Recognition of β-hairpin motifs in proteins by using the composite vector

A composite vector method for predicting β-hairpin motifs in proteins is proposed by combining the score of matrix, increment of diversity, the value of distance and auto-correlation information to express the information of sequence. The prediction is based on analysis of data from 3,088 non-homologous protein chains including 6,035 β-hairpin motifs and 2,738 non-β-hairpin motifs. The overall accuracy of prediction and Matthew’s correlation coefficient are 83.1% and 0.59, respectively. In addition, by using the same methods, the accuracy of 80.7% and Matthew’s correlation coefficient of 0.61 are obtained for other dataset with 2,878 non-homologous protein chains, which contains 4,884 β-hairpin motifs and 4,310 non-β-hairpin motifs. Better results are also obtained in the prediction of the β-hairpin motifs of proteins by analysis of the CASP6 dataset.     

A Short Polybasic Segment between the Two Conserved Domains of the β2a-Subunit Modulates the Rate of Inactivation of R-type Calcium Channel

Besides opening and closing, high voltage-activated calcium channels transit to a nonconducting inactivated state from which they do not re-open unless the plasma membrane is repolarized. Inactivation is critical for temporal regulation of intracellular calcium signaling and prevention of a deleterious rise in calcium concentration. R-type high voltage-activated channels inactivate fully in a few hundred milliseconds when expressed alone. However, when co-expressed with a particular β-subunit isoform, β_2a, inactivation is partial and develops in several seconds. Palmitoylation of a unique di-cysteine motif at the N terminus anchors β_2a to the plasma membrane. The current view is that membrane-anchored β_2a immobilizes the channel inactivation machinery and confers slow inactivation phenotype. β-Subunits contain one Src homology 3 and one guanylate kinase domain, flanked by variable regions with unknown structures. Here, we identified a short polybasic segment at the boundary of the guanylate kinase domain that slows down channel inactivation without relocating a palmitoylation-deficient β_2a to the plasma membrane. Substitution of the positively charged residues within this segment by alanine abolishes its slow inactivation-conferring phenotype. The linker upstream from the polybasic segment, but not the N- and C-terminal variable regions, masks the effect of this determinant. These results reveal a novel mechanism for inhibiting voltage-dependent inactivation of R-type calcium channels by the β_2a-subunit that might involve electrostatic interactions with an unknown target on the channel''s inactivation machinery or its modulatory components. They also suggest that intralinker interactions occlude the action of the polybasic segment and that its functional availability is regulated by the palmitoylated state of the β_2a-subunit.     

A Study of the Influence of Charged Residues on β-Hairpin Formation by Nuclear Magnetic Resonance and Molecular Dynamics

Chain reversals are often nucleation sites in protein folding. The β-hairpins of FBP28 WW domain and IgG are stable and have been proved to initiate the folding and are, therefore, suitable for studying the influence of charged residues on β-hairpin conformation. In this paper, we carried out NMR examination of the conformations in solution of two fragments from the FPB28 protein (PDB code: 1E0L) (N-terminal part) namely KTADGKT-NH₂ (1E0L 12–18, D7) and YKTADGKTY-NH₂ (1E0L 11–19, D9), one from the B3 domain of the protein G (PDB code: 1IGD), namely DDATKT-NH₂ (1IGD 51–56) (Dag1), and three variants of Dag1 peptide: DVATKT-NH₂ (Dag2), OVATKT-NH₂ (Dag3) and KVATKT-NH₂ (Dag4), respectively, in which the original charged residue were replaced with non-polar residues or modified charged residues. It was found that both the D7 and D9 peptides form a large fraction bent conformations. However, no hydrophobic contacts between the terminal Tyr residues of D9 occur, which suggests that the presence of a pair of like-charged residues stabilizes chain reversal. Conversely, only the Dag1 and Dag2 peptides exhibit some chain reversal; replacing the second aspartic-acid residue with a valine and the first one with a basic residue results in a nearly extended conformation. These results suggest that basic residues farther away in sequence can result in stabilization of chain reversal owing to screening of the non-polar core. Conversely, smaller distance in sequence prohibits this screening, while the presence oppositely-charged residues can stabilize a turn because of salt-bridge formation.     

