Conformational States of Trifluoroacetic Acid–Treated Cytochrome c in the Presence of Salts and Alcohols

We have carried out a systematic investigation of salts- and alcohols-induced conformational alterations on the trifluoroacetic acid (TFA)-treated ferricytochrome c by soret absorption spectroscopy, far UV circular dichroism (CD), tryptophan fluorescence, and 1-anilino-8-naphthalene sulfonate (ANS) binding. TFA induces the unfolding of native cytochrome c obtained from horse heart leading to loss of secondary structure. The addition of increasing concentration of salts and alcohols leads to increase in MRE value at 222 and 208 nm indicating an increase in the alpha-helical content leading to formation of compact dimensional structure. Cytochrome c is a heme protein in which the resonance energy of tryptophan is transferred to heme resulting in quenched tryptophan fluorescence. Addition of alcohols leads to increase in tryptophan and ANS fluorescence. The tryptophan and ANS fluorescence in case of salts shows decreased fluorescence intensity. TFA-induced unfolded cytochrome c showed the soret absorption maximum at 394 nm. However, an intermediate state in presence of alcohols and salts showed the absorption maxima at 398 nm and 402 nm, respectively. Among all the salts and alcohols studied, K3Fe(CN)6 and butanol were found to be most effective as examined by the above-mentioned spectroscopic techniques. The order of effectiveness of alcohols was found to be butanol > propanol > ethanol > methanol. The following effective trend in the case of salts was obtained: K3Fe(CN)6 > K2SO4>KClO4 > KCl. These results suggest that alcohols induce an intermediate with molten globule-like conformation on the TFA unfolded state, whereas salts induce a refolded intermediate approaching native-like conformation.     

Molecular Evolution of the Photolyase–Blue-Light Photoreceptor Family

The photolyase–blue-light photoreceptor family is composed of cyclobutane pyrimidine dimer (CPD) photolyases, (6-4) photolyases, and blue-light photoreceptors. CPD photolyase and (6-4) photolyase are involved in photoreactivation for CPD and (6-4) photoproducts, respectively. CPD photolyase is classified into two subclasses, class I and II, based on amino acid sequence similarity. Blue-light photoreceptors are essential light detectors for the early development of plants. The amino acid sequence of the receptor is similar to those of the photolyases, although the receptor does not show the activity of photoreactivation. To investigate the functional divergence of the family, the amino acid sequences of the proteins were aligned. The alignment suggested that the recognition mechanisms of the cofactors and the substrate of class I CPD photolyases (class I photolyases) are different from those of class II CPD photolyases (class II photolyases). We reconstructed the phylogenetic trees based on the alignment by the NJ method and the ML method. The phylogenetic analysis suggested that the ancestral gene of the family had encoded CPD photolyase and that the gene duplication of the ancestral proteins had occurred at least eight times before the divergence between eubacteria and eukaryotes. Received: 23 October 1996 / Accepted: 1 April 1997     

Calcium Modulation of Ligand Affinity in the Cyclic GMP–gated Ion Channels of Cone Photoreceptors

To investigate modulation of the activation of cGMP-gated ion channels in cone photoreceptors, we measured currents in membrane patches detached from the outer segments of single cones isolated from striped bass retina. The sensitivity of these channels to activation by cGMP depends on the history of exposure to divalent cations of the membrane''s cytoplasmic surface. In patches maintained in 20 μM Ca⁺⁺ and 100 μM Mg⁺⁺ after excision, the current amplitude dependence on cGMP is well described by a Hill equation with average values of K _1/2, the concentration necessary to activate half the maximal current, of 86 μM and a cooperativity index, n, of 2.57. Exposing the patch to a solution free of divalent cations irreversibly increases the cGMP sensitivity; the average value of K _1/2 shifts to 58.8 μM and n shifts to 1.8. Changes in cGMP sensitivity do not affect other functional parameters of the ion channels, such as the interaction and permeation of mono- and divalent cations. Modulation of cGMP activation depends on the action of an endogenous factor that progressively dissociates from the channel as Ca⁺⁺ concentration is lowered below 1 μM. The activity of the endogenous modulator is not well mimicked by exogenously added calmodulin, although this protein competes with the endogenous modulator for a common binding site. Thus, the modulation of cGMP affinity in cones depends on the activity of an unidentified molecule that may not be calmodulin.     

