FTIR Difference Spectroscopy Research Articles

Probing Local Environments with the Infrared Probe: l-4-Nitrophenylalanine

The genetic incorporation of unnatural amino acids (UAAs) with high efficiency and fidelity is a powerful tool for the study of protein structure and dynamics with site-specificity in a relatively nonintrusive manner. Here, we illustrate the ability of L-4-nitrophenylalanine to serve as a sensitive IR probe of local protein environments in the 247 residue superfolder green fluorescent protein (sfGFP). Specifically, the nitro symmetric stretching frequency of L-4-nitrophenylalanine was shown to be sensitive to both solvents that mimic different protein environments and (15)N isotopic labeling of the three-atom nitro group of this UAA. (14)NO(2) and (15)NO(2) variants of this UAA were incorporated utilizing an engineered orthogonal aminoacyl-tRNA synthetase/tRNA pair into a solvent exposed and a partially buried position in sfGFP with high efficiency and fidelity. The combination of isotopic labeling and difference FTIR spectroscopy permitted the nitro symmetric stretching frequency of L-4-nitrophenylalanine to be experimentally measured at either site in sfGFP. The (14)NO(2) symmetric stretching frequency red-shifted 7.7 cm(-1) between the solvent exposed and partially buried position, thus illustrating the ability of this UAA to serve as an effective IR probe of local protein environments.

Probing Local Protein Environments with the Infrared Probe: L-4-Nitrophenylalanine

The genetic incorporation of unnatural amino acids (UAAs) with high efficiency and fidelity is a powerful tool for the study of protein structure and dynamics with site-specificity in a relatively nonintrusive manner. Here, we illustrate the ability of l-4-nitrophenylalanine to serve as a sensitive IR probe of local protein environments in the 247 residue superfolder green fluorescent protein (sfGFP). Specifically, the nitro symmetric stretching frequency of l-4-nitrophenylalanine was shown to be sensitive to both solvents that mimic different protein environments and 15N isotopic labeling of the three-atom nitro group of this UAA. 14NO2 and 15NO2 variants of this UAA were incorporated utilizing an engineered orthogonal aminoacyl−tRNA synthetase/tRNA pair into a solvent exposed and a partially buried position in sfGFP with high efficiency and fidelity. The combination of isotopic labeling and difference FTIR spectroscopy permitted the nitro symmetric stretching frequency of l-4-nitrophenylalanine to be ex...

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

The melibiose carrier from Escherichia coli (MelB) couples the accumulation of the disaccharide melibiose to the downhill entry of H(+), Na(+), or Li(+). 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(+) binding. Secondly, though Asp124 is not essential for Na(+) binding, this acidic residue may play a critical role, possibly by its interaction with the bound cation, in the full Na(+)-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(+) 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.

Evidence from FTIR Difference Spectroscopy of an Extensive Network of Hydrogen Bonds near the Oxygen-Evolving Mn4Ca Cluster of Photosystem II Involving D1-Glu65, D2-Glu312, and D1-Glu329