Recognition of β-calcineurin by the domains of calmodulin: thermodynamic and structural evidence for distinct roles

Calcineurin (CaN, PP2B, PPP3), a heterodimeric Ca²⁺‐calmodulin‐dependent Ser/Thr phosphatase, regulates swimming in Paramecia, stress responses in yeast, and T‐cell activation and cardiac hypertrophy in humans. Calcium binding to CaN_B (the regulatory subunit) triggers conformational change in CaN_A (the catalytic subunit). Two isoforms of CaN_A (α, β) are both abundant in brain and heart and activated by calcium‐saturated calmodulin (CaM). The individual contribution of each domain of CaM to regulation of calcineurin is not known. Hydrodynamic analyses of (Ca²⁺)₄‐CaM_1–148 bound to βCaNp, a peptide representing its CaM‐binding domain, indicated a 1:1 stoichiometry. βCaNp binding to CaM increased the affinity of calcium for the N‐ and C‐domains equally, thus preserving intrinsic domain differences, and the preference of calcium for sites III and IV. The equilibrium constants for individual calcium‐saturated CaM domains dissociating from βCaNp were ～1 μM. A limiting K_d ≤ 1 nM was measured directly for full‐length CaM, while thermodynamic linkage analysis indicated that it was approximately 1 pM. βCaNp binding to ¹⁵N‐(Ca²⁺)₄‐CaM_1–148 monitored by ¹⁵N/¹HN HSQC NMR showed that association perturbed the N‐domain of CaM more than its C‐domain. NMR resonance assignments of CaM and βCaNp, and interpretation of intermolecular NOEs observed in the ¹³C‐edited and ¹²C‐¹⁴N‐filtered 3D NOESY spectrum indicated anti‐parallel binding. The sole aromatic residue (Phe) located near the βCaNp C‐terminus was in close contact with several residues of the N‐domain of CaM outside the hydrophobic cleft. These structural and thermodynamic properties would permit the domains of CaM to have distinct physiological roles in regulating activation of βCaN. Proteins 2011. © 2010 Wiley‐Liss, Inc.     

Beyond the Binding Site: The Role of the β2 – β3 Loop and Extra-Domain Structures in PDZ Domains

A general paradigm to understand protein function is to look at properties of isolated well conserved domains, such as SH3 or PDZ domains. While common features of domain families are well understood, the role of subtle differences among members of these families is less clear. Here, molecular dynamics simulations indicate that the binding mechanism in PSD95-PDZ3 is critically regulated via interactions outside the canonical binding site, involving both the poorly conserved loop and an extra-domain helix. Using the CRIPT peptide as a prototypical ligand, our simulations suggest that a network of salt-bridges between the ligand and this loop is necessary for binding. These contacts interconvert between each other on a time scale of a few tens of nanoseconds, making them elusive to X-ray crystallography. The loop is stabilized by an extra-domain helix. The latter influences the global dynamics of the domain, considerably increasing binding affinity. We found that two key contacts between the helix and the domain, one involving the loop, provide an atomistic interpretation of the increased affinity. Our analysis indicates that both extra-domain segments and loosely conserved regions play critical roles in PDZ binding affinity and specificity.     

Keeping Them All Together: β-Propeller Domains in Histone Methyltransferase Complexes

Histone methyltransferases (HKMTs) residing in multi-subunit protein complexes frequently require the presence of β-propeller proteins to achieve their biological functions. Recent biochemical studies have highlighted the functional diversity of these scaffolding proteins in maintaining the integrity of the complexes, allosterically regulating HKMT enzymatic activity and acting as “histone tethering devices” to facilitate the interaction between HKMTs and their substrates. Structural studies have revealed that, while β-propeller domain proteins share structural similarity, they employ divergent mechanisms to achieve their functions. This review focuses on the progress made in the last decade to identify the biochemical determinants underlying the functions of these important proteins.     

