Melanie J. Cocco

Interhelical hydrogen bonding drives strong interactions in membrane proteins

Polar residues in transmembrane α-helices may strongly influence the folding or association of integral membrane proteins. To test whether a motif that promotes helix association in a soluble protein could do the same within a membrane, we designed a model transmembrane helix based on the GCN4 leucine zipper. We found in both detergent miscelles and biological membranes that helix association is driven strongly by asparagine, independent of the rest of the hydrophobic leucine and/or valine sequence. Hydrogen bonding between membrane helices gives stronger associations than the packing of surfaces in glycophorin A helices, creating an opportunity to stabilize structures, but also implying a danger that non-specific interactions might occur. Thus, membrane proteins may fold to avoid exposure of strongly hydrogen bonding groups at their lipid exposed surfaces.

Design of stable alpha-helical arrays from an idealized TPR motif.

The tetratricopeptide repeat (TPR) is a 34-amino acid alpha-helical motif that occurs in over 300 different proteins. In the different proteins, three to sixteen or more TPR motifs occur in tandem arrays and function to mediate protein-protein interactions. The binding specificity of each TPR protein is different, although the underlying structural motif is the same. Here we describe a statistical approach to the design of an idealized TPR motif. We present the high-resolution X-ray crystal structures (to 1.55 and 1.6 A) of designed TPR proteins and describe their solution properties and stability. A detailed analysis of these structures provides an understanding of the TPR motif, how it is repeated to give helical arrays with different superhelical twists, and how a very stable framework may be constructed for future functional designs.

Amphipols From A to Z

Amphipols (APols) are short amphipathic polymers that can substitute for detergents to keep integral membrane proteins (MPs) water soluble. In this review, we discuss their structure and solution behavior; the way they associate with MPs; and the structure, dynamics, and solution properties of the resulting complexes. All MPs tested to date form water-soluble complexes with APols, and their biochemical stability is in general greatly improved compared with MPs in detergent solutions. The functionality and ligand-binding properties of APol-trapped MPs are reviewed, and the mechanisms by which APols stabilize MPs are discussed. Applications of APols include MP folding and cell-free synthesis, structural studies by NMR, electron microscopy and X-ray diffraction, APol-mediated immobilization of MPs onto solid supports, proteomics, delivery of MPs to preexisting membranes, and vaccine formulation.

Structure and Stability Changes of Human IgG1 Fc as a Consequence of Methionine Oxidation

The Fc region has two highly conserved methionine residues, Met 33 (C(H)3 domain) and Met 209 (C(H)3 domain), which are important for the Fcs structure and biological function. To understand the effect of methionine oxidation on the structure and stability of the human IgG1 Fc expressed in Escherichia coli, we have characterized the fully oxidized Fc using biophysical (DSC, CD, and NMR) and bioanalytical (SEC and RP-HPLC-MS) methods. Methionine oxidation resulted in a detectable secondary and tertiary structural alteration measured by circular dichroism. This is further supported by the NMR data. The HSQC spectral changes indicate the structures of both C(H)2 and C(H)3 domains are affected by methionine oxidation. The melting temperature (Tm) of the C(H)2 domain of the human IgG1 Fc was significantly reduced upon methionine oxidation, while the melting temperature of the C(H)3 domain was only affected slightly. The change in the C(H)2 domain T m depended on the extent of oxidation of both Met 33 and Met 209. This was confirmed by DSC analysis of methionine-oxidized samples of two site specific methionine mutants. When incubated at 45 degrees C, the oxidized Fc exhibited an increased aggregation rate. In addition, the oxidized Fc displayed an increased deamidation (at pH 7.4) rate at the Asn 67 and Asn 96 sites, both located on the C(H)2 domain, while the deamidation rates of the other residues were not affected. The methionine oxidation resulted in changes in the structure and stability of the Fc, which are primarily localized to the C(H)2 domain. These changes can impact the Fcs physical and covalent stability and potentially its biological functions; therefore, it is critical to monitor and control methionine oxidation during manufacturing and storage of protein therapeutics.

