Sequence-specific resonance assignment and secondary structure of (1–71) bacterioopsin

Sobol, A. A.; Arseniev, Alexander S.; Abdulaeva, Galina V.; Musina, Larisa Yu.; Bystrov, V. F.

doi:10.1007/bf01875527

Cited by 18 publications

(8 citation statements)

References 29 publications

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“…It was ascertained that a possible aggregation is not responsible for the behavior of the C2 fragment, as an exchange curve obtained at a lower concentration showed similar results (data not shown). The data corresponding to the fragment C2 are consistent with the NMR results obtained under identical conditions by Sobol et al (1992), who reported that about 34% of the amide protons have exchange half-time between 10 and 100 h and the remaining ones less than 30 min. The differences in the exchange rates of Cl and C2 should be reflected in the deconvoluted spectra taken at different times after addition of deuterated C/M.…”

Section: Fourth-derivative Spectrophotometrysupporting

confidence: 90%

“…These bands are assigned to helical structure, as their frequencies are within the range normally accepted for these structures (1650-1657 cm-1; Byler and Susi, 1986;Surewicz and Mantsch, 1988). Furthermore, the sum of their relative areas is comparable to the predicted a-helical content in this solvent (Arseniev et al, 1988;Pervushin and Arseniev, 1992;Sobol et al, 1992).…”

Section: Fourth-derivative Spectrophotometrymentioning

confidence: 51%

“…It is worth mentioning that the differences observed in the exchange rate for the two fragments could be attributed to an increased tendency of the C2 fragment to aggregate in the C/M solvent, thus decreasing the accessibility of some amide protons to the medium. However, this possibility can be excluded because the interactions between helices from different C2 fragments in this solvent have not been detected by NMR (Sobol et al, 1992). On the other hand, if the interaction between helices from the same fragment made some amide protons belonging to interacting faces inaccessible to the solvent, this fact should be reflected in NMR data, but it is clear that the exchange resistance does 1600 1700 1680 1660 1640 1620wavenumber (cm-f') 1600 not depend on the face in which the residue is located (Sobol et al, 1992).…”

Section: Discussionmentioning

confidence: 99%

“…Arseniev et al (1987) showed by CD spectroscopy and 19F-NMR that BR solubilized in organic solvents could have a secondary and tertiary structure quite similar to the native state. Following that work, conformational analysis of several synthetic fragments, e.g., B (Arseniev et al, 1988), A (Pervushin and Arseniev, 1992), and proteolytic fragments BP2 (Barsukov et al, 1990) and C2 (Sobol et al, 1992) by 2D 1H-NMR have been carried out. These works show the existence of a predominant structure, a right-handed a-helix that fits well with Receivedforpublication 22 August 1994 and infinalform 7 February 1995.…”

Section: Introductionmentioning

confidence: 99%

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Spectroscopic studies of bacteriorhodopsin fragments dissolved in organic solution

Torres

Padrós

1995

Biophysical Journal

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Fourier transform infrared and UV fourth-derivative spectroscopies were used to study the secondary structure of bacteriorhodopsin and its chymotryptic and one of the sodium borohydride fragments dissolved in chloroform-methanol (1:1, v/v), 0.1 M LiClO4. The C1 fragment (helices C, D, E, F, and G) showed an alpha-helical content of about 53%, whereas C2 (helices A and B) had about 60%, and B2 (helices F and G) about 65% alpha-helix. The infrared main band indicated differences in alpha-helical properties between these fragments. These techniques were also used to obtain information on the interactions among helices. According to the results obtained from the hydrogen/deuterium exchange kinetics, about 40% of the amide protons of C2 are particularly protected against exchange, whereas for the C1 fragment this process is unexpectedly fast. UV fourth-derivative spectra of these samples were used to obtain information about the environment of Trp side chains. The results showed that the Trp residues of C2 are more shielded from the solvent than those of C1 or B2. The results of this work indicate that the specific interactions existing between the transmembrane segments induce different types of helical conformations in native bacteriorhodopsin.