Analyses of the refined X-ray crystallographic structures of photosystem II (PSII) at 2.9-3.5 A have revealed the presence of possible channels for the removal of protons from the catalytic Mn(4)Ca cluster during the water-splitting reaction. As an initial attempt to verify these channels experimentally, the presence of a network of hydrogen bonds near the Mn(4)Ca cluster was probed with FTIR difference spectroscopy in a spectral region sensitive to the protonation states of carboxylate residues and, in particular, with a negative band at 1747 cm(-1) that is often observed in the S(2)-minus-S(1) FTIR difference spectrum of PSII from the cyanobacterium Synechocystis sp. PCC 6803. On the basis of its 4 cm(-1) downshift in D(2)O, this band was assigned to the carbonyl stretching vibration (C horizontal lineO) of a protonated carboxylate group whose pK(a) decreases during the S(1) to S(2) transition. The positive charge that forms on the Mn(4)Ca cluster during the S(1) to S(2) transition presumably causes structural perturbations that are transmitted to this carboxylate group via electrostatic interactions and/or an extended network of hydrogen bonds. In an attempt to identify the carboxylate group that gives rise to this band, the FTIR difference spectra of PSII core complexes from the mutants D1-Asp61Ala, D1-Glu65Ala, D1-Glu329Gln, and D2-Glu312Ala were examined. In the X-ray crystallographic models, these are the closest carboxylate residues to the Mn(4)Ca cluster that do not ligate Mn or Ca and all are highly conserved. The 1747 cm(-1) band is present in the S(2)-minus-S(1) FTIR difference spectrum of D1-Asp61Ala but absent from the corresponding spectra of D1-Glu65Ala, D2-Glu312Ala, and D1-Glu329Gln. The band is also sharply diminished in magnitude in the wild type when samples are maintained at a relative humidity of </=85%. It is proposed that D1-Glu65, D2-Glu312, and D1-Glu329 participate in a common network of hydrogen bonds that includes water molecules and the carboxylate group that gives rise to the 1747 cm(-1) band. It is further proposed that the mutation of any of these three residues, or partial dehydration caused by maintaining samples at a relative humidity of <or=85%, disrupts the network sufficiently that the structural perturbations associated with the S(1) to S(2) transition are no longer transmitted to the carboxylate group that gives rise to the 1747 cm(-1) band. Because D1-Glu329 is located approximately 20 A from D1-Glu65 and D2-Glu312, the postulated network of hydrogen bonds must extend for at least 20 A across the lumenal face of the Mn(4)Ca cluster. The D1-Asp61Ala, D1-Glu65Ala, and D2-Glu312Ala mutations also appear to substantially decrease the fraction of PSII reaction centers that undergo the S(3) to S(0) transition in response to a saturating flash. This behavior is consistent with D1-Asp61, D1-Glu65, and D2-Glu312 participating in a dominant proton egress channel that links the Mn(4)Ca cluster with the thylakoid lumen.

The Zn2+ inhibitive effects on the cytochrome bc1 complex from Rhodobacter capsulatus as revealed by the FTIR difference spectroscopy

The Zn2+ inhibitive effects on the cytochrome bc1 complex from Rhodobacter capsulatus as revealed by the FTIR difference spectroscopy

Light‐Induced Activation of Bacterial Phytochrome Agp1 Monitored by Static and Time‐Resolved FTIR Spectroscopy

Phytochromes, which regulate many biological processes in plants, bacteria, and fungi, can exist in two stable states, Pr and Pfr, that can be interconverted by light, via a number of intermediates such as meta-Rc. Herein we employ FTIR spectroscopy to study the Pr-to-Pfr conversion of the bacteriophytochrome Agp1 from Agrobacterium tumefaciens. Static FTIR Pfr/Pr and meta-Rc/Pr difference spectra are disentangled in terms of cofactor and protein structural changes. Guided by DFT calculations on cofactor models, the chromophore conformational changes can be grouped into structural adjustments of the cofactor-protein interactions localized in the C-D dipyrrole moiety, that is, the photoisomerisation site, and in the A-B dipyrrole moiety including the protein attachment site. Whereas changes at the C and D rings appear to be largely completed in the meta-Rc state, the structural changes in the A-B unit occur during the transition from meta-Rc to Pfr, concomitant with the main protein structural changes, as demonstrated by static and time-resolved FTIR difference spectroscopy. We employ this technique to monitor, for the first time, the dynamics of the photocycle of phytochrome on the millisecond timescale. By extending the studies to genetically engineered protein variants of Agp1, we further demonstrate that H250 and D197 as well as the PHY domain are essential for formation of the Pfr state. Based on the IR spectroscopic and available crystallographic data we discuss the role of critical amino acid residues for the protein-cofactor interactions during the photoinduced reaction cycle.

