Proteins: Structure, Function, Bioinformatics

Wiley Online Library : Proteins: Structure, Function, and Bioinformatics
  • Crystal structure of a Baeyer–Villiger flavin-containing monooxygenase from Staphylococcus aureus MRSA strain MU50
    [Aug 2014]

    Abstract

    Flavin-containing Monooxygenase (FMO) catalyzed the oxygenation of broad spectrum of substrates. FMO can also serve as biocatalysts in the Baeyer–Villiger reaction in organic synthesis. Here, we report the high-resolution crystal structure of a Baeyer–Villiger Flavin-containing Monooxygenase (BVFMO) from methicillin- and vancomycin-resistant Staphylococcus aureus strain MU50. The structure of S. aureus FMO should facilitate further development of BVFMO as biocatalysts. A possible role of S. aureus FMO in methicillin and vancomycin resistance is discussed. Proteins 2014. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles
  • Influence of oligomerization state on the structural properties of invasion plasmid antigen B from Shigella flexneri in the presence and absence of phospholipid membranes
    [Aug 2014]

    ABSTRACT

    Shigella flexneri causes bacillary dysentery, an important cause of mortality among children in the developing world. Shigella secretes effector proteins via its type III secretion system (T3SS) to promote bacterial uptake into human colonic epithelial cells. The T3SS basal body spans the bacterial cell envelope anchoring a surface-exposed needle. A pentamer of invasion plasmid antigen D lies at the nascent needle tip and invasion plasmid antigen B (IpaB) is recruited into the needle tip complex on exposure to bile salts. From here, IpaB forms a translocon pore in the host cell membrane. Although the mechanism by which IpaB inserts into the membrane is unknown, it was recently shown that recombinant IpaB can exist as either a monomer or tetramer. Both of these forms of IpaB associate with membranes, however, only the tetramer forms pores in liposomes. To reveal differences between these membrane-binding events, Cys mutations were introduced throughout IpaB, allowing site-specific fluorescence labeling. Fluorescence quenching was used to determine the influence of oligomerization and/or membrane association on the accessibility of different IpaB regions to small solutes. The data show that the hydrophobic region of tetrameric IpaB is more accessible to solvent relative to the monomer. The hydrophobic region appears to promote membrane interaction for both forms of IpaB, however, more of the hydrophobic region is protected from solvent for the tetramer after membrane association. Limited proteolysis demonstrated that changes in IpaB's oligomeric state may determine the manner by which it associates with phospholipid membranes and the subsequent outcome of this association. Proteins 2014. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles
  • Structure-kinetic relationship of carbapenem antibacterials permeating through E. coli OmpC porin
    [Aug 2014]

    ABSTRACT

    The emergence of Gram-negative “superbugs” exhibiting resistance to known antibacterials poses a major public health concern. Low molecular weight Gram-negative antibacterials are believed to penetrate the outer bacterial membrane (OM) through porin channels. Therefore, intracellular exposure needed to drive antibacterial target occupancy should depend critically on the translocation rates through these proteins and avoidance of efflux pumps. We used electrophysiology to study the structure-translocation kinetics relationships of a set of carbapenem antibacterials through purified porin OmpC reconstituted in phospholipid bilayers. We also studied the relative susceptibility of OmpC+ and OmpC- E. coli to these compounds as an orthogonal test of translocation. Carbapenems exhibit good efficacy in OmpC-expressing E. coli cells compared with other known antibacterials. Ertapenem, which contains an additional acidic group compared to other analogs, exhibits the fastest entry into OmpC (kon ≈ 2 × 104 M−1 s−1). Zwitterionic compounds with highly polar groups attached to the penem-2 ring, including panipenem, imipenem and doripenem exhibit faster kon (>104 M−1 s−1), while meropenem and biapenem with fewer exposed polar groups exhibit slower kon (∼5 × 103 M−1 s−1). Tebipenem pivoxil and razupenem exhibit ∼13-fold slower kon (∼1.5 × 103 M−1 s−1) than ertapenem. Overall, our results suggest that (a) OmpC serves as an important route of entry of these antibacterials into E. coli cells; and (b) that the structure-kinetic relationships of carbapenem translocation are governed by H-bond acceptor/donor composition (in accordance with our previous findings that the enthalpic cost of transferring water from the constriction zone to bulk solvent increases in the presence of exposed nonpolar groups). Proteins 2014. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles
  • Rubredoxin refolding on nanostructured hydrophobic surfaces: Evidence for a new type of biomimetic chaperones
    [Aug 2014]

