Proteins in Action Monitored by Time‐Resolved FTIR Spectroscopy

Kötting, Carsten; Gerwert, Klaus

doi:10.1002/cphc.200400504

Cited by 136 publications

(108 citation statements)

References 63 publications

(74 reference statements)

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“…S2). Given the large and widely distributed number of IR active vibrations in a protein, almost any interaction with the substrate will induce an IR diff spectrum (40), in contrast to other spectroscopic methods relying on localized probes. Information about protein structural changes is mainly constrained to the 1;700-1;500 cm −1 region (amide I and II), whereas changes in amino acid side chains are more broadly distributed in frequencies (Fig.…”

Section: Resultsmentioning

confidence: 99%

Structural insights into the activation mechanism of melibiose permease by sodium binding

Granell

León²,

Leblanc³

et al. 2010

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

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The melibiose carrier from Escherichia coli (MelB) couples the accumulation of the disaccharide melibiose to the downhill entry of H þ , Na þ , or Li þ . In this work, substrate-induced FTIR difference spectroscopy was used in combination with fluorescence spectroscopy to quantitatively compare the conformational properties of MelB mutants, implicated previously in sodium binding, with those of a fully functional Cys-less MelB permease. The results first suggest that Asp55 and Asp59 are essential ligands for Na þ binding. Secondly, though Asp124 is not essential for Na þ binding, this acidic residue may play a critical role, possibly by its interaction with the bound cation, in the full Na þ -induced conformational changes required for efficient coupling between the ion-and sugar-binding sites; this residue may also be a sugar ligand. Thirdly, Asp19 does not participate in Na þ binding but it is a melibiose ligand. The location of these residues in two independent threading models of MelB is consistent with their proposed role.infrared spectroscopy | ligand binding | membrane proteins | sugar/cation symporter A ccording to the chemiosmotic principles, secondary active transporters comprise membrane proteins that couple in an obligatory fashion the discharge of an ionic gradient (or that of a solute gradient) to the "uphill" translocation of different solutes in the same direction (symporters or cotransporters) or in the opposite one (antiporters or exchangers) (1). Thermodynamic considerations and a wealth of kinetic, biochemical, and biophysical studies have led to the consensual view that substrate translocation relies on the alternating-access concept (2), stating that at any moment a single binding site in a polar cavity is accessible to only one side of the membrane (see for example, recent reviews and references therein in refs. 3-8). The recent elucidation of the atomic structure of almost a dozen of transporters provides strong support to the validity of the alternatingaccess concept (see reviews cited above). Finally, the diversity of conformation(s) adopted in the different transporters crystals has yielded insights into the structural basis of the various steps of the symporter cycle. Still, many issues regarding the conformational changes, especially those involved in ligand binding and in the coupling of the ligand binding sites, remain largely unanswered.In this context, the melibiose permease (MelB) of Escherichia coli, which belongs to the Glycoside-Pentoside-Hexuronide: Cation symporter family (9) (a submember of the major facilitator superfamily, MFS), is a convenient Na þ symporter to analyze the molecular and structural basis of the interaction of the coupling ion with the transporter. MelB efficiently couples the uphill transport of α-or β-galactosides to the favorable entry of Na þ , Li þ , or H þ (H 3 O þ ) (10,11). In the past, this property has been extensively exploited to investigate the molecular and structural basis of the ion-MelB interaction and implications in the coupling propert...

