Dependence of the size of a protein-SDS complex on detergent and Na+ concentrations

Artificial Proteins Designed from G3LEA Contribute to Enhancement of Oxidation Tolerance in E. coli in a Chaperone-like Manner

G3LEA is a family of proteins that exhibit chaperone-like activity when under distinct stress. In previous research, DosH was identified as a G3LEA protein from model extremophile-Deinococcus radiodurans R1 with a crucial core HD domain consisting of eight 11-mer motifs. However, the roles of motifs participating in the process of resistance to stress and their underlying mechanisms remain unclear. Here, eight different proteins with tandem repeats of the same motif were synthesized, named Motif1-8, respectively, whose function and structure were discussed. In this way, the role of each motif in the HD domain can be comprehensively analyzed, which can help in finding possibly crucial amino acid sites. Circular dichroism results showed that all proteins were intrinsically ordered in phosphate buffer, and changed into more α-helical ordered structures with the addition of trifluoroethanol and glycerol. Transformants expressing artificial proteins had significantly higher stress resistance to oxidation, desiccation, salinity and freezing compared with the control group; E. coli with Motif1 and Motif8 had more outstanding performance in particular. Moreover, enzymes and membrane protein protection viability suggested that Motif1 and Motif8 had more positive influences on various molecules, demonstrating a protective role in a chaperone-like manner. Based on these results, the artificial proteins synthesized according to the rule of 11-mer motifs have a similar function to wildtype protein. Regarding the sequence in all motifs, there are more amino acids to produce H bonds and α-helices, and more amino acids to promote interaction between proteins in Motif1 and Motif8; in addition, considering linkers, there are possibly more amino acids forming α-helix and binding substrates in these two proteins, which potentially provides some ideas for us to design potential ideal stress-response elements for synthetic biology. Therefore, the amino acid composition of the 11-mer motif and linker is likely responsible for its biological function.

Structural, kinetic and thermodynamic characterizations of SDS-induced molten globule state of a highly negatively charged cytochrome c

This study presents the structural, kinetic and thermodynamic characterizations of previously unknown submicellar concentrations of SDS-induced molten globule (MGSDS) state of a highly negatively charged base-denatured ferricytochrome c (UB-state) at pH ∼12.8 (±0.2). The far-UV CD, near-UV CD, ANS-fluorescence data of UB-state in the presence of different concentrations of SDS indicate that the submicellar concentrations of SDS (≤0.4 mM) transform the UB-state to MGSDS-state. The MGSDS-state has native-like α-helical secondary structure but lacks tertiary structure. The free energy change (ΔG°D) for UB→ MGSDS transition determined by far-UV CD (∼2.7 kcal mol-1) is slightly higher than those determined by fluorescence (∼2.0 kcal mol-1) at 25°C. At very low SDS and NaCl concentrations, the MGSDS-state undergoes cold denaturation. As SDS concentration is increased, the thermal denaturation temperature increases and the cold denaturation temperature decrease. Kinetic experiments involving the measurement of the CO-association rate to the base-denatured ferrocytochrome c at pH ≈12.8 (±0.2), 25°C indicate that the submicellar concentrations of SDS restrict the internal dynamics of base-denatured protein.

Impact of Differential Detergent Interactions on Transmembrane Helix Dimerization Affinities

Interactions between transmembrane (TM) helices play a critical role in the fundamental processes required for cells to communicate and exchange materials with their surroundings. Our understanding of the factors that promote TM helix interactions has greatly benefited from our ability to study these interactions in the solution phase through the use of membrane-mimetic micelles. However, less is known about the potential influence of juxtamembrane regions flanking the interacting TM helices that may modulate dimerization affinities, even when the interacting surface itself is not altered. To investigate this question, we used solution NMR to quantitate the dimerization affinity of the major coat protein from the M13 bacteriophage in sodium dodecyl sulfate (SDS), a well-characterized model of a single-spanning self-associating TM protein. Here, we showed that a shorter construct lacking the N-terminal amphipathic helix has a higher dimerization affinity relative to that of the full-length protein, with no change in the helical structure between the monomeric and dimeric states in both cases. Although this translated into a 0.6 kcal/mol difference in free energy when the SDS solvent was approximated as a continuous phase, there were deviations from this model at high protein to detergent ratios. Instead, the equilibria were better fit to a model that treats the empty micelle as an active participant in the reaction, giving rise to standard free energies of association that were the same for both full-length and TM-segment constructs. According to this model, the higher apparent affinity of the shorter peptide could be completely explained by the enhanced detergent binding by the monomer relative to that bound by the dimer. Therefore, differential detergent binding between the monomeric and dimeric states provides a mechanism by which TM helix interactions can be modulated by noninteracting juxtamembrane regions.