Structural and Functional Analyses of the Major Outer Membrane Protein of Chlamydia trachomatis

Chlamydia trachomatis is a major pathogen throughout the world, and preventive measures have focused on the production of a vaccine using the major outer membrane protein (MOMP). Here, in elementary bodies and in preparations of the outer membrane, we identified native trimers of the MOMP. The trimers were stable under reducing conditions, although disulfide bonds appear to be present between the monomers of a trimer and between trimers. Cross-linking of the outer membrane complex demonstrated that the MOMP is most likely not in a close spatial relationship with the 60- and 12-kDa cysteine-rich proteins. Extraction of the MOMP from Chlamydia isolates under nondenaturing conditions yielded the trimeric conformation of this protein as shown by cross-linking and analysis by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis with different concentrations of acrylamide. Using circular dichroism spectroscopy, we determined that the trimers were formed mainly of beta-pleated sheet structures in detergent micelles. Using a liposomal swelling assay, the MOMP was found to have porin activity, and the size of the pore was estimated to be approximately 2 nm in diameter. The trimers were found to be stable in SDS at temperatures ranging from 4 to 37 degrees C and over a pH range of 5.0 to 8.0. In addition, the trimers of MOMP were found to be resistant to digestion with trypsin. In conclusion, these results show that the native conformation of the MOMP of C. trachomatis is a trimer with predominantly a beta-sheet structure and porin function.

Electropositive Charge in α-Defensin Bactericidal Activity: Functional Effects of Lys-for-Arg Substitutions Vary with the Peptide Primary Structure

ABSTRACT Cationic amino acids contribute to α-defensin bactericidal activity. Curiously, although Arg and Lys have equivalent electropositive charges at neutral pH, α-defensins contain an average of nine Arg residues per Lys residue. To investigate the role of high α-defensin Arg content, all Arg residues in mouse Paneth cell α-defensin cryptdin 4 (Crp4) and rhesus myeloid α-defensin 4 (RMAD-4) were replaced with Lys to prepare (R/K)-Crp4 and (R/K)-RMAD-4, respectively. Lys-for-Arg replacements in Crp4 attenuated bactericidal activity and slowed the kinetics of Escherichia coli ML35 cell permeabilization, and (R/K)-Crp4 required longer exposure times to reduce E. coli cell survival. In marked contrast, Lys substitutions in RMAD-4 improved microbicidal activity against certain bacteria and permeabilized E. coli more effectively. Therefore, Arg→Lys substitutions attenuated activity in Crp4 but not in RMAD-4, and the functional consequences of Arg→Lys replacements in α-defensins are dependent on the peptide primary structure. In addition, the bactericidal effects of (R/K)-Crp4 and (R/K)-RMAD-4 were more sensitive to inhibition by NaCl than those of the native peptides, suggesting that the high Arg content of α-defensins may be under selection to confer superior microbicidal function under physiologic conditions.

Differential Effects on Human Immunodeficiency Virus Type 1 Replication by α-Defensins with Comparable Bactericidal Activities

ABSTRACT In addition to their antibacterial activities, certain antimicrobial peptides inactivate enveloped viruses, including the human immunodeficiency virus (HIV). To determine whether peptide bactericidal activities are predictive of antiviral activity, the anti-HIV properties of recombinant human α-defensin 5, mouse α-defensins, cryptdins (Crp) 3 and 4, and rhesus macaque myeloid α-defensins (RMADs) 3 and 4 were determined in vitro. The peptides, purified to homogeneity, had equivalent bactericidal activities that were similar to those of the native molecules. Nuclear magnetic resonance spectroscopy showed RMAD-4 and Crp3 had characteristic α-defensin tridisulfide arrays. Of the peptides analyzed, only RMAD-4 inhibited HIV infectivity at 150 μg/ml, and Crp3 unexpectedly increased HIV replication. Quantitative real-time PCRs for minus-strand strong stop DNA and complete viral cDNA synthesis were used to distinguish between preentry and postentry anti-HIV effects by RMAD-4. Viral exposure to RMAD-4 for 1 h prior to infection reduced HIV minus-strand strong stop DNA and HIV cDNA by 4- to 20-fold during the first round of replication, showing that RMAD-4-exposed virions were not entering cells during the first 24 h. On the other hand, when RMAD-4 was added coincident with HIV inoculation, no anti-HIV activity was detected. Viral exposure to Crp3 resulted in a threefold increase in both HIV minus-strand strong stop DNA and HIV cDNA over the first round of replication. Therefore, two α-defensins, RMAD-4 and Crp3, inhibit or augment HIV replication, respectively, by mechanisms that precede reverse transcription.