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Section: Resultsmentioning

confidence: 99%

Structural insights into the activation mechanism of melibiose permease by sodium binding

Granell

León²,

Leblanc³

et al. 2010

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

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“…Protonated and deprotonated carboxylates can be easily distinguished by FT-IR spectroscopy (67,91). Protonation of the carboxylate side chain gives rise to C ϭ O stretching bands in the 1720 -1700 cm Ϫ1 region, whereas deprotonated carboxylates have delocalized asymmetric and symmetric CO stretching vibrations at ϳ1560 and 1390 cm Ϫ1 (65).…”

Section: Discussionmentioning

confidence: 99%

An Intrinsically Disordered Photosystem II Subunit, PsbO, Provides a Structural Template and a Sensor of the Hydrogen-bonding Network in Photosynthetic Water Oxidation

Offenbacher

Polander

Barry

2013

Journal of Biological Chemistry

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Background:PsbO is an intrinsically disordered subunit of photosystem II. Results: Temperature-sensitive PsbO dynamics are identified by reaction-induced Fourier transform infrared spectroscopy and the removal and reconstitution of PsbO. Conclusion: PsbO serves as an organizational template and undergoes flash-induced hydrogen-bonding changes, coupled with the catalytic cycle of water oxidation. Significance: PsbO samples a rough conformational landscape when bound to its target, the photosystem II reaction center.

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“…1,2 The unique value of IR spectroscopy becomes more transparent with the rapid development of various multidimensional techniques in recent years. [3][4][5][6][7] For condensed phase applications, however, the interpretation of IR spectra is not always straightforward, which highlights the importance of developing effective computational techniques that can compute linear and nonlinear IR spectra in complex molecular systems.…”

Section: Introductionmentioning

confidence: 99%

The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding

Cui

2007

The Journal of Chemical Physics

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The vibrational spectra of protonated water clusters: A benchmark for selfconsistent-charge density-functional tight binding AbstractProton transfers are involved in many chemical processes in solution and in biological systems. Although water molecules have been known to transiently facilitate proton transfers, the possibility that water molecules may serve as the "storage site" for proton in biological systems has only been raised in recent years. To characterize the structural and possibly the dynamic nature of these protonated water clusters, it is important to use effective computational techniques to properly interpret experimental spectroscopic measurements of condensed phase systems. Bearing this goal in mind, we systematically benchmark the self-consistent-charge density-functional tight-binding �SCC-DFTB� method for the description of vibrational spectra of protonated water clusters in the gas phase, which became available only recently with infrared multiphoton photodissociation and infrared predissociation spectroscopic experiments. It is found that SCC-DFTB qualitatively reproduces the important features in the vibrational spectra of protonated water clusters, especially concerning the characteristic signatures of clusters of various sizes. In agreement with recent ab initio molecular dynamics studies, it is found that dynamical effects play an important role in determining the vibrational properties of these water clusters. Considering computational efficiency, these benchmark calculations suggest that the SCC-DFTB/molecular mechanical approach can be an effective tool for probing the structural and dynamic features of protonated water molecules in biomolecular systems. The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding Proton transfers are involved in many chemical processes in solution and in biological systems. Although water molecules have been known to transiently facilitate proton transfers, the possibility that water molecules may serve as the "storage site" for proton in biological systems has only been raised in recent years. To characterize the structural and possibly the dynamic nature of these protonated water clusters, it is important to use effective computational techniques to properly interpret experimental spectroscopic measurements of condensed phase systems. Bearing this goal in mind, we systematically benchmark the self-consistent-charge density-functional tight-binding ͑SCC-DFTB͒ method for the description of vibrational spectra of protonated water clusters in the gas phase, which became available only recently with infrared multiphoton photodissociation and infrared predissociation spectroscopic experiments. It is found that SCC-DFTB qualitatively reproduces the important features in the vibrational spectra of protonated water clusters, especially concerning the characteristic signatures of clusters of various sizes. In agreement with recent ab initio molecular dynamics studies, it is found that dynamic...

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Proteins in Action Monitored by Time‐Resolved FTIR Spectroscopy

Cited by 136 publications

References 63 publications

Structural insights into the activation mechanism of melibiose permease by sodium binding

Structural insights into the activation mechanism of melibiose permease by sodium binding

An Intrinsically Disordered Photosystem II Subunit, PsbO, Provides a Structural Template and a Sensor of the Hydrogen-bonding Network in Photosynthetic Water Oxidation

The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding

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