Elucidating the Role of Val-Asn 95 and Arg-Gly 52 Mutations on Structure and Stability of Fibroblast Growth Factor Homologous Factor 2

Background: Fibroblast growth Factor Homologous Factors (FHFs) belong to a subclass of Fibroblast Growth Factor (FGF) family owing to their high sequence and structural similarities with FGFs. However, despite these similarities, there are properties which set them apart from FGFs. FHFs lack the secretion signal sequence unlike other FGF members, except FGF1 and 2. Unlike FGFs, FHFs are not able to bind to FGF Receptors (FGFRs) and instead have been implicated in binding to Voltage-Gated Sodium Channels (VGSCs), neuronal MAP kinase scaffold protein and islet-brain-2 (IB2). The two amino acids Arg-52 and Val95 are conserved in all FHFs and mutation of these residues lead to its inability to bind with VGSC/IB2. However, it is not clear whether the loss of binding is due to destabilization of the protein on mutation or due to involvement of Arg52 and Val95 in conferring functionality to FHFs. Objective: In the present study, we have mutated these two conserved residues of FHF2 with its corresponding FGF counterpart amino acids and studied the effects of the mutations on the structure and stability of the protein. Methods: Several biophysical methods like isothermal equilibrium denaturation study, ANS fluorescence, intrinsic fluorescence, acrylamide quenching, circular dichroism studies as well as using computational approaches were employed. Results: The single mutations were found to affect the overall stability, conformation and functionality of the protein. Conclusion: Thus, the studies throw light on the role of specific amino acids in deciding the stability, structure and functionality of proteins and will be useful for development of therapeutically engineered proteins.

Phytolacca americana lectin (Pa-2; pokeweed mitogen): an intrinsically unordered protein and its conversion into partial order at low pH

This is the first report of its kind that well demonstrates that a lectin from Phytolacca americana [Pa-2 (P. americana lectin-2)] can also be intrinsically unordered, based on the results obtained by CD, tryptophan fluorescence, ANS (8-anilinonaphthalene-1-sulfonic acid) binding, acrylamide quenching, DLS (dynamic light scattering) and its amino acid composition database analyses. Pa-2 is an acidic monomeric lectin and acquires random coil conformation at neutral pH without any regular secondary structure. As confirmed by different spectroscopic techniques, on lowering the pH, some secondary structures, predominantly α-helices, are detected by far-UV CD that adopt a marginally stable partially folded collapsed conformation possessing the characteristics of a premolten globule state. It is in accordance with coil–helix transition that is commonly observed when these intrinsically unordered proteins interact with their partner molecules in vivo.

Examination of EmrE conformational differences in various membrane mimetic environments

Ethidium multidrug resistance protein (EmrE) is a member of the small multidrug resistance family of proteins and is responsible for resistance in Escherichia coli to a diverse group of lipophilic cations. Research is beginning to elucidate structural information as well as substrate binding and extrusion mechanisms for this protein. However, the choice of membrane mimetic environment to perform structural studies needs to be made. In this study EmrE was solubilized in different membrane mimetic environments to investigate the influence of environment on the structure and dynamics of the protein by comparing the fluorescence properties of emission maxima, peak shifts, relative intensities, acrylamide quenching constants, and polarization. Taken together, the different fluorescence observations on EmrE in the various membrane mimetic systems tested suggest that the tryptophan residues in EmrE are present in the most flexible and exposed state when solubilized in methanol, followed by sodium dodecyl sulfate and urea. The two detergents N-dodecyl-β-D-maltoside (DM) and polyoxyethylene(8)dodecyl ether, for the most part, only display subtle differences between the spectral properties with DM best representing the lipid environment. The conformation of EmrE is clearly more open and dynamic in detergent relative to being reconstituted in small unilamellar vesicles. The fluorescence observations of EmrE solubilized in trifluoroethanol shows an environment that is similar to that of EmrE solubilized in detergents. Additionally, secondary structure was monitored by circular dichroism (CD). The CD spectra were similar among the different solubilizing conditions, suggesting little difference in α-helical content. This work establishes groundwork for the choice of solubilizing conditions for future structural, folding, and ligand binding studies.Key words: SMR, EmrE, tryptophan fluorescence, membrane proteins, detergent solubilization, membrane mimetic.

Muscarinic Toxin-Like Proteins from Taiwan Banded Krait (Bungarus multicinctus) Venom: Purification, Characterization and Gene Organization

Two novel proteins, BM8 and BM14, were isolated from Bungarus multicinctus (Taiwan banded krait) venom using the combination of chromatography on a SPSephadex C-25 column and a reversephase HPLC column. Both proteins contained 82 amino acid residues including 10 cysteine residues, but there were two amino acid substitutions at positions 37 and 38 (Glu37Ala38 in BM8; Lys37Lys38 in BM14). CD spectra and acrylamide quenching studies revealed that the gross conformation of BM8 and BM14 differed. In contrast to BM8, BM14 inhibited the binding of [3H]quinuclidinyl benzilate to the M2 muscarinic acetylcholine (mAchR) receptor subtype. Trinitrophenylation of Lys residues abolished the mAchRbinding activity of BM14, indicating that the Lys substitutions at positions 37 and 38 played a crucial role in the activity of BM14. The genomic DNA encoding the precursor of BM14 was amplified by PCR. The gene shared virtually identical structural organization with αneurotoxin and cardiotoxin genes. The intron sequences of these genes shared a sequence identity up to 84%, but the proteincoding regions were highly variable. These results suggest that BM8, BM14, neurotoxins and cardiotoxins may have originated from a common ancestor, and the evolution of snake venom proteins shows a tendency to diversify their functions.

Tryptophan rotamers that report the conformational dynamics of proteins

The binding of acetyl­pepstatin to the Q7K/L33I/L63I mutant of HIV-1 protease was studied by fluorescence, phosphorescence, and 500-ps molecular dynamics. The protease is a homodimer with two tryptophans per monomer. Maximum entropy method (MEM) analysis and acrylamide quenching results show two tryptophyl, tryptophan (Trp) populations in the apoenzyme that merge into one in the complex. These results are in agreement with molecular dynamics simulations indicative of Trp asymmetry in the apoenzyme as revealed by the occurrence of nonequivalent Trp42 indole rotamer interconversions, not observed for the complex. Analysis of the local Trp42B environments of the apoenzyme with respect to possible quencher groups shows that the c2 interconversions do not influence the lifetime, while the c1 interconversions do. Upon binding the inhibitor, Trp42B acquires a single conformation with the same lifetime and orientation as that of Trp42, and also with less quenching accessibility. Thus, protein conformational dynamics become constrained with inhibitor binding. This conclusion is supported by red-edge effect experiments and phosphorescence lifetime measurements. The low temperature tp (~5.8 s) is quenched to ~200 ms as protein motions become activated around the glass transition temperature. In the case of the complex, the phosphorescence lifetime data show a more cooperative activation of the quenching mechanisms.