    Abstract

    Rubredoxins (Rds) are small proteins containing a tetrahedral Fe(SCys)4 site. Folded forms of metal free Rds (apoRds) show greatly impaired ability to incorporate iron compared to chaotropically unfolded apoRds. In this study, formation of the Rd holoprotein (holoRd) upon addition of iron to a structured, but iron-uptake incompetent apoRd was investigated in the presence of polystyrene nanoparticles (NP). In our rationale, hydrophobic contacts between apoRd and the NP surface would expose protein regions (including ligand cysteines) buried in the structured apoRd, allowing iron incorporation and folding to the native holoRd. Burial of the hydrophobic regions in the folded holoRd would allow its detachment from the NP surface. We found that both rate and yield of holoRd formation increased significantly in the presence of NP and were influenced by the NP concentration and size. Rates and yields had an optimum at “catalytic” NP concentrations (0.2 g/L NP) when using relatively small NP (46 nm diameter). At these optimal conditions, only a fraction of the apoRd was bound to the NP, consistent with the occurrence of turnover events on the NP surface. Lower rates and yields at higher NP concentrations or when using larger NP (200 nm) suggest that steric effects and molecular crowding on the NP surface favor specific “iron-uptake-competent” conformations of apoRd on the NP surface. This bio-mimetic chaperone system may be applicable to other proteins requiring an unfolding step prior to cofactor-triggered refolding, particularly when over-expressed under limited cofactor accessibility. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles
  • Unbinding and unfolding of adhesion protein complexes through stretching: Interplay between shear and tensile mechanical clamps
    [Aug 2014]

    Abstract

    Using coarse-grained molecular dynamics simulations, we analyze mechanically induced dissociation and unfolding of the protein complex CD48-2B4. This heterodimer is an indispensable component of the immunological system: 2B4 is a receptor on natural killer cells whereas CD48 is expressed on surfaces of various immune cells. So far, its mechanostability has not been assessed either experimentally or theoretically. We find that the dissociation processes strongly depend on the direction of pulling and may take place in several pathways. Interestingly, the CD48-2B4 interface can be divided into three distinct patches that act as units when resisting the pulling forces. At experimentally accessible pulling speeds, the characteristic mechanostability forces are in the range between 100 and 200˜pN, depending on the pulling direction. These characteristic forces need not be associated with tensile forces involved in the act of separation of the complex because prior shear-involving unraveling within individual proteins may give rise to a higher force peak. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles
  • Crystal structure of juvenile hormone epoxide hydrolase from the silkworm Bombyx mori
    [Aug 2014]

    Abstract

    The juvenile hormone (JH) epoxide hydrolase (JHEH) catalyzes the degradation of JH, which regulates the metamorphosis development of insects. Here we report the 2.30 Å crystal structure of JHEH from the silkworm Bombyx mori (BmJHEH). The overall structure of BmJHEH is composed of an N-terminal segment followed by a core hydrolase domain, which is interrupted by an all-α lid domain. Structural analyses together with molecular simulation reveal insights into the conservation and specificity of the active-site pocket. These findings increase our understanding of the substrate recognition and catalysis of microsomal epoxide hydrolase family and might help the design of JH-derived pesticides. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles
  • Finding off-targets, biological pathways & target diseases for chymase inhibitors via structure-based systems biology approach
    [Aug 2014]

    Abstract

    Off-target binding connotes the binding of a small molecule of therapeutic significance to a protein target in addition to the primary target for which it was proposed. Progressively such off-targeting is emerging to be regular practice to reveal side effects. Chymase is an enzyme of hydrolase class that catalyzes hydrolysis of peptide bonds. A link between heart failure and chymase is ascribed, and a chymase inhibitor is in clinical phase II for treatment of heart failure. However, the underlying mechanisms of the off-target effects of human chymase inhibitors are still unclear. Here, we develop a robust computational strategy that is applicable to any enzyme system and that allows the prediction of drug effects on biological processes. Putative off-targets for chymase inhibitors were identified through various structural and functional similarity analyses along with molecular docking studies. Finally, literature survey was performed to incorporate these off-targets into biological pathways and to establish links between pathways and particular adverse effects. Off-targets of chymase inhibitors are linked to various biological pathways such as classical and lectin pathways of complement system, intrinsic and extrinsic pathways of coagulation cascade, and fibrinolytic system. Tissue kallikreins, granzyme M, neutrophil elastase, and mesotrypsin are also identified as off-targets. These off-targets and their associated pathways are elucidated for the effects of inflammation, cancer, hemorrhage, thrombosis and central nervous system diseases (Alzheimer’s disease). Prospectively, our approach is helpful not only to better understand the mechanisms of chymase inhibitors but also for drug repurposing exercises to find novel uses for these inhibitors. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles
  • Effective discrimination between biologically relevant contacts and crystal packing contacts using new determinants
    [Aug 2014]

