A server and database for dipole moments of proteins

Felder, Clifford E.; Prilusky, Jaime; Silman, Israel; Sussman, Joel L.

doi:10.1093/nar/gkm307

Cited by 176 publications

(220 citation statements)

References 21 publications

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“…5), and the average p grows at higher z, as may be expected from the increase of both the maximum protein dimensions and total charge. For comparison, one can find near-native protein structures in the Protein Data Bank (PDB) and calculate their dipole moments by using the dedicated web server (48). The result for ubiquitin is 189 D, which is comparable with the typical values for ion geometries with higher z (Fig.…”

Section: Comparison Of Theory and Experimentssupporting

confidence: 56%

Pendular proteins in gases and new avenues for characterization of macromolecules by ion mobility spectrometry

Shvartsburg

Noskov

Purves

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

110

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Polar molecules align in electric fields when the dipole energy (proportional to field intensity E ؋ dipole moment p) exceeds the thermal rotational energy. Small molecules have low p and align only at inordinately high E or upon extreme cooling. Many biomacromolecules and ions are strong permanent dipoles that align at E achievable in gases and room temperature. The collision cross-sections of aligned ions with gas molecules generally differ from orientationally averaged quantities, affecting ion mobilities measured in ion mobility spectrometry (IMS). Field asymmetric waveform IMS (FAIMS) separates ions by the difference between mobilities at high and low E and hence can resolve and identify macroion conformers based on the mobility difference between pendular and free rotor states. The exceptional sensitivity of that difference to ion geometry and charge distribution holds the potential for a powerful method for separation and characterization of macromolecular species. Theory predicts that the pendular alignment of ions in gases at any E requires a minimum p that depends on the ion mobility, gas pressure, and temperature. At ambient conditions used in current FAIMS systems, p for realistic ions must exceed Ϸ300 -400 Debye. The dipole moments of proteins statistically increase with increasing mass, and such values are typical above Ϸ30 kDa. As expected for the dipole-aligned regime, FAIMS analyses of protein ions and complexes of Ϸ30 -130 kDa show an order-of-magnitude expansion of separation space compared with smaller proteins and other ions. mass spectrometry ͉ protein structure S eparation and characterization of ions by using their drift in gases forced by electric field, called ion mobility spectrometry (IMS), is becoming common in analytical and structural chemistry (1-6). As with mass spectrometry (MS), initial applications were to small molecules (1, 5, 7) that could be readily ionized. Coupling to MS and to electrospray (ESI) and matrix-assisted laser desorption ionization (MALDI) ion sources in the 1990s (8, 9) brought IMS to biological analyses (2, 4, 6). In particular, peptide and protein folding (2, 4, 9-14) and amyloidogenic misfolding (15) were explored. Application of IMS and IMS/MS is expanding to ever-larger macromolecules, including noncovalent assemblies with mass (m) Ͼ 1 MDa (16-18). Such studies have used both drift tube (DT) IMS (1-5, 7-15) and differential mobility analyzers (DMA) (17, 18) to separate ions by absolute mobility (K). In DT IMS, ions are separated while being pulled through still gas by an electric field. In DMA (17-19) ions traverse a space between 2 electrodes while being displaced laterally by gas flow. Only ions of specific K (determined by the voltage across the gap and flow speed) exit the gap, and mobility spectra are obtained by scanning the voltage.Recently, field asymmetric waveform ion mobility spectrometry (FAIMS) or differential mobility spectrometry has emerged as a major analytical tool (6,(20)(21)(22)(23)(24)(25)(26)(27)(28). FAIMS filters ions based on th...