Synthesis and characterization of injectable bioadhesive hydrogels for nucleus pulposus replacement and repair of the damaged intervertebral disc

Bioadhesive polymers are natural or synthetic materials that can be used for soft tissue repair. The aim of this investigation was to develop an injectable, bioadhesive hydrogel with the potential to serve as a synthetic replacement for the nucleus pulposus of the intervertebral disc or as an annulus closure material. Branched copolymers of poly(N-isopropylacrylamide) (PNIPAAm) and poly(ethylene glycol) (PEG) were blended with poly(ethylene imine) (PEI). This three component injectable system can form a precipitated gel at physiological temperature due to the phase transition of PNIPAAm. The injection of glutaraldehyde into the gel core will adhere the implant to the surrounding tissues. (1)H NMR results indicated the successful physical incorporation of PEI into the PNIPAAm-PEG network by blending. In addition, the covalent crosslinking between the amine functionalities on the PEI and the aldehyde functionalities on the glutaraldehyde was verified using FTIR difference spectroscopy. Mechanical characterization of these blends showed a significant increase (p < 0.05) in compressive modulus following glutaraldehyde injection. The in vitro bioadhesive force studies with porcine skin showed a significant increase (p < 0.05) in the mean maximum force of detachment for PNIPAAm-PEG/PEI gels when glutaraldehyde was injected into the gel core. The results of this study indicate that the reactivity between amines and aldehyde functionalities can be exploited to impart bioadhesive properties to PNIPAAm-PEG/PEI copolymers.

Redox-induced conformational changes within the Escherichia coli NADH ubiquinone oxidoreductase (complex I): An analysis by mutagenesis and FT-IR spectroscopy

The proton-pumping NADH:ubiquinone oxidoreductase couples the transfer of electrons from NADH to ubiquinone with the translocation of protons across the membrane. This process is suggested to be accompanied by conformational changes of the enzyme that may be monitored by redox-induced FT-IR difference spectroscopy. Signals observed in the amide I range are partially attributed to local rearrangements that occur as an electrostatic response to the redox reactions of the FeS clusters. In addition, conformational changes can be reported that depend on pH and at the same time can be perturbed by site-directed mutagenesis of residue E67 on subunit B (the bacterial homologue of the mitochondrial PSST subunit). This residue is located in the vicinity of the cluster N2. Re-evaluating these previous data we here discuss a mechanism, by which the redox reaction of N2 induces conformational changes possibly leading to proton translocation.

Rapid-scan FTIR difference spectroscopy applied to ubiquinone reduction in photosynthetic reaction centers: role of redox mediators

Rapid-scan FTIR difference spectroscopy was used to investigate light-induced reduction of the ubiquinone QB ,a nd the oxidation kinetics of QB − and QH2 by external mediators in isolated reaction centers (RCs) from R. sphaeroides. As redox mediators, a Ferrocyanide/N,N,N � ,N � -tetramethyl-p-phenylenediamine (TMPD) mixture and an Ascorbate/2,3,5,6-tetramethyl- p-phenylenediamine (DAD) mixture are compared. Results show that TMPD red rapidly reduces the photoproduced P870 + primary donor. The process is fast enough to record rapid-scan FTIR spectra devoid of P870 + bands down to 260 K. Results show also that TMPD ox oxidises both QB − and QH2 faster than DAD ox . In particular, QB − is oxidised faster than QH2 at all temperatures studied. Results are discussed in the framework of time-resolved infrared studies on R. sphaeroides RCs, showing advan- tages/drawbacks of the proposed experimental approach.

Rapid-scan FTIR difference spectroscopy applied to ubiquinone reduction in photosynthetic reaction centers: Role of redox mediators

Rapid-scan FTIR difference spectroscopy was used to investigate light-induced reduction of the ubiquinone QB, and the oxidation kinetics of QB–and QH2by external mediators in isolated reaction centers (RCs) fromR. sphaeroides. As redox mediators, a Ferrocyanide/N,N,Nʹ,Nʹ-tetramethyl-p-phenylenediamine (TMPD) mixture and an Ascorbate/2,3,5,6-tetramethyl-p-phenylenediamine (DAD) mixture are compared.Results show that TMPDredrapidly reduces the photoproduced P870+primary donor. The process is fast enough to record rapid-scan FTIR spectra devoid of P870+bands down to 260 K. Results show also that TMPDoxoxidises both QB–and QH2faster than DADox. In particular, QB–is oxidised faster than QH2at all temperatures studied.Results are discussed in the framework of time-resolved infrared studies onR. sphaeroidesRCs, showing advantages/drawbacks of the proposed experimental approach.