    Abstract

    In the structural models determined by X-ray crystallography, contacts between molecules can be divided into two categories: biologically relevant contacts and crystal packing contacts. With the growth in the number and quality of available large crystal packing contacts structures, distinguishing crystal packing contacts from biologically relevant contacts remains a difficult task, which can lead to wrong interpretation of structural models. In this study, we performed a systematic analysis on the biologically relevant contacts and crystal packing contacts. The analysis results reveal that biologically contacts are more tightly packed than crystal packing contacts. This property of biologically contacts may contribute to the formation of their interfacial core region. Meanwhile, the differences between the core and surface region of biologically contacts in amino acid composition and evolutionary measure are more dramatic than crystal packing contacts and these differences appear to be useful in distinguishing these two categories of contacts. Based on the features derived from our analysis, we developed a random forest model to classify biological relevant contacts and crystal packing contacts. Our method can achieve a high receiver operating curve of 0.923 in the 5-fold cross validation and accuracies of 91.4% and 91.7% for two different test sets. Moreover, in a comparison study, our model outperforms other existing methods, such as DiMoVo, Pita, Pisa and Eppic. We believe that this study will provide useful help in the validation of oligomeric proteins and protein complexes. The model and all data used in this paper are freely available at http://cic.scu.edu.cn/bioinformatics/bio-cry.zip. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles
  • Characterization of the near native conformational states of the SAM domain of Ste11 protein by NMR spectroscopy
    [Aug 2014]

    ABSTRACT

    The sterile alpha motif or SAM domain is one of the most frequently present protein interaction modules with diverse functional attributions. SAM domain of the Ste11 protein of budding yeast plays important roles in mitogen-activated protein kinase cascades. In the current study, urea-induced, at subdenaturing concentrations, structural, and dynamical changes in the Ste11 SAM domain have been investigated by nuclear magnetic resonance spectroscopy. Our study revealed that a number of residues from Helix 1 and Helix 5 of the Ste11 SAM domain display plausible alternate conformational states and largest chemical shift perturbations at low urea concentrations. Amide proton (H/D) exchange experiments indicated that Helix 1, loop, and Helix 5 become more susceptible to solvent exchange with increased concentrations of urea. Notably, Helix 1 and Helix 5 are directly involved in binding interactions of the Ste11 SAM domain. Our data further demonstrate that the existence of alternate conformational states around the regions involved in dimeric interactions in native or near native conditions. Proteins 2014. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles
  • Multivariate sequence analysis reveals additional function impacting residues in the SDR superfamily
    [Aug 2014]

    ABSTRACT

    The “extended” type of short chain dehydrogenases/reductases (SDR), share a remarkable similarity in their tertiary structures inspite of being highly divergent in their functions and sequences. We have carried out principal component analysis (PCA) on structurally equivalent residue positions of 10 SDR families using information theoretic measures like Jensen–Shannon divergence and average shannon entropy as variables. The results classify residue positions in the SDR fold into six groups, one of which is characterized by low Shannon entropies but high Jensen–Shannon divergence against the reference family SDR1E, suggesting that these positions are responsible for the specific functional identities of individual SDR families, distinguishing them from the reference family SDR1E. Site directed mutagenesis of three residues from this group in the enzyme UDP-Galactose 4-epimerase belonging to SDR1E shows that the mutants promote the formation of NADH containing abortive complexes. Finally, molecular dynamics simulations have been used to suggest a mechanism by which the mutants interfere with the re-oxidation of NADH leading to the formation of abortive complexes. Proteins 2014. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles
  • Structure-based investigation into the functional roles of the extended loop and substrate-recognition sites in an endo-β-1,4-d-mannanase from the Antarctic springtail, Cryptopygus antarcticus
    [Aug 2014]

