Insight into protein structure and protein-ligand recognition by Fourier transform infrared spectroscopy

The tailspike protein of Shigella phage Sf6. A structural homolog of Salmonella phage P22 tailspike protein without sequence similarity in the beta-helix domain

Bacteriophage Sf6 tailspike protein is functionally equivalent to the well characterized tailspike of Salmonella phage P22, mediating attachment of the viral particle to host cell-surface polysaccharide. However, there is significant sequence similarity between the two 70-kDa polypeptides only in the N-terminal putative capsid-binding domains. The major, central part of P22 tailspike protein, which forms a parallel beta-helix and is responsible for saccharide binding and hydrolysis, lacks detectable sequence homology to the Sf6 protein. After recombinant expression in Escherichia coli as a soluble protein, the Sf6 protein was purified to homogeneity. As shown by circular dichroism and Fourier transform infrared spectroscopy, the secondary structure contents of Sf6 and P22 tailspike proteins are very similar. Both tailspikes are thermostable homotrimers and resist denaturation by SDS at room temperature. The specific endorhamnosidase activities of Sf6 tailspike protein toward fluorescence-labeled dodeca-, deca-, and octasaccharide fragments of Shigella O-antigen suggest a similar active site topology of both proteins. Upon deletion of the N-terminal putative capsid-binding domain, the protein still forms a thermostable, SDS-resistant trimer that has been crystallized. The observations strongly suggest that the tailspike of phage Sf6 is a trimeric parallel beta-helix protein with high structural similarity to its functional homolog from phage P22.

Role of protein and substrate dynamics in catalysis by Pseudomonas putida cytochrome P450cam

The role of protein structural flexibility and substrate dynamics in catalysis by cytochrome P450 enzymes is an area of current interest. We have addressed these in cytochrome P450(cam) (P450(cam)) and its Y96A mutant with camphor and its related compounds using fluorescence spectroscopy. Previously [Prasad et al. (2000) FEBS Lett. 477, 157-160], we provided experimental support to dynamic fluctuations in P450(cam), and substrate access into the active site region via the channel next to the flexible F-G helix-loop-helix segment. In the investigation described here, we show that the dynamic fluctuations in the enzyme are substrate dependent as reflected by tryptophan fluorescence quenching experiments. The orientation of tryptophan relative to heme (kappa(2)) for W42 obtained from time-resolved tryptophan fluorescence measurements show variation with type of substrate bound to P450(cam) suggesting regions distant from heme-binding site are affected by physicochemical and steric characteristics/protein-substrate interactions of P450(cam) active site. We monitored substrate dynamics in the active site region of P450(cam) by time-resolved substrate anisotropy measurements. The anisotropy decay of substrates bound to P450(cam) indicate that mobility of substrates is modulated by physicochemical and steric characteristics/protein-substrate interactions of local active site structure, and provides an understanding of factors controlling observed hydroxylated products for substrate bound P450(cam) complexes. The present study shows that P450(cam) local and peripheral structural flexibility and heterogeneity along with substrate mobility play an important role in regulating substrate binding orientation during catalysis and accommodating diverse range of substrates within P450(cam) heme pocket.

A new approach to the study of protein-protein interaction by FTIR: complex formation between cytochrome P450BM-3 heme domain and FMN reductase domain

We describe a new approach to the study of protein-protein interaction using Fourier transform infrared spectroscopy (FTIR). This approach is based on the combination of FTIR technique with both protein titration experiments and the principal component analysis (factor analysis) of the IR absorption spectra in the 1500-1800 cm(-1) region for the protein mixtures. We have applied this approach to the interaction of the heme domain with the FMN domain of bacterial monooxygenase cytochrome P450BM-3 (CYP102A1). The analysis reveals that the first principal component reflects the protein-protein complex formation because the loading factors show a clear systematic dependence on the concentration of the heme domain according to a titration curve with a dissociation constant of approximately 5 microM. The spectrum of the first principal component has been assigned to structural changes in the secondary structure (increase of beta-sheet and alpha-helix and decrease of turn structures), amino acid side chains (protonation of aspartate and C-terminal COO group), and deprotonation of a propionic acid COOD group in the heme.

Intermolecular electron transfer in cytochrome P450cam covalently bound with Tris(2,2'-bipyridyl)ruthenium(II): structural changes detected by FTIR spectroscopy

Using Fourier transform infrared spectroscopy (FTIR) we have monitored the changes in the protein structure following photoinduced electron transfer from Ru(bpy)(3)(2+) covalently attached to cysteine 334 on the surface of cytochrome P450cam (CYP101). The FTIR difference spectra between the oxidized and reduced form indicate changes in a salt link and the secondary structure (alpha-helix and turn regions). Photoreduction was carried out in the presence of carbon monoxide in order to prove the reduction of the heme iron by means of the appearance of the characteristic CO stretch vibration infrared band at 1940 cm(-1) for the camphor-bound protein. This infrared band has also been used to estimate electron transfer rates. The observed rates depend on the protein concentration, indicating that intermolecular electron transfer occurs between the labeled molecules.

Substrates modulate the rate-determining step for CO binding in cytochrome P450cam (CYP101). A high-pressure stopped-flow study

The high-pressure stopped-flow technique is applied to study the CO binding in cytochrome P450cam (P450cam) bound with homologous substrates (1R-camphor, camphane, norcamphor and norbornane) and in the substrate-free protein. The activation volume DeltaV # of the CO on-rate is positive for P450cam bound with substrates that do not contain methyl groups. The kon rate constant for these substrate complexes is in the order of 3 x 10(6) M(-1) x s(-1). In contrast, P450cam complexed with substrates carrying methyl groups show a negative activation volume and a low kon rate constant of approximately 3 x 10(4) M(-1) x s(-1). By relating kon and DeltaV # with values for the compressibility and the influx rate of water for the heme pocket of the substrate complexes it is concluded that the positive activation volume is indicative for a loosely bound substrate that guarantees a high solvent accessibility for the heme pocket and a very compressible active site. In addition, subconformers have been found for the substrate-free and camphane-bound protein which show different CO binding kinetics.

Cytochrome P-450-CO and substrates: lessons from ligand binding under high pressure

An overview of the application of high-pressure studies on the carbon monoxide complex of cytochrome P-450 is given. Different approaches to characterize ligand binding steps, the conformational states and substates and the compressibility of the ligand-bound complex are reviewed. A particular focus is the effect of substrates on these properties. It is shown that substrate mobility, compressibility and water accessibility are interrelated and may have functional meaning.