A Retroviral Chimeric Capsid Protein Reveals the Role of the N-Terminal β-Hairpin in Mature Core Assembly

The human immunodeficiency virus (HIV) is an enveloped virus constituted by two monomeric RNA molecules that encode for 15 proteins. Among these are the structural proteins that are translated as the gag polyprotein. In order to become infectious, HIV must undergo a maturation process mediated by the proteolytic cleavage of gag to give rise to the isolated structural protein matrix, capsid (CA), nucleocapsid as well as p6 and spacer peptides 1 and 2. Upon maturation, the 13 N-terminal residues from CA fold into a β-hairpin, which is stabilized mainly by a salt bridge between Pro1 and Asp51. Previous reports have shown that non-formation of the salt bridge, which potentially disrupts proper β-hairpin arrangement, generates noninfectious virus or aberrant cores. To date, however, there is no consensus on the role of the β-hairpin. In order to shed light in this subject, we have generated mutations in the hairpin region to examine what features would be crucial for the β-hairpin's role in retroviral mature core formation. These features include the importance of the proline at the N-terminus, the amino acid sequence, and the physical structure of the β-hairpin itself. The presented experiments provide biochemical evidence that β-hairpin formation plays an important role in regard to CA protein conformation required to support proper mature core arrangement. Hydrogen/deuterium exchange and in vitro assembly reactions illustrated the importance of the β-hairpin structure, its dynamics, and its influence on the orientation of helix 1 for the assembly of the mature CA lattice.     

Inclusion of Many-Body Effects in the Additive CHARMM Protein CMAP Potential Results in Enhanced Cooperativity of α-Helix and β-Hairpin Formation

Folding simulations on peptides and proteins using empirical force fields have demonstrated the sensitivity of the results to details of the backbone potential. A recently revised version of the additive CHARMM protein force field, which includes optimization of the backbone CMAP potential to achieve good balance between different types of secondary structure, correcting the α-helical bias present in the former CHARMM22/CMAP energy function, is shown to result in improved cooperativity for the helix-coil transition. This is due to retention of the empirical corrections introduced in the original CMAP to reproduce folded protein structures—corrections that capture many-body effects missing from an energy surface fitted to gas phase calculations on dipeptides. The experimental temperature dependence of helix formation in (AAQAA)₃ and parameters for helix nucleation and elongation are in much better agreement with experiment than those obtained with other recent force fields. In contrast, CMAP parameters derived by fitting to a vacuum quantum mechanical surface for the alanine dipeptide do not reproduce the enhanced cooperativity, showing that the empirical backbone corrections, and not some other feature of the force field, are responsible. We also find that the cooperativity of β-hairpin formation is much improved relative to other force fields we have studied. Comparison with (ϕ,ψ) distributions from the Protein Data Bank further justifies the inclusion of many-body effects in the CMAP. These results suggest that the revised energy function will be suitable for both simulations of unfolded or intrinsically disordered proteins and for investigating protein-folding mechanisms.     

An Inducible System for the Hydrolysis and Transport of β-Glucosides in Yeast : I. Characteristics of the β-glucosidase activity of intact and of lysed cells

A strain of bakers'' yeast was isolated which could utilize cellobiose and other β-D-glucosides quantitatively as carbon and energy sources for growth. Cellobiose-grown cells contained a largely cryptic enzyme active against the chromogenic substrate p-nitrophenyl-β-D-glucoside. The patent (intact cell) activity of such cells was inhibited by azide and, competitively, by cellobiose; neither agent inhibited the β-glucosidase activity of lysed cells or of extracts. The enzyme induced by growth in cellobiose medium had no affinity for cellobiose as either substrate or inhibitor; its substrate specificity classifies it as an aryl-β-glucosidase. It was concluded that growth in cellobiose also induced the formation of a stereospecific and energy-dependent system whose function determined the rate at which intact cells could hydrolyze substrates of the intracellular β-glucosidase.     