    ABSTRACT

    Endo-β-1,4-d-mannanase from the Antarctic springtail, Cryptopygus antarcticus (CaMan), is a cold-adapted β-mannanase that has the lowest optimum temperature (30°C) of all known β-mannanases. Here, we report the apo- and mannopentaose (M5) complex structures of CaMan. Structural comparison of CaMan with other β-mannanases from the multicellular animals reveals that CaMan has an extended loop that alters topography of the active site. Structural and mutational analyses suggest that this extended loop is linked to the cold-adapted enzymatic activity. From the CaMan-M5 complex structure, we defined the mannose-recognition subsites and observed unreported M5 binding site on the surface of CaMan. Proteins 2014. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles
  • pH Dependence of Conformational Fluctuations of the Protein Backbone
    [Aug 2014]

    Abstract

    Proton binding equilibria (pKa values) of ionizable groups in proteins are exquisitely sensitive to their microenvironments. Apparent pKa values measured for individual ionizable residues with NMR spectroscopy are actually population-weighted averages of the pKa in different conformational microstates. NMR spectroscopy experiments with staphylococcal nuclease were used to test the hypothesis that pKa values of surface Glu and Asp residues are affected by pH-sensitive fluctuations of the backbone between folded and locally unfolded conformations. 15N spin relaxation studies showed that as the pH decreases from the neutral into the acidic range the amplitudes of backbone fluctuations in the ps-ns timescale increase near carboxylic residues. Hydrogen exchange experiments suggested that backbone conformational fluctuations promoted by decreasing pH also reflect slower local or sub-global unfolding near carboxylic groups. This study has implications for structure-based pKa calculations: (1) The timescale of the backbone's response to ionization events in proteins can range from ps to ms, and even longer; (2) pH-sensitive fluctuations of the backbone can be localized to both the segment the ionizable residue is attached to or the one that occludes the ionizable group; (3) Structural perturbations are not necessarily propagated through Coulomb interactions; instead, local fluctuations appear to be coupled through the cooperativity inherent to elements of secondary structure and to networks of hydrogen bonds. These results are consistent with the idea that local conformational fluctuations and stabilities are important determinants of apparent pKa values of ionizable residues in proteins. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles
  • Dual effects of familial Alzheimer’s disease mutations (D7H, D7N, and H6R) on amyloid β peptide: Correlation dynamics and zinc binding
    [Aug 2014]

    ABSTRACT

    Short Title: Effects of C-terminal mutations of amyloid β peptide

    Although the N-terminal region of Amyloid β (Aβ) peptides plays dual roles as metal-coordinating sites and conformational modulator, few studies have been performed to explore the effects of mutations at this region on the overall conformational ensemble of Aβ and the binding propensity of metal ions. In this work, we focus on how three familial Alzheimer disease mutations (D7H, D7N, and H6R) alter the structural characteristics and thermodynamic stabilities of Aβ42 using molecular dynamics simulations. We observe that each mutation displays increased β-sheet structures in both N and C termini. In particular, both the N terminus and central hydrophobic region of D7H can form stable β-hairpin structures with its C terminus. The conserved turn structure at Val24–Lys28 in all peptides and Zn2+-bound Aβ42 is confirmed as the common structural motif to nucleate folding of Aβ. Each mutant can significantly increase the solvation free energy and thus enhance the aggregation of Aβ monomers. The correlation dynamics between Aβ(1–16) and Aβ(17–42) fragments are elucidated by linking the domain motions with the corresponding structured conformations. We characterize the different populations of correlated domain motions for each mutant from a more macroscopic perspective, and unexpectedly find that Zn2+-bound Aβ42 ensemble shares the same populations as Aβ42, indicating the binding of Zn2+ to Aβ follows the conformational selection mechanism, and thus is independent of domain motions, even though the structures of Aβ have been modified at a residue level. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles
  • Structural and mutational analysis of a monomeric and dimeric form of a single domain antibody with implications for protein misfolding
    [Aug 2014]