Time-resolved flow-flash FT-IR difference spectroscopy: the kinetics of CO photodissociation from myoglobin revisited

Time-resolved flow-flash FT-IR difference spectroscopy: the kinetics of CO photodissociation from myoglobin revisited

FTIR analysis of GPCR activation using azido probes

We demonstrate the site-directed incorporation of an IR-active amino acid, p-azido-L-phenylalanine (azidoF, 1), into the G protein-coupled receptor rhodopsin using amber codon suppression technology. The antisymmetric stretch vibration of the azido group absorbs at approximately 2,100 cm(-1) in a clear spectral window and is sensitive to its electrostatic environment. We used FTIR difference spectroscopy to monitor the azido probe and show that the electrostatic environments of specific interhelical networks change during receptor activation.

Monitoring and Interpretation of Photoinduced Biochemical Processes by Rapid-Scan FTIR Difference Spectroscopy and Hybrid Hard and Soft Modeling

Natural photochemical processes often require special instrumentation to monitor them at a suitable time scale. Rapid-scan FTIR difference spectroscopy is one of the preferred techniques to obtain rich structural information in the scale of milliseconds about photochemical processes of complex natural systems. The difference spectra obtained by this technique enhance the fine spectroscopic changes undergone during the process but require powerful data analysis methodologies to take full advantage of the information provided. Hybrid hard- and soft-modeling methodologies allow for coping with difficulties linked to the nature of the time-resolved measurement and to the complexity of the kinetic model describing the natural photochemical process. Thus, this methodology presents the following advantages: (a) handles difference spectra, taking into account the consequences of the lack of measurement about the initial stage of the process, (b) models events of the process that may be defined by a kinetic model (by hard modeling) and events that do not obey a mechanistic behavior (by soft modeling), (c) adapts to the photoaccumulation/relaxation stages of reversible photochemical processes, and (d) works simultaneously with series of experiments performed in different conditions and showing different kinetic behavior. The results of this data treatment provide complete kinetic information on the photochemical processes, e.g., rate constants, and a global picture of the difference spectra and the concentration profiles linked to each of the events (hard or soft modeled) contributing to the measured signal. The performance of the combination of time-resolved differential FTIR and hybrid hard and soft modeling is shown in a complex case study related to the photosynthetic activity of the reaction center of the purple bacteria Rhodobacter sphaeroides.

Low-Frequency Heme, Iron-Ligand, and Ligand Modes of Imidazole and Imidazolate Complexes of Iron Protoporphyrin and Microperoxidase in Aqueous Solution. An Analysis by Far-Infrared Difference Spectroscopy

FTIR difference spectroscopy, notably in the far-IR domain, is appealing for the analysis of hemoproteins, since it permits us to directly probe the properties of the heme and its ligands but also those of aminoacids remote from the heme. We recently set a thin path-length electrochemical cell with diamond windows allowing the far-IR analysis of proteins in aqueous solutions using FTIR difference spectroscopy (Berthomieu, C,; Marboutin, L.; Dupeyrat, F.; Bouyer, P. Biopolymers 2006 82, 363-367). In this study, we used this cell to identify redox-sensitive low-frequency IR modes of imidazole complexes of Fe-protoporphyrin IX and microperoxidase-8 and analyzed the pH dependence of these modes. The far-IR bands of the heme and the axial imidazole ligands were assigned using (15)N(2)-, and d(3)-imidazole isotopic substitution, as well as imidazole substitution by 4(5)-methylimidazole. Internal modes of the axial histidine and imidazole ligands were identified in the 670-580 cm(-1) region, which are sensitive to the iron coordination (five-coordinated high-spin heme or six-coordinated low-spin heme) and the protonation states of the axial ligands. We showed that deformation modes of the heme pyrroles dominate the 420-370 cm(-1) region of the difference spectra. These modes were highly sensitive to the coordination and redox states of the heme iron and the conformation of the tetrapyrrole. While no nu(as)(Fe-axial ligand) IR mode was detected in the difference spectra of the neutral imidazole complexes of Fe-protoporphyrin and microperoxidase, a new mode at 312 and 334 cm(-1) was found specific of the imidazolate complexes of Fe(3+)-protoporphyrin and Fe(3+)-microperoxidase-8, respectively. On the basis of isotope shifts observed upon ligand deuteration, this band was assigned to a mode mixing the asymmetric stretching of the axial bonds with an internal deformation of the imidazolate rings. These data set the bases for the analysis of the IR low-frequency modes of hemoproteins, and specifically the electronic properties of the heme axial histidine ligands.