Separate Domains for Desensitization of GABA ρ1 and β2 Subunits Expressed in Xenopus Oocytes

Desensitization of ligand-gated receptor channels is an intrinsic feedback mechanism and prevents the receptor/channels from becoming overly activated thereby maintaining biological function of the nervous system. Desensitization also plays an important role in neuronal plasticity. By taking advantage of biophysical and pharmacological diversities of GABA β₂ subunits from the brain and ρ₁ subunits from the retina, structural determinants that confer agonist-induced desensitization were identified. A synthetic chimeric receptor/channel was created from the β₂ and ρ₁ subunits for this investigation. The chimera was constructed from the extracellular N-domain of the β₂ subunit, extending from the amino terminus to the beginning region of the M1 transmembrane segment, and from the C-domain of the ρ₁ subunit extending from the M1 transmembrane segment to the carboxyl terminus. The C-domain region included the M1 to M4 transmembrane regions and the large intracellular loop between the M3 and M4 transmembrane segments. Homo-oligomeric GABA β₂, ρ₁, and β₂/ρ₁ chimeric receptor/channels were individually expressed in Xenopus oocytes, and the desensitization characteristics attributable to each type of subunit were compared. Results from the present study reveal that motifs in the amino-terminal and carboxyl-terminal domains of the β₂ subunit conferred the agonist-induced desensitization; chloroform modulation was linked to specific phases of the GABA-activated current decay. Received: 2 April 1997/Revised: 27 March 1998     

Regulation of contractility and metabolic signaling by the β2-adrenergic receptor in rat ventricular muscle

AimsCardiac function is modulated by the sympathetic nervous system through β-adrenergic receptor (β-AR) activity and this represents the main regulatory mechanism for cardiac performance. To date, however, the metabolic and molecular responses to β₂-agonists are not well characterized. Therefore, we studied the inotropic effect and signaling response to selective β₂-AR activation by tulobuterol.Main methodsStrips of rat right ventricle were electrically stimulated (1 Hz) in standard Tyrode solution (95% O₂, 5% CO₂) in the presence of the β₁-antagonist CGP-20712A (1 μM). A cumulative dose–response curve for tulobuterol (0.1–10 μM), in the presence or absence of the phosphodiesterase (PDE) inhibitor IBMX (30 μM), or 10 min incubation (1 μM) with the β₂-agonist tulobuterol was performed.Key findingsβ₂-AR stimulation induced a positive inotropic effect (maximal effect = 33 ± 3.3%) and a decrease in the time required for half relaxation (from 45 ± 0.6 to 31 ± 1.8 ms, ? 30%, p < 0.001) after the inhibition of PDEs. After 10 min of β₂-AR stimulation, p-AMPKα^T172 (54%), p-PKB^T308 (38%), p-AS160^T642 (46%) and p-CREB^S133 (63%) increased, without any change in p-PKA^T197.SignificanceThese results suggest that the regulation of ventricular contractility is not the primary function of the β₂-AR. Rather, β₂-AR could function to activate PKB and AMPK signaling, thereby modulating muscle mass and energetic metabolism of rat ventricular muscle.     

Recognition of the Helical Structure of β-1,4-Galactan by a New Family of Carbohydrate-binding Modules

The microbial enzymes that depolymerize plant cell wall polysaccharides, ultimately promoting energy liberation and carbon recycling, are typically complex in their modularity and often contain carbohydrate-binding modules (CBMs). Here, through analysis of an unknown module from a Thermotoga maritima endo-β-1,4-galactanase, we identify a new family of CBMs that are most frequently found appended to proteins with β-1,4-galactanase activity. Polysaccharide microarray screening, immunofluorescence microscopy, and biochemical analysis of the isolated module demonstrate the specificity of the module, here called TmCBM61, for β-1,4-linked galactose-containing ligands, making it the founding member of family CBM61. The ultra-high resolution x-ray crystal structures of TmCBM61 (0.95 and 1.4 Å resolution) in complex with β-1,4-galactotriose reveal the molecular basis of the specificity of the CBM for β-1,4-galactan. Analysis of these structures provides insight into the recognition of an unexpected helical galactan conformation through a mode of binding that resembles the recognition of starch.     