    ABSTRACT

    Camelid single domain antibodies (sdAb) are known for their thermal stability and reversible refolding. We have characterized an unusually stable sdAb recognizing Staphylococcal enterotoxin B with one of the highest reported melting temperatures (Tm = 85 °C). Unexpectedly, ~10-20% of the protein formed a dimer in solution. Three other cases where <20% of the sdAb dimerized have been reported; however, this is the first report of both the monomeric and dimeric X-ray crystal structures. Concentration of the monomer did not lead to the formation of new dimer suggesting a stable conformationally distinct species in a fraction of the cytoplasmically expressed protein. Comparison of periplasmic and cytoplasmic expression showed that the dimer was associated with cytoplasmic expression. The disulfide bond was partially reduced in the WT protein purified from the cytoplasm and the protein irreversibly unfolded. Periplasmic expression produced monomeric protein with a fully formed disulfide bond and mostly reversible refolding. Crystallization of a disulfide-bond free variant, C22A/C99A, purified from the periplasm yielded a structure of a monomeric form, while crystallization of C22A/C99A from the cytoplasm produced an asymmetric dimer. In the dimer, a significant conformational asymmetry was found in the loop residues of the edge β-strands (S50-Y60) containing the highly variable complementarity determining region, CDR2. Two dimeric assemblies were predicted from the crystal packing. Mutation of a residue at one of the interfaces, Y98A, disrupted the dimer in solution. The pleomorphic homodimer may yield insight into the stability of misfolded states and the importance of the conserved disulfide bond in preventing their formation. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles
  • Characterizing of functional human coding RNA editing from evolutionary, structural and dynamic perspectives
    [Aug 2014]

    Abstract

    A-to-I RNA editing has been recently shown to be a widespread phenomenon with millions of sites spread in the human transcriptome. However, only few are known to be located in coding sequences and modify the amino acid sequence of the protein product. Here, we used high-throughput data, variant prediction tools and protein structural information in order to find structural and functional preferences for coding RNA editing. We show that RNA editing has a unique pattern of amino-acid changes characterized by enriched stop-to-tryptophan changes, positive-to-neutral and neutral-to-positive charge changes. RNA editing tends to have stronger structural effect than equivalent A-to-G SNPs but weaker effect than random A-to-G mutagenesis events. Sites edited at low level tend to be located at conserved positions with stronger predicted deleterious effect on proteins comparing to sites edited at high frequencies. Lowly edited sites tend to destabilize the protein structure and affect amino acids with larger number of intra-molecular contacts. Still, some highly edited sites are predicted also to prominently affect structure and tend to be located at critical positions of the protein matrix and are likely to be functionally important. Using our pipeline, we identify and discuss several novel putative functional coding changing editing sites in the genes COPA (I164V), GIPC1 (T62A), ZN358 (K382R) and CCNI (R75G). © Proteins 2014;. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles
  • Solution and crystal structure of BA42, a protein from the Antarctic bacterium Bizionia argentinensis comprised of a stand-alone TPM domain
    [Aug 2014]

    Abstract

    The structure of the BA42 protein belonging to the Antarctic flavobacterium Bizionia argentinensis was determined by Nuclear Magnetic Resonance and X-ray crystallography. This is the first structure of a member of the PF04536 family comprised of a stand-alone TPM domain. The structure reveals a new topological variant of the four β-strands constituting the central β-sheet of the αβα architecture and a double metal binding site stabilizing a pair of crossing loops, not observed in previous structures of proteins belonging to this family. BA42 shows differences in structure and dynamics in the presence or absence of bound metals. The affinity for divalent metal ions is close to that observed in proteins that modulate their activity as a function of metal concentration, anticipating a possible role for BA42. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles
  • Binding mode analysis of a major T3SS translocator protein PopB with its chaperone PcrH from Pseudomonas aeruginosa
    [Aug 2014]

    Abstract

    Pseudomonas aeruginosa, a gram-negative pathogen utilizes a specialized set of T3SS translocator proteins to establish virulence in the host cell. An understanding of the factors that govern translocation by the translocator protein-chaperone complex is thus, of immense importance. In the present work, experimental and computational techniques were employed to probe into the structure of the major translocator protein PopB from P. aeruginosa and to identify the important regions involved in functioning of the translocator protein. This study reveals that the binding sites of the common chaperone PcrH, needed for maintenance of the translocator PopB within the bacterial cytoplasm, which are primarily localized within the N-terminal domain. However, disordered and flexible residues located both at the N- and C-terminal domains are also observed to be involved in association with the chaperone. This intrinsic disorderliness of the terminal domains is conserved for all the major T3SS translocator proteins and is functionally important to maintain the intrinsically disordered state of the translocators. Our experimental and computational analyses suggest that a ‘disorder-to-order’ transition of PopB protein might take place upon PcrH binding. The long helical coiled-coil part of PopB protein perhaps helps in pore formation while the flexible apical region is involved in chaperone interaction. Thus, our computational model of translocator protein PopB and its binding analyses provide crucial functional insights into the T3SS translocation mechanism. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles
  • Terminal sialic acids on CD44 N-glycans can block hyaluronan binding by forming competing intramolecular contacts with arginine sidechains
    [Aug 2014]