Structural Changes of Cephalopod Rhodopsin and β-Arrestin Measured by FTIR Difference Spectroscopy and Isotope Editing

Invertebrate rhodopsin is the primary photoreceptor found in the eyes of cephalopods. Importantly, unlike vertebrate rhodopsin, invertebrate rhodopsins such as sepia rhodopsin (s-Rh) can be activated by light and then rapidly cycled back to the original state with a second red-shifted photon, thereby facilitating a variety of novel biophysical studies. Additionally, invertebrate rhodopsins can bind to the ubiquitous β-Arrestin2 which is used in regulating signal transduction in many GCPRs. In this study, we used static and time-resolved FTIR difference spectroscopy to investigate the photocycle of s-Rh complexed to β-Arrestin2. In the spectrum of s-Rh alone, difference spectra obtained using two colors to cycle between the ground (rho) and acid meta state show an 11-cis to all-trans photocycle as previously described. Several bands between 1750-1700 cm-1 are assigned using a D2O induced shift to an as yet unknown carboxyl groups. Other large bands are seen especially in the amide I and II regions which indicate significant backbone structural changes. Upon addition of β-Arrestin2, the difference spectrum is altered, especially in the amide I and II regions, reflecting additional structural changes occurring in β-Arrestin2 upon photoactivation. A negative band at 1742 cm-1 was shifted higher in the complex indicating the β-Arrestin2 is perturbing at least one carboxyl group in s-Rh. In order to assign these changes, total 15N isotope labeling of β-Arrestin2 was utilized. Comparison of difference spectra from s-Rh complexes containing unlabelled and 15N labeled β-Arrestin2 reveals ∼ 3 cm-1 downshift of a negative/positive feature at 1668/1655 cm-1 indicating that these bands reflect at least partially conformational changes of the β -arrestin involving α-helical structure. These results offer a promising new tool to investigate the molecular mechanism of β-Arrestin interactions with GCPRs to regulate downstream signaling.

1P-233 除草剤効果を使用した植物の光傷害メカニズムの解明(光生物-光合成,第47回日本生物物理学会年会)

1P-233 除草剤効果を使用した植物の光傷害メカニズムの解明(光生物-光合成,第47回日本生物物理学会年会)

Substrate interaction with recombinant amidase from Pseudomonas aeruginosa during biocatalysis

The interaction of a variety of substrates with Pseudomonas aeruginosa native amidase (E.C. 3.5.1.4), overproduced in an Escherichia coli strain, was investigated using difference FTIR spectroscopy. The amides used as substrates showed an increase in hydrogen bonding upon association in multimers, which was not seen with esters. Evidence for an overall reduction or weakening of hydrogen bonding while amide and ester substrates are interacting with the enzyme is presented. The results describe a spectroscopic approach for analysis of substrate–amidase interaction and in situ monitoring of the hydrolysis and transferase reaction when amides or esters are used as substrates.

