Equilibrium unfolding of a small low-potential cytochrome, cytochrome c553 from Desulfovibrio vulgaris

Heme-bound SiaA from Streptococcus pyogenes: Effects of mutations and oxidation state on protein stability

The protein SiaA (HtsA) is part of a heme uptake pathway in Streptococcus pyogenes. In this report, we present the heme binding of the alanine mutants of the axial histidine (H229A) and methionine (M79A) ligands, as well as a lysine (K61A) and cysteine (C58A) located near the heme propionates (based on homology modeling) and a control mutant (C47A). pH titrations gave pKa values ranging from 9.0 to 9.5, close to the value of 9.7 for WT SiaA. Resonance Raman spectra of the mutants suggested that the ferric heme environment may be distinct from the wild-type; spectra of the ferrous states were similar. The midpoint reduction potential of the K61A mutant was determined by spectroelectrochemical titration to be 61±3mV vs. SHE, similar to the wild-type protein (68±3mV). The addition of guanidine hydrochloride showed two processes for protein denaturation, consistent with heme loss from protein forms differing by the orientation of the heme in the binding pocket (the half-life for the slower process ranged from less than half a day to two days). The ease of protein unfolding was related to the strength of interaction of the residues with the heme. We hypothesize that kinetically facile but only partial unfolding, followed by a very slow approach to the completely unfolded state, may be a fundamental attribute of heme trafficking proteins. Small motions to release/transfer the heme accompanied by resistance to extensive unfolding may preserve the three dimensional form of the protein for further uptake and release.

Role of cofactors in protein folding

Although cofactors are essential components of many proteins to attain biological activity, the role of cofactors in protein folding is not well understood. Biophysical characterization of four types of cofactor-binding proteins (with copper, flavin moiety, iron-sulfur cluster, and heme cofactors, respectively) provides the following insights. (1) The presence of the cofactor often stabilizes the native protein. (2) The cofactor has the ability to interact specifically with the unfolded polypeptide. (3) The presence of the cofactor is sometimes essential for the polypeptide to fold. (4) Coordination of the cofactor prior to polypeptide folding can dramatically accelerate formation of the functional protein.

Unfolding the unique c-type heme protein, Chlamydomonas reinhardtii cytochrome f

We have studied the unfolding reaction of cytochrome f from the green alga Chlamydomonas reinhardtii. Cytochrome f is different from all other c-type heme proteins in that it is a large, two-domain protein with predominantly beta-sheet structure. Moreover, the sixth axial ligand to the heme-iron is unique in cytochrome f: it is provided by the N-terminal alpha-amino group. Unfolding of oxidized and reduced cytochrome f by guanidine hydrochloride (GuHCl) was monitored by far-UV circular dichroism (CD), Soret absorption, and tyrosine emission: the same unfolding curves were obtained regardless of method. Neither oxidized nor reduced unfolded cytochrome f can be refolded at neutral pH. At pH 3.5 refolding takes place (upon dilution to lower denaturant concentrations or by electron injection to the unfolded, oxidized form), although the reaction is extremely slow. Reduced cytochrome f appears much more resistant towards denaturant perturbation than the oxidized form (in pH range 7-3.5). The heme in unfolded cytochrome f remains low-spin to pH 4 but turns high-spin at pH 3.5 (presumably due to protonation of the N-terminal amino group). Our results suggest that the unfolding process for cytochrome f is complex, involving kinetically trapped intermediates not resolvable by spectroscopy.

Structural and Biochemical Characterization of the Lungfish (Lepidosiren paradoxa) Liver Basic Fatty Acid Binding Protein

Only one fatty acid-binding protein (FABP) from the liver of the lungfish (Lepidosiren paradoxa) was isolated and characterized. The sequence comparison of lungfish FABP with that of the known members of the liver FABP (L-FABP) and liver basic FABP (Lb-FABP) subfamilies indicates that it is more closely related to chicken, iguana, frog, axolotl, catfish, and shark Lb-FABPs than to mammalian and axolotl L-FABPs. Lungfish liver expression of this single Lb-FABP contrasts with the other fish studied so far which coexpress an Lb-FABP with heart-adipocyte and/or intestinal FABP types. The lungfish liver FABP expression pattern resembles that of tetrapods, which only expresses liver type FABPs. Lungfish Lb-FABP is one of the two FABPs reported to have a disulfide bridge. The molecular modeling of lungfish Lb-FABP predicts that nine of the conserved residues of Lb-FABPs are oriented toward the binding cavity, thus suggesting they are related to the protein binding characteristics.

Cytochrome c(553), a small heme protein that lacks misligation in its unfolded state, folds with rapid two-state kinetics

Cytochrome c(553) (cyt c(553)) from Desulfovibrio vulgaris is a small helical heme protein that displays apparent two-state equilibrium-unfolding behavior. The covalently attached heme is low-spin, ligated by Met and His residues, in the native state but becomes high-spin upon unfolding at pH 7. Here, we show that in contrast to other c-type heme proteins, where misligations in the unfolded states are prominent, cyt c(553) refolding kinetics at pH 7 proceeds rapidly without detectable intermediates. The extrapolated folding rate constant in water for oxidized cyt c(553) matches exactly that predicted from the cyt c(553) native-state topology: 5300 s(-1 )(experimental) versus 5020 s(-1) (predicted). We therefore conclude that the presence of the oxidized cofactor does not affect the intrinsic formation speed of the cyt c(553 )structural motif.

Isolation, characterization and binding properties of two rat liver fatty acid-binding protein isoforms

Mammalian liver has only one fatty acid-binding protein (L-FABP) while the liver of non-mammalian vertebrates expresses a liver basic FABP (Lb-FABP) in addition to other members of the FABP family. We explore the possibility that L-FABP isoforms accomplish, in the liver of mammals, the metabolic functions corresponding to the different FABPs present in the liver of non-mammalian vertebrates. We have isolated isoforms I and II which have a different residue 105, Asn in the former and Asp in the latter. We made a conformational comparison of the apo-isoforms by intrinsic fluorescence emission and fourth-derivative spectroscopy, native-state proteolysis and unfolding curves. Ligand affinity was studied by measuring cis-parinaric acid displacement by different ligands. They have differences in their molecular conformation, including the environment of the binding site. Isoform II has probably a more open conformation than isoform I, thus allowing the binding of a greater variety of ligands. The affinity of isoform II for lysophospholipids, prostaglandins, retinoids, bilirubin and bile salts is greater than that of isoform I. These characteristics of rat L-FABP isoforms I and II suggest that they may accomplish different functions as happens with those of the different FABP types in non-mammalian species.