Enhanced production of thermostable β-amylase and pullulanase in the presence of surfactants by Clostridium thermosulfurogenes SV2

The addition of the surfactants Triton X-100, CHAPS, Tween-80 and sodium taurocholate to Clostridium thermosulfurogenes SV2 culture individually resulted in a marked increase in the yields of thermostable β-amylase and pullulanase. The stimulation of enzymes production was greater when the surfactants were added after 18 h of incubation of the culture. Upon treatment with 1.0 mM Triton X-100, 0.1 mM CHAPS, 0.1 mM Tween-80 and 0.1 mM sodium taurocholate, C. thermosulfurogenes SV2 produced 140, 34, 88 and 28% more β-amylase and 114, 146, 47 and 28% more pullulanase than the control (lacking surfactants), respectively. Besides stimulation, the surfactants caused an increased secretion of the enzymes into the extracellular fluid. These surfactants also further enhanced the stability of the enzymes. All the surfactants tested were found to have a little inhibitory effect on the growth of the bacterium.     

Recognition of peptidoglycan and β-lactam antibiotics by the extracellular domain of the Ser/Thr protein kinase StkP from Streptococcus pneumoniae

The eukaryotic-type serine/threonine kinase StkP from Streptococcus pneumoniae is an important signal-transduction element that regulates the expression of numerous pneumococcal genes. We have expressed the extracellular C-terminal domain of StkP kinase (C-StkP), elaborated a three-dimensional structural model and performed a spectroscopical characterization of its structure and stability. Biophysical experiments show that C-StkP binds to synthetic samples of the cell wall peptidoglycan (PGN) and to β-lactam antibiotics, which mimic the terminal portions of the PGN stem peptide. This is the first experimental report on the recognition of a minimal PGN unit by a PASTA-containing kinase, suggesting that non-crosslinked PGN may act as a signal for StkP function and pointing to this protein as an interesting target for β-lactam antibiotics.     

Regulation of the β-ketoadipate pathway in Rhizobium japonicum and bacteroids by succinate

Rhizobium japonicum 61-A-101 and its bacteroids catabolize phenol and p-hydroxybenzoate. With phenol as a carbon source, utilization started only after a prolonged lag phase while p-hydroxybenzoate was almost instantancously metabolized. Succinate, which supports rapid growth of Rhizobium japonicum, completely repressed respication of phenol; the oxidation of p-hydroxybenzoate was partially inhibited. Pyruvate, supporting slower growth than succinate, retarded the onset of phenol consumption but did not affect its maximum rate.Catabolite repression of phenol utilization by succinate appears to be a characteristic feature of rhizobia. In Pseudomonas putida which also actively metabolizes phenol, succinate had no effect on phenol utilization.     

Plasticity of the ��-Trefoil Protein Fold in the Recognition and Control of Invertebrate Predators and Parasites by a Fungal Defence System