Vitamin B12 diffusion and binding in crosslinked poly(acrylic acid)s and poly(acrylic acid-co- N-vinyl pyrrolidinone)s

The diffusion mechanism of vitamin B12 in two types of crosslinked hydrogels, poly(acrylic acid) (cPAA) and copolymers of acrylic acid and N-vinyl pyrrolidinone (cP(AA-NVP)) was studied. The PAA and P(AA-NVP) synthesized by three different degrees of crosslinking have limited water absorption capabilities ranging from 3% to 18%. In the copolymers permeability of B12 is controlled by both intramolecular and intermolecular hydrogen-bonding between the pyrrolidinone and carboxylic acid side chains. The diffusion kinetic data in two types of polymers were best described by Peppas models instead of Higuchi models. Permeation from both crosslinked PAA and P(AA-co-NVP) copolymers followed a Super Case II transport mechanism, most likely driven by macromolecular chain relaxation and swelling of hydrophilic polymers. A special FTIR spectroscopic method for drug binding study, FTIR difference spectroscopy, is used to probe the strong interactions between vitamin B12 and the side chains of the hydrogels. The FTIR differential spectra of B12 in PAA hydrogels revealed dramatic changes of the spectral marker bands of B12 after binding in the crosslinked gels, indicating significant interactions occurring in the amide and phosphate moieties of B12. Such interactions retard the diffusion of vitamin B12.

Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin

The positions of protons are not available in most high-resolution structural data of biomolecules, thus the identity of proton storage sites in biomolecules that transport proton is generally difficult to determine unambiguously. Using combined quantum mechanical/molecular mechanical computations, we demonstrate that a pair of conserved glutamate residues (Glu 194/204) bonded by a delocalized proton is the proton release group that has been long sought in the proton pump, bacteriorhodopsin. This model is consistent with all available experimental structural and infrared data for both the wild-type bacteriorhodopsin and several mutants. In particular, the continuum infrared band in the 1,800- to 2,000-cm(-1) region is shown to arise due to the partially delocalized nature of the proton between the glutamates in the wild-type bacteriorhodopsin; alternations in the flexibility of the glutamates and electrostatic nature of nearby residues in various mutants modulate the degree of proton delocalization and therefore intensity of the continuum band. The strong hydrogen bond between Glu 194/204 also significantly shifts the carboxylate stretches of these residues well <1,700 cm(-1), which explains why carboxylate spectral shift was not observed experimentally in the typical >1,700-cm(-1) region upon proton release. By contrast, simulations with the proton restrained on the nearby water cluster, as proposed by several recent studies [see, for example, Garezarek K, Gerwert K (2006) Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy. Nature 439:109], led to significant structural deviations from available X-ray structures. This study establishes a biological function for strong, low-barrier hydrogen bonds.

Different Structural Changes Occur in Blue- and Green-Proteorhodopsins during the Primary Photoreaction

We examine the structural changes during the primary photoreaction in blue-absorbing proteorhodopsin (BPR), a light-driven retinylidene proton pump, using low-temperature FTIR difference spectroscopy. Comparison of the light-induced BPR difference spectrum recorded at 80 K to that of green-absorbing proteorhodopsin (GPR) reveals that there are several differences in the BPR and GPR primary photoreactions despite the similar structure of the retinal chromophore and all-trans --> 13-cis isomerization. Strong bands near 1700 cm(-1) assigned previously to a change in hydrogen bonding of Asn230 in GPR are still present in BPR. However, additional bands in the same region are assigned on the basis of site-directed mutagenesis to changes occurring in Gln105. In the amide II region, bands are assigned on the basis of total (15)N labeling to structural changes of the protein backbone, although no such bands were previously observed for GPR. A band at 3642 cm(-1) in BPR, assigned to the OH stretching mode of a water molecule on the basis of H2(18)O substitution, appears at a different frequency than a band at 3626 cm(-1) previously assigned to a water molecule in GPR. However, the substitution of Gln105 for Leu105 in BPR leads to the appearance of both bands at 3642 and 3626 cm(-1), indicating the waters assigned in BPR and GPR exist in separate distinct locations and can coexist in the GPR-like Q105L mutant of BPR. These results indicate that there exist significant differences in the conformational changes occurring in these two types proteorhodopsin during the initial photoreaction despite their similar chromophore structures, which might reflect a different arrangement of water in the active site as well as substitution of a hydrophilic for hydrophobic residue at residue 105.