    Abstract

    Specific sugar residues and their linkages form the basis of molecular recognition for interactions of glycoproteins with other biomolecules. Seemingly small changes, like the addition of a single monosaccharide in the covalently attached glycan component of glycoproteins, can greatly affect these interactions. For instance, the sialic acid capping of glycans affects protein-ligand binding involved in cell-cell and cell-matrix interactions. CD44 is a single-pass transmembrane glycoprotein whose binding with its carbohydrate ligand hyaluronan (HA), an extracellular matrix component, mediates processes such as leukocyte homing, cell adhesion, and tumor metastasis. This binding is highly regulated by glycosylation of the N-terminal extracellular hyaluronan-binding domain (HABD); specifically, sialic acid capped N-glycans of HABD inhibit ligand binding. However, the molecular mechanism behind this sialic acid mediated regulation has remained unknown. Two of the five N-glycosyation sites of HABD have been previously identified as having the greatest inhibitory effect on HA binding, but only if the glycans contain terminal sialic acid residues. These two sites, Asn25 and Asn120, were chosen for in silico glycosylation in this study. Here, from extensive standard molecular dynamics simulations and biased simulations, we propose a molecular mechanism for this behavior based on spontaneously-formed charge-paired hydrogen bonding interactions between the negatively-charged sialic acid residues and positively-charged Arg sidechains known to be critically important for binding to HA, which itself is negatively charged. Such intramolecular hydrogen bonds would preclude associations critical to hyaluronan binding. This observation suggests how CD44 and related glycoprotein binding is regulated by sialylation as cellular environments fluctuate. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles
  • Helix stability of oligoglycine, oligoalanine and oligo-β-alanine dodecamers reflected by hydrogen-bond persistence
    [Aug 2014]

    Abstract

    Helices are important structural/recognition elements in proteins and peptides. Stability and conformational differences between helices composed of α- and β-amino acids as scaffolds for mimicry of helix recognition has become a theme in medicinal chemistry. Furthermore, helices formed by β-amino acids are experimentally more stable than those formed by α-amino acids. This is paradoxical because the larger sizes of the hydrogen-bonding rings required by the extra methylene groups should lead to entropic destabilization. In this study, molecular dynamics simulations using the second-generation force field, AMOEBA [1], explored the stability and hydrogen-bonding patterns of capped oligo-β-alanine, oligoalanine and oligoglycine dodecamers in water. The MD simulations showed that oligo-β-alanine has strong acceptor+2 hydrogen bonds, but surprisingly did not contain a large content of 312-helical structures, possibly due to the sparse distribution of the 312-helical structure and other structures with acceptor+2 hydrogen bonds. On the other hand, despite its backbone flexibility, the β-alanine dodecamer had more stable and persistent <3.0 Å hydrogen bonds. Its structure was dominated more by multicentered hydrogen bonds than either oligoglycine and oligoalanine helices. The 31 (PII) helical structure, prevalent in oligoglycine and oligoalanine, does not appear to be stable in oligo-β-alanine indicating its competition with other structures (stacking structure as indicated by MD analyses). These differences are among the factors that shape helical structural preferences and the relative stabilities of these three oligopeptides. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles
  • Solution and high-pressure NMR studies of the structure, dynamics and stability of the cross-reactive allergenic cod parvalbumin Gad m 1
    [Aug 2014]

    Abstract

    Beta-parvalbumins from different fish species have been identified as the main elicitors of IgE-mediated reactions in fish-allergic individuals. Here, we report for the first time the NMR determination of the structure and dynamics of the major Atlantic cod (Gadus morhua) allergen Gad m 1 and compare them with other known parvalbumins. Although the Gad m 1 structure and accessibility of putative IgE epitopes are similar to parvalbumins in mackerel and carp, the charge distribution at the putative epitopes is different. The determination of the Gad m 1 structure contributes to a better understanding of cross-reactivity among fish parvalbumins. In addition, the high-pressure NMR and temperature variation experiments revealed the important contribution of the AB motif and other regions to the protein folding. This structural information could assist the future identification of hot spots for targeted mutations to develop hypoallergenic Ca2+-free forms for potential use in immunotherapy. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.

    Categories: Journal Articles