Modeling Protein-Micelle Systems in Implicit Water

Several membrane proteins and numerous membrane-active peptides have been studied in detergent micelles by solution NMR. However, the detailed structure of these complexes remains unknown. We propose a modeling approach that treats the protein and detergent in atomistic detail and the solvent implicitly. The model is based on previous work on dodecylphosphocholine micelles, adapted for use with the CHARMM36 force field and extended to sodium dodecyl sulfate micelles. Solvation parameters were slightly adjusted to reproduce experimental data on aggregation numbers and critical micelle concentrations. To test the approach, several membrane-active peptides and three β-barrel membrane proteins were subjected to molecular dynamics simulations in the presence of a large number of detergent molecules. Their experimentally determined secondary structure was maintained and the RMSD values were less than 2 Å. Deformations were commonly observed in the N or C termini. The atomistic view of the protein-micelle systems that this approach provides could be useful in interpreting biophysical experiments carried out in the presence of detergent.

'q-Titration' of long-chain and short-chain lipids differentiates between structured and mobile residues of membrane proteins studied in bicelles by solution NMR spectroscopy

'q-Titration' refers to the systematic comparison of signal intensities in solution NMR spectra of uniformly (15)N labeled membrane proteins solubilized in micelles and isotropic bicelles as a function of the molar ratios (q) of the long-chain lipids (typically DMPC) to short-chain lipids (typically DHPC). In general, as q increases, the protein resonances broaden and correspondingly have reduced intensities due to the overall slowing of protein reorientation. Since the protein backbone signals do not broaden uniformly, the differences in line widths (and intensities) enable the narrower (more intense) signals associated with mobile residues to be differentiated from the broader (less intense) signals associated with "structured" residues. For membrane proteins with between one and seven trans-membrane helices in isotropic bicelles, we have been able to find a value of q between 0.1 and 1.0 where only signals from mobile residues are observed in the spectra. The signals from the structured residues are broadened so much that they cannot be observed under standard solution NMR conditions. This q value corresponds to the ratio of DMPC:DHPC where the signals from the structured residues are "titrated out" of the spectrum. This q value is unique for each protein. In magnetically aligned bilayers (q>2.5) no signals are observed in solution NMR spectra of membrane proteins because the polypeptides are "immobilized" by their interactions with the phospholipid bilayers on the relevant NMR timescale (∼10(5)Hz). No signals are observed from proteins in liposomes (only long-chain lipids) either. We show that it is feasible to obtain complementary solution NMR and solid-state NMR spectra of the same membrane protein, where signals from the mobile residues are present in the solution NMR spectra, and signals from the structured residues are present in the solid-state NMR spectra. With assigned backbone amide resonances, these data are sufficient to describe major features of the secondary structure and basic topology of the protein. Even in the absence of assignments, this information can be used to help establish optimal experimental conditions.

On the mechanism of SDS-induced protein denaturation

To understand the mechanism of ionic detergent-induced protein denaturation, this study examines the action of sodium dodecyl sulfate on ferrocytochrome c conformation under neutral and strongly alkaline conditions. Equilibrium and stopped-flow kinetic results consistently suggest that tertiary structure unfolding in the submicellar and chain expansion in the micellar range of SDS concentrations are the two major and discrete events in the perturbation of protein structure. The nature of interaction between the detergent and the protein is predominantly hydrophobic in the submicellar and exclusively hydrophobic at micellar levels of SDS concentration. The observation that SDS also interacts with a highly denatured and negatively charged form of ferrocytochrome c suggests that the interaction is independent of structure, conformation, and ionization state of the protein. The expansion of the protein chain at micellar concentration of SDS is driven by coulombic repulsion between the protein-bound micelles, and the micelles and anionic amino acid side chains.

Dynamic alpha-helix structure of micelle-bound human amylin

Amylin is an endocrine hormone that regulates metabolism. In patients afflicted with type 2 diabetes, amylin is found in fibrillar deposits in the pancreas. Membranes are thought to facilitate the aggregation of amylin, and membrane-bound oligomers may be responsible for the islet beta-cell toxicity that develops during type 2 diabetes. To better understand the structural basis for the interactions between amylin and membranes, we determined the NMR structure of human amylin bound to SDS micelles. The first four residues in the structure are constrained to form a hairpin loop by the single disulfide bond in amylin. The last nine residues near the C terminus are unfolded. The core of the structure is an alpha-helix that runs from about residues 5-28. A distortion or kink near residues 18-22 introduces pliancy in the angle between the N- and C-terminal segments of the alpha-helix. Mobility, as determined by (15)N relaxation experiments, increases from the N to the C terminus and is strongly correlated with the accessibility of the polypeptide to spin probes in the solution phase. The spin probe data suggest that the segment between residues 5 and 17 is positioned within the hydrophobic lipid environment, whereas the amyloidogenic segment between residues 20 and 29 is at the interface between the lipid and solvent. This orientation may direct the aggregation of amylin on membranes, whereas coupling between the two segments may mediate the transition to a toxic structure.