Matrix metalloproteinase-7 activation of mouse paneth cell Pro-α-defensins: Ser43*Ile44 proteolysis enables membrane disruptive activity

Small intestinal Paneth cells secrete α-defensin microbicidal peptides as mediators of innate enteric immunity. In mice, production of mature Paneth cell α-defensins, termed cryptdins (Crps), requires proteolytic activation of inactive precursors (pro-Crps) by the convertase matrix metalloproteinase-7. Proteolysis of mouse (pro-Crp4)20-92 produces the specific cleavage intermediates pro-Crp444-92, pro-Crp454-92, and pro-Crp459-92. To identify which cleavage event enables bactericidal activity, recombinant pro-Crp4-processing intermediates were purified to homogeneity and assayed for bactericidal peptide activity. The in vitro bactericidal activities of pro-Crp4-processing intermediates were very similar to fully processed Crp4, contrasting the lack of bactericidal and membrane-disruptive activity shown by pro-Crp420-92. Thus, cleavage of pro-Crp420-92 at Ser43↓Ile44 is sufficient to activate bactericidal activity, and amino acids in the pro-Crp420-43 of the proregion maintain the precursor in an inactive state. Because cationic Arg residues are determinants of Crp4 bactericidal peptide activity, we hypothesized that Asp and Glu residues in pro-Crp420-43 neutralize Crp4 Arg side chains in pro-Crp420-92. Therefore, a pro-Crp420-92 variant with Gly substitutions at all pro-Crp420-43 Asp and Glu positions ((DE/G)-pro-Crp4) was prepared, and it was bactericidal and lysed phospholipid vesicles under conditions where native pro-Crp420-92 lacks activity. These findings show that MMP-7 proteolysis of pro-Crp420-92 at Ser43↓Ile44 converts inactive precursors to bactericidal forms by removal of covalently associated, inhibitory acidic amino acids from proximity with the Crp4 component of the molecule.

Amphipols stabilize the Chlamydia major outer membrane protein and enhance its protective ability as a vaccine.

The native major outer membrane protein (nMOMP) from Chlamydia was purified in its trimeric form using the zwitterionic detergent Z3-14. In aliquots from this preparation, Z3-14 was exchanged for amphipol (APol) A8-35. CD analysis showed that trapping with A8-35 improved the thermostability of nMOMP without affecting its secondary structure. Recombinant MOMP (rMOMP) was also formulated with Z3-14 or A8-35. Four groups of mice were vaccinated with nMOMP/Z3-14, nMOMP/A8-35, rMOMP/Z3-14 or rMOMP/A8-35 using CpG and Montanide as adjuvants. A positive control group was inoculated intranasally with live Chlamydia and a negative control group with culture medium. Mice were challenged intranasally with live Chlamydia and protection was assessed based on changes in body weight, the weight of the lungs and the number of chlamydial inclusion forming units recovered from the lungs 10 days after the challenge. Overall, vaccines formulated with nMOMP elicited better protection than those using rMOMP. Furthermore, the protection afforded by nMOMP/A8-35 was more robust than that achieved with nMOMP/Z3-14. In contrast, no differences in protection were observed between rMOMP/Z3-14 and rMOMP/A8-35 preparations. These findings suggest that the higher protection conferred by nMOMP/A8-35 complexes most likely results from a better preservation of the native structure of MOMP and/or from a more efficient presentation of the antigen to the immune system, rather than from an adjuvant effect of the amphipol. Thus, amphipols can be used in vaccine formulations to stabilize a membrane-protein component and enhance its immunogenicity.

THE NATIVE STATE OF APOMYOGLOBIN DESCRIBED BY PROTON NMR SPECTROSCOPY : THE A-B-G-H INTERFACE OF WILD-TYPE SPERM WHALE APOMYOGLOBIN

Proton nuclear magnetic resonance spectroscopy was applied to sperm whale apomyoglobin to describe the conformation adopted by the protein under native conditions. The study focused on the A‐B‐G‐H interface, a region known to form a compact subdomain in the apoprotein (Hughson and Baldwin, Biochemistry 28:4415–4422, 1989). Two histidine residues located in this subdomain, His24 and His119, interact and are thought to play a role in the acid denaturation process (Barrick et al., J. Mol. Biol. 237:588–601, 1994). A stable double mutant at these positions (His24Va1/His119Phe sperm whale apomyoglobin) was compared with wild‐type apomyoglobin. The amino acid replacements result in chemical shift perturbations near the mutations, in particular in the AB interhelical region, and in a deceleration of backbone amide hydrogen exchange in the B helix from position 27 to position 33. The double mutant data were used to expand and confirm the wild‐type spectral analysis. Signals from the D helix were identified that demonstrate the formation of holoprotein‐like structure. The assigned wild‐type nuclear Overhauser effects, although in small number, were sufficient to construct a model of the compact subdomain of the apoprotein. This was achieved by using the structure of the holoprotein and restraining it with the geometrical information on the apoprotein in a simulated annealing procedure. The experimental restraints define a low‐resolution model of the A‐B‐G‐H interface in apomyoglobin.