Negative surface potential produced by self-assembled monolayers of helix peptides oriented vertically to a surface

Miura, Yoshiko; Kimura, Shunsaku; Kobayashi, Shiro; Iwamoto, Mitsumasa; Imanishi, Yukio; Umemura, Junzo

doi:10.1016/s0009-2614(99)01191-4

Cited by 59 publications

(50 citation statements)

References 20 publications

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“…In contrast to inversion of b-strand orientation, the inversion of an a-helix axis goes along with the inversion of the large helix dipole (Chakrabarti 1994). The helix dipole can have a strong influence on protein stability, its intrinsic function (Chou et al 1988;Fairman et al 1989;Aqvist et al 1991;Ben-Tal and Honig 1996;Sengupta 2005), and ability of complex formation with other proteins (Miura et al 1999). b-Strands in proteins can be organized in alternative orientations (parallel or antiparallel), which indicates functional robustness of proteins toward inverse orientations of b-strands.…”

Section: Discussionmentioning

confidence: 99%

Novel protein folds and their nonsequential structural analogs

Guerler

Knapp

2008

Protein Science

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Newly determined protein structures are classified to belong to a new fold, if the structures are sufficiently dissimilar from all other so far known protein structures. To analyze structural similarities of proteins, structure alignment tools are used. We demonstrate that the usage of nonsequential structure alignment tools, which neglect the polypeptide chain connectivity, can yield structure alignments with significant similarities between proteins of known three-dimensional structure and newly determined protein structures that possess a new fold. The recently introduced protein structure alignment tool, GANGSTA, is specialized to perform nonsequential alignments with proper assignment of the secondary structure types by focusing on helices and strands only. In the new version, GANGSTA+, the underlying algorithms were completely redesigned, yielding enhanced quality of structure alignments, offering alignment against a larger database of protein structures, and being more efficient. We applied DaliLite, TM-align, and GANGSTA+ on three protein crystal structures considered to be novel folds. Applying GANGSTA+ to these novel folds, we find proteins in the ASTRAL40 database, which possess significant structural similarities, albeit the alignments are nonsequential and in some cases involve secondary structure elements aligned in reverse orientation. A web server is available at http:// agknapp.chemie.fu-berlin.de/gplus for pairwise alignment, visualization, and database comparison.

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Section: Discussionmentioning

confidence: 99%

Novel protein folds and their nonsequential structural analogs

Guerler

Knapp

2008

Protein Science

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“…Because both helix types display a large dipole moment along the helical axis, [22] it is expected that the polarity of the applied voltage between the STM tip and the gold substrate influences the STM image of the peptides. [23,24] BL12S was observed by STM under application of the positive sample bias as described above. When the sample bias was inverted from positive to negative, the bright spots of BL12S disappeared within a few scans, but they reappeared with a return to the positive bias (Figure 4 a).…”

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confidence: 99%

A Helical Molecule That Exhibits Two Lengths in Response to an Applied Potential

2005

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“…In fact, negative potential means a dipole oriented with the negative side towards the analyzed surface [61].…”

Section: Resultsmentioning

confidence: 99%

“…This could explain why the asymmetric isomers of pyrene such as chrysene or benzo(a)anthracene are retained stronger on C 18 compared to pyrene (symmetric). Also Jinno and Kawasaki [61] stated that there is a high correlation between retention times for PAHs in RPLC and their molecular polarizability.…”

Section: Retention Mechanism In Rpc Through Spontaneous Surface Polarmentioning

confidence: 99%

Reverse-High Performance Liquid Chromatography Mechanism Explained by Polarization of Stationary Phase

Andrade-Eiroa¹

2011

CheM

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Original results and conclusions on Reverse Phase High Performance Liquid Chromatography (RPLC) mechanism are here presented. So far, none of the theoretical approaches applied to the RPLC mechanism can explain the retention and elution mechanisms of most of the analytes by RPLC, especially neutral organic compounds. Our experiences allowed us to state that RPLC retention mechanism most likely occurs through polarization of stationary phase (usually dielectric surfaces) submerged into solvents with huge dielectric constant and high dipole moment (i.e. water and/or acetonitrile) at high pressures as those applied in RPLC systems. The surface polarized interacts with polarizable target analytes (i.e. naphthalene, pyrene or benzo(ghi)perylene) in such a way that the retention depends on the medium polarizability of the target compound. The higher is the medium polarizability of the compound retained the higher is its retention time.By using Polycyclic Aromatic Hydro-carbons (PAHs) and 6-nitrochrysene as probes, we found that although the dependence of retention times on pressure is not evident in most cases, the interaction between pressure and the mobile phase dipole moment is evidenced at the light of the constructed mathematical models. Two very different cases can be distinguished:1. On one hand, when low dipole moment mobile phases are used, high pressure means big work developed by the system in such a way that high pressures inside the system reduce retention times compared to low pressures.2. On the another one, when high dipole moment solvents are used as mobile phase, high pressure entails an outstanding increase of the retention times compared to low dipole moment mobile phases. This is most likely due to high pressures that entail closer alignment of mobile phase dipoles and lesser tilt of them, originating an outstanding electric field inside the analytical column.In addition to this, reduced retention times for dipole solutes (6-nitrochrysene, dipole molecule) compared to non-polar solutes (PAHs) were observed when pressure drops. This conclusions would allow to extend the model to basic/acid molecules at different pH. In this case, electrostatic repulsions among analyte molecules should be considered.

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Negative surface potential produced by self-assembled monolayers of helix peptides oriented vertically to a surface

Cited by 59 publications

References 20 publications

Novel protein folds and their nonsequential structural analogs

Novel protein folds and their nonsequential structural analogs

A Helical Molecule That Exhibits Two Lengths in Response to an Applied Potential

Reverse-High Performance Liquid Chromatography Mechanism Explained by Polarization of Stationary Phase

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