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Section: Comparison Of Theory and Experimentssupporting

confidence: 56%

Pendular proteins in gases and new avenues for characterization of macromolecules by ion mobility spectrometry

Shvartsburg

Noskov

Purves

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

110

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“…The higher hydrophobicity of the yeast cyt c pocket could favor an increase of protein affinity for CL (as is indeed observed experimentally) and, thus, a decreased propensity of the complex to dissociate even at high ionic strength. Furthermore, yeast cyt c has a larger dipole moment than the horse protein (531 Debye in yeast and 253 Debye in horse cyt c, as calculated using the Protein Dipole Moments Server described in [42]). Dipole moment values have been shown to be an important factor in determining the interaction of cyt c on charged surfaces [43], and electrostatic interactions of the former protein with the negatively charged phosphate groups of CL might be very strong and less affected by ionic strength.…”

Section: Discussionmentioning

confidence: 99%

The effects of ATP and sodium chloride on the cytochrome c–cardiolipin interaction: The contrasting behavior of the horse heart and yeast proteins

Sinibaldi¹,

Droghetti²,

Polticelli³

et al. 2011

Journal of Inorganic Biochemistry

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In cells a portion of cytochrome c (cyt c) (15-20%) is tightly bound to cardiolipin (CL), one of the phospholipids constituting the mitochondrial membrane. The CL-bound protein, which has nonnative tertiary structure, altered heme pocket, and disrupted Fe(III)-M80 axial bond, is thought to play a role in the apoptotic process. This has attracted considerable interest in order to clarify the mechanisms governing the cyt c-CL interaction. Herein we have investigated the binding reaction of CL with the c-type cytochromes from horse heart and yeast. Although the two proteins possess a similar tertiary architecture, yeast cyt c displays lower stability and, contrary to the equine protein, it does not bind ATP and lacks pro-apoptotic activity. The study has been performed in the absence and in the presence of ATP and NaCl, two compounds that influence the (horse cyt c)-CL binding process and, thus, the pro-apoptotic activity of the protein. The two proteins behave differently: while CL interaction with horse cyt c is strongly influenced by the two effectors, no effect is observed for yeast cyt c. It is noteworthy that NaCl induces dissociation of the (horse cyt c)-CL complex but has no influence on that of yeast cyt c. The differences found for the two proteins highlight that specific structural factors, such as the different local structure conformation of the regions involved in the interactions with either CL or ATP, can significantly affect the behavior of cyt c in its reaction with liposomes and the subsequent pro-apoptotic action of the protein.

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“…The only remaining mechanisms are structural vibrations of electrically polar molecules or larger structures. Certain proteins manifest high electric dipole moments [14] which can therefore represent a good candidate for the sought-after substrate. The vibration modes of proteins themselves lie in the THz part of the spectrum [15], therefore beyond the frequency region of interest; however, we may consider larger polar biomacromolecular structures composed of proteins [12], for instance cytoskeletal filaments [11,13], which are theoretically predicted to have vibration modes in the range from MHz to GHz [16,17].…”

Section: Substrate For Biological Radiofrequency Activitymentioning

confidence: 99%

Radiofrequency and microwave interactions between biomolecular systems

Kučera

Cifra

2015

J Biol Phys

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The knowledge of mechanisms underlying interactions between biological systems, be they biomacromolecules or living cells, is crucial for understanding physiology, as well as for possible prevention, diagnostics and therapy of pathological states. Apart from known chemical and direct contact electrical signaling pathways, electromagnetic phenomena were proposed by some authors to mediate non-chemical interactions on both intracellular and intercellular levels. Here, we discuss perspectives in the research of nanoscale electromagnetic interactions between biosystems on radiofrequency and microwave wavelengths. Based on our analysis, the main perspectives are in (i) the micro and nanoscale characterization of both passive and active radiofrequency properties of biomacromolecules and cells, (ii) experimental determination of viscous damping of biomacromolecule structural vibrations and (iii) detailed analysis of energetic circumstances of electromagnetic interactions between oscillating polar biomacromolecules. Current cutting-edge nanotechnology and computational techniques start to enable such studies so we can expect new interesting insights into electromagnetic aspects of molecular biophysics of cell signaling.

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A server and database for dipole moments of proteins

Cited by 176 publications

References 21 publications

Pendular proteins in gases and new avenues for characterization of macromolecules by ion mobility spectrometry

Pendular proteins in gases and new avenues for characterization of macromolecules by ion mobility spectrometry

The effects of ATP and sodium chloride on the cytochrome c–cardiolipin interaction: The contrasting behavior of the horse heart and yeast proteins

Radiofrequency and microwave interactions between biomolecular systems

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