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Section: Fourth-derivative Spectrophotometrysupporting

confidence: 90%

Section: Fourth-derivative Spectrophotometrymentioning

confidence: 51%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Spectroscopic studies of bacteriorhodopsin fragments dissolved in organic solution

Torres

Padrós

1995

Biophysical Journal

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“…In contrast to their observation, in our simulation the Gly 2~ carbonyl oxygen atom is stabilized not by a hydrogen bond to surrounding water molecules (which are absent in the current simulations), but to the H~IO group of Thr 24. A remarkable feature of C2 (Sobol et al, 1992) and of sA (Pervushin and Arseniev, 1992) formation of COi_3,4-H~'lOi hydrogen bonds (Sobol et al, 1992;Pervushin and Arseniev, 1992). Formation of these hydrogen bonds weakens the ~x-helical backbone hydrogen bonds, due to competition between the n'tlo and HN groups for the C=O group.…”

Section: Models Of Sa and C2mentioning

confidence: 99%

Manifestation of intramolecular motions on pico- and nanosecond time scales in 1H?15N NMR relaxation: Analysis of dynamic models of one- and two-helical subunits of bacterioopsin

Pervushin

Orekhov²,

Korzhnev³

et al. 1995

J Biomol NMR

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The influence of the internal dynamics of two polypeptides comprising transmembrane α-helix A or two α-helices A and B of bacterioopsin on experimentally accessible (15)N NMR relaxation rates was investigated by molecular dynamics (MD) simulations, combined with more simple mechanic considerations. 'Model-free' order parameters and correlation times of internal motions [Lipari, G. and Szabo, A. (1982) J. Am. Chem. Soc., 104, 4546-4559] were calculated for these models. It was found that both peptides exhibit two types of internal motions of the amide bonds, on the pico- and nanosecond time scales, affecting (15)N NMR relaxation. The fast fluctuations are local and correspond to the librational motions of the individual N-H vectors in an effective potential of atoms of the surrounding matrix. In contrast, the motions on the nanosecond time scale imply concerted collective vibrations of a large number of atoms and could be represented as bending oscillation of α-helices, strongly overdamped by the ambient solvent. A few other molecular mechanisms of slow internal motion were found, such as local distortions of the α-helices (e.g., α-aneurysm), delocalized distortions of the α-helical backbone, as well as oscillations of the tilt angle between the axes of the α-helices A and B. The results are compared with (15)N NMR relaxation data measured for the (1-36)bacterioopsin and (1-71)bacterioopsin polypeptides in chloroform-methanol (1:1) and in SDS micelles [Orekhov, V.Yu., Pervushin, K.V. and Arseniev, A.S. (1994) Eur. J. Biochem., 219, 887-896].

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The stability of transmembrane helices: A molecular dynamics study on the isolated helices of bacteriorhodopsin

Iyer

Vishveshwara

1998

Biopolymers

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Bacteriorhodopsin (bR) continues to be a proven testing ground for the study of integral membrane proteins (IMPs). It is important to study the stability of the individual helices of bR, as they are postulated to exist as independently stable transmembrane helices (TMHs) and also for their utility as templates for modeling other IMPs with the postulated seven‐helix bundle topology. Toward this purpose, the seven helices of bR have been studied by molecular dynamics simulation in this study. The suitability of using the backbone‐dependent rotamer library of side‐chain conformations arrived at from the data base of globular protein structures in the case TMHs has been tested by another set of 7 helix simulations with the side‐chain orientations taken from this library. The influence of the residue's net charge on the helix stability was examined by simulating the helices III, IV, and VI (from both of the above sets of helices) with zero net charge on the side chains. The results of these 20 simulations demonstrate in general the stability of the isolated helices of bR in conformity with the two‐stage hypothesis of IMP folding. However, the helices I, II, V, and VII are more stable than the other three helices. The helical nature of certain regions of III, IV, and VI are influenced by factors such as the net charge and orientation of several residues. It is seen that the residues Arg, Lys, Asp, and Glu (charged residues), and Ser, Thr, Gly, and Pro, play a crucial role in the stability of the helices of bR. The backbone‐dependent rotamer library for the side chains is found to be suitable for the study of TMHs in IMP. © 1996 John Wiley & Sons, Inc.

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Sequence-specific resonance assignment and secondary structure of (1–71) bacterioopsin

Cited by 18 publications

References 29 publications

Spectroscopic studies of bacteriorhodopsin fragments dissolved in organic solution

Spectroscopic studies of bacteriorhodopsin fragments dissolved in organic solution

Manifestation of intramolecular motions on pico- and nanosecond time scales in 1H?15N NMR relaxation: Analysis of dynamic models of one- and two-helical subunits of bacterioopsin

The stability of transmembrane helices: A molecular dynamics study on the isolated helices of bacteriorhodopsin

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