI-contacting phosphate and appear to dictate DNA backbone conformation were mutated. Next, a hydrophobic residue in helix H1 that is expected to position the N terminus of the helix was altered. Finally, a residue on the surface of helix 111 that may contact the inhibitory elements was changed. In each case DNA binding and autoinhibition was affected. Taken together, the results demonstrate the role of the dipole-facilitated phosphate contact in DNA binding. Furthermore, the findings support a model in which helix H1 links the inhibitory elements to the ETS domain. We speculate that this helix, which is conserved in all Ets proteins, provides a common route to regulation.},
	keywords = {ALPHA-HELIX, AUTO-INHIBITION, COMPLEX, DOMAIN, FACTORS ELK-1, INDIRECT READOUT, MURINE ETS-1, PROTEINS, RECOGNITION, TRANSCRIPTION FACTOR},
	isbn = {0021-9258},
	url = {<Go to ISI>://000173421300083},
	author = {Wang, H. and McIntosh, L. P. and Graves, B. J.}
}
@article {5004,
	title = {The methanol-induced conformational transitions of beta-lactoglobulin, cytochrome c, and ubiquitin at low pH: A study by electrospray ionization mass spectrometry},
	journal = {Journal of the American Society for Mass Spectrometry},
	volume = {12},
	number = {3},
	year = {2001},
	note = {ISI Document Delivery No.: 408WBTimes Cited: 45Cited Reference Count: 51},
	month = {Mar},
	pages = {317-328},
	type = {Article},
	abstract = {The methanol-induced conformational transitions under acidic conditions for beta -lactoglobulin, cytochrome c, and ubiquitin, representing three different classes of proteins with beta -sheets, alpha -helices, and both alpha -helices and beta -sheets, respectively, are studied under equilibrium conditions by electrospray ionization mass spectrometry (ESI-MS). The folding states of proteins in solution are monitored by the charge state distributions that they produce during ESI and by hydrogen/deuterium (H/D) exchange followed by ESI-MS. The changes in charge state distributions are correlated with earlier studies by optical and other methods which have shown that, in methanol, these proteins form partially unfolded intermediates with induced ct-helix structure. Intermediate states formed at about 35\% methanol concentration are found to give bimodal charge state distributions. The same rate of H/D exchange is shown by the two contributions to the bimodal distributions. This suggests the intermediates are highly flexible and may consist of a mixture of two or more rapidly interconverting conformers. H/D exchange of proteins followed by ESI-MS shows that helical denatured states, populated at around 50\% methanol concentration, transform into more protected structures with further increases in methanol concentration, consistent with previous circular dicroism studies. These more protected structures still produce high charge states in ESI, similar to those of the fully denatured proteins. (C) 2001 American Society for Mass Spectrometry.},
	keywords = {2-DIMENSIONAL NMR, ALPHA-HELIX, AMIDE HYDROGEN-EXCHANGE, COMPLETE SEQUENCE, DENATURED STATES, DEUTERIUM-EXCHANGE, INTERMEDIATE, MYOGLOBIN, PROTEIN, SOLVENT},
	isbn = {1044-0305},
	url = {<Go to ISI>://000167349200010},
	author = {Babu, K. R. and Moradian, A. and Douglas, D. J.}
}
@article {4029,
	title = {Acid-induced unfolding of cytochrome c at different methanol concentrations: Electrospray ionization mass spectrometry specifically monitors changes in the tertiary structure},
	journal = {Biochemistry},
	volume = {36},
	number = {40},
	year = {1997},
	note = {ISI Document Delivery No.: YA264Times Cited: 132Cited Reference Count: 51},
	month = {Oct},
	pages = {12296-12302},
	type = {Article},
	abstract = {The acid-induced denaturation of ferricytochrome c (cyt c) was examined in aqueous solutions containing different concentrations of methanol by electrospray ionization mass spectrometry (ESI MS) and optical spectroscopy. Circular dichroism, fluorescence, and absorption spectroscopy show that at a low concentration of methanol (3\%) a decrease in pH induces a cooperative unfolding transition at around pH 2.6 that is accompanied by a breakdown of the native secondary and tertiary structure of the protein. In 50\% methanol the breakdown of the tertiary structure occurs at around pH 4.0, whereas the alpha-helical content remains largely intact over the whole pH range studied. In ESI MS different protein conformations in solution are monitored by the different charge state distributions they generate during ESI. The ESI mass spectra recorded at near-neutral pH for both methanol concentrations are very similar and show a maximum at (cyt c + 8H(+))8(+). Despite the different conformations of the protein in solution, the acid-denatured states for the two methanol concentrations also show very similar mass spectra with a maximum at (cyt c + 17H(+))17(+). This indicates that the charge state distribution generated during EST is not sensitive to the differences in the secondary structure of the denatured protein. The observed transition from low to high charge states is due to the breakdown of the tertiary structure in both cases. These findings suggest that ESI MS might be a general method to selectively monitor changes in the tertiary structure of proteins.},
	keywords = {ALPHA-HELIX, BETA-LACTOGLOBULIN, CIRCULAR-DICHROISM, DENATURED, FERRICYTOCHROME-C, HEME, PARTIALLY FOLDED STATE, PROBING CONFORMATIONAL-CHANGES, PROTEIN, STATE, TRIFLUOROETHANOL},
	isbn = {0006-2960},
	url = {<Go to ISI>://A1997YA26400034},
	author = {Konermann, L. and Douglas, D. J.}
}
@article {2925,
	title = {CIRCULAR-DICHROISM ANALYSIS OF A SYNTHETIC PEPTIDE CORRESPONDING TO THE ALPHA,ALPHA-CORNER MOTIF OF HEMOGLOBIN},
	journal = {Biochemical and Biophysical Research Communications},
	volume = {196},
	number = {1},
	year = {1993},
	note = {ISI Document Delivery No.: MC105Times Cited: 1Cited Reference Count: 16},
	month = {Oct},
	pages = {435-439},
	type = {Article},
	keywords = {ALPHA-HELIX, GLOBULAR-PROTEINS, INTERMEDIATE, POLYPEPTIDE-CHAIN, SECONDARY STRUCTURE, STABILITY},
	isbn = {0006-291X},
	url = {<Go to ISI>://A1993MC10500062},
	author = {Tsai, F. C. S. and Sherman, J. C.}
}