Discrimination between self and non-self is a prerequisite for any defence mechanism; in innate defence, this discrimination is often mediated by lectins recognizing non-self carbohydrate structures and so relies on an arsenal of host lectins with different specificities towards target organism carbohydrate structures. Recently, cytoplasmic lectins isolated from fungal fruiting bodies have been shown to play a role in the defence of multicellular fungi against predators and parasites. Here, we present a novel fruiting body lectin, CCL2, from the ink cap mushroom Coprinopsis cinerea. We demonstrate the toxicity of the lectin towards Caenorhabditis elegans and Drosophila melanogaster and present its NMR solution structure in complex with the trisaccharide, GlcNAcβ1,4[Fucα1,3]GlcNAc, to which it binds with high specificity and affinity in vitro. The structure reveals that the monomeric CCL2 adopts a β-trefoil fold and recognizes the trisaccharide by a single, topologically novel carbohydrate-binding site. Site-directed mutagenesis of CCL2 and identification of C. elegans mutants resistant to this lectin show that its nematotoxicity is mediated by binding to α1,3-fucosylated N-glycan core structures of nematode glycoproteins; feeding with fluorescently labeled CCL2 demonstrates that these target glycoproteins localize to the C. elegans intestine. Since the identified glycoepitope is characteristic for invertebrates but absent from fungi, our data show that the defence function of fruiting body lectins is based on the specific recognition of non-self carbohydrate structures. The trisaccharide specifically recognized by CCL2 is a key carbohydrate determinant of pollen and insect venom allergens implying this particular glycoepitope is targeted by both fungal defence and mammalian immune systems. In summary, our results demonstrate how the plasticity of a common protein fold can contribute to the recognition and control of antagonists by an innate defence mechanism, whereby the monovalency of the lectin for its ligand implies a novel mechanism of lectin-mediated toxicity.     

Positions of β2 and β3 subunits in the large-conductance calcium- and voltage-activated BK potassium channel

Large-conductance voltage- and Ca²⁺-gated K⁺ channels are negative-feedback regulators of excitability in many cell types. They are complexes of α subunits and of one of four types of modulatory β subunits. These have intracellular N- and C-terminal tails and two transmembrane (TM) helices, TM1 and TM2, connected by an ∼100-residue extracellular loop. Based on endogenous disulfide formation between engineered cysteines (Cys), we found that in β2 and β3, as in β1 and β4, TM1 is closest to αS1 and αS2 and TM2 is closest to αS0. Mouse β3 (mβ3) has seven Cys in its loop, one of which is free, and this Cys readily forms disulfides with Cys substituted in the extracellular flanks of each of αS0–αS6. We identified by elimination mβ3-loop Cys152 as the only free Cys. We inferred the disulfide-bonding pattern of the other six Cys. Using directed proteolysis and fragment sizing, we determined this pattern first among the four loop Cys in β1. These are conserved in β2–β4, which have four additional Cys (eight in total), except that mβ3 has one fewer. In β1, disulfides form between Cys at aligned positions 1 and 8 and between Cys at aligned positions 5 and 6. In mβ3, the free Cys is at position 7; position 2 lacks a Cys present in all other β2–β4; and the disulfide pattern is 1–8, 3–4, and 5–6. Presumably, Cys 2 cross-links to Cys 7 in all other β2–β4. Cross-linking of mβ3 Cys152 to Cys substituted in the flanks of αS0–S5 attenuated the protection against iberiotoxin (IbTX); cross-linking of Cys152 to K296C in the αS6 flank and close to the pore enhanced protection against IbTX. In no case was N-type inactivation by the N-terminal tail of mβ3 perturbed. Although the mβ3 loop can move, its position with Cys152 near αK296, in which it blocks IbTX binding, is likely favored.     

Impacts of Environmental Colloids on the Transport of 17 β-estradiol in Intact Soil Cores

Estrogens such as 17-β estradiol (E2) are endocrine-disrupting compounds and can affect the reproductive systems of aquatic organisms. Therefore, it is important to understand the mechanisms of their transport in the environment. E2 and its daughter product estrone (E1) are both strongly adsorbed by soil organic matter and have relatively short half-lives. Reduced contact time with soil makes transport of E2 and E1 in soil more likely. In this study, intact soil cores from three soils representing a range of particle size distribution, structure, and organic matter content were used to compare the transport of E2 with and without the presence of colloidal material fractionated from soil or swine manure. In chemical transport experiments conducted with undisturbed soil columns, E2 and E1 were measured both in solution and attached to suspended solids in column effluent. During the transport experiments, colloids carrying E2 passed through all soils, with the exception of the sandy soil. The presence of colloids decreased the first detection time of E2 in the aqueous phase, was correlated with greater peak E2 concentrations in the effluent of both loamy and clayey soils, but not through the sandy soil, and increased mass fractions of the E2 that was transported.