Structure–Critical Distribution of Aromatic Residues in the Fibronectin Type III Protein Family

Over a thousand individual Fibronectin type III (FnIII) domain sequences, extracted from more than 60 different FnIII-dependent protein super-structures, were downloaded from curated database resources. Three regions of extreme sequence conservation within the well-characterized FnIII β-sandwich structure were respectively defined by near absolute conservation of a tryptophan (Trp) in β-strand-B, tyrosines (Tyr) in both β-strand-C and β-strand-F, and a leucine (Leu) residue in the unstructured region immediately preceding β-strand-F. Employing these four conserved landmarks, the entire FnIII sequence dataset was vertically registered to align the three conserved regions, and the cumulative distribution of all other amino acid functionality was determined and plotted relative to these landmark residues. Conserved aromatic sites were each found to be flanked by aliphatic residues that assure localization of these sites to the inaccessible hydrophobic interface between major sheet structures. Mapping the location of conserved aromatic sites in numerous PDB structures demonstrated the consistent pair-wise co-localization of the indole side-chain of the conserved strand-B Trp site to within 0.35 nm of the phenolic side-chain of the strand-C Tyr site located 8–14 amino acids distal. Likewise, the side-chain of the strand-F Tyr site co-localized to within 0.45 nm of the aliphatic side-chain of the conserved Leu that uniformly precedes it by six residues. While classic hydropathy-based theories would deem the “burying” of Tyr and Trp side-chains and/or their association with hydrophobic FnIII core residues thermodynamically unnecessary, alternative contributions of conserved Trp and Tyr residues, and particularly the role of the absolutely conserved tyrosine phenolic –OH in native FnIII structure–function are considered. A more global role for conserved FnIII aromaticity is also discussed in light of the aromatic conservation observed in other well-established protein families.     

Conformational Dynamics of Dioxygenase AlkB and DNA in the Course of Catalytically Active Enzyme–Substrate Complex Formation

Russian Journal of Bioorganic Chemistry - Fe2+/2-ketoglutarate-dependent DNA-dioxygenase AlkB from Escherichia coli is able to restore the native structure of alkylated DNA bases. The enzymatic...     

SH3 domains: modules of protein–protein interactions

Src homology 3 (SH3) domains are involved in the regulation of important cellular pathways, such as cell proliferation, migration and cytoskeletal modifications. Recognition of polyproline and a number of noncanonical sequences by SH3 domains has been extensively studied by crystallography, nuclear magnetic resonance and other methods. High-affinity peptides that bind SH3 domains are used in drug development as candidates for anticancer treatment. This review summarizes the latest achievements in deciphering structural determinants of SH3 function.     

Evolution of High-Affinity Peptide Probes to Detect the SH3 Domain of Cancer Biomarker BCR–ABL

The BCR–ABL fusion protein is closely associated with the pathological progression of chronic myelogenous leukaemia and some other myeloproliferative diseases, which has long been recognized as one of the most important cancer biomarkers in the tumor diagnosis community. The SH3 domain of BCR–ABL is a small, conserved protein module that specifically recognizes and binds proline-rich peptide fragments. In the current study, we used a synthetic strategy to discover new peptide probes with high affinity binding to the BCR–ABL SH3 domain. In the procedure, a sequence-based machine learning predictor was developed based on a set of affinity-known SH3 binders, and the predictor was then used to guide the evolutional optimization of numerous virtual peptides to enrich high binding potency for the SH3 domain. Subsequently, a evolved peptide population was generated, from which ten peptides with the highest affinity scores were selected and their interaction free energies with SH3 domain were characterized systematically using a combination of molecular dynamics simulation and binding free energy analysis. Consequently, four peptides were suggested as promising candidates and their affinities toward SH3 domain were assayed; two peptides, APTYTPPPPP and APTYAPPPPP, were identified to have potent binding capability with dissociation constants K _d of 3 and 8 μM, respectively. Further, the structural basis and energetic property of SH3 domain in complex with APTYTPPPPP were examined in detail, revealing a non-specific interaction in SH3–peptide recognition that should render a broad ligand spectrum for the domain.     

Detecting Protein–Protein Interactions in Living Cells: Development of a Bioluminescence Resonance Energy Transfer Assay to Evaluate the PSD-95/NMDA Receptor Interaction

The PDZ domain mediated interaction between the NMDA receptor and its intracellular scaffolding protein, PSD-95, is a potential target for treatment of ischemic brain diseases. We have recently developed a number of peptide analogues with improved affinity for the PDZ domains of PSD-95 compared to the endogenous C-terminal peptide of the NMDA receptor, as evaluated by a cell-free protein–protein interaction assay. However, it is important to address both membrane permeability and effect in living cells. Therefore a bioluminescence resonance energy transfer (BRET) assay was established, where the C-terminal of the NMDA receptor and PDZ2 of PSD-95 were fused to green fluorescent protein (GFP) and Renilla luciferase (Rluc) and expressed in COS7 cells. A robust and specific BRET signal was obtained by expression of the appropriate partner proteins and subsequently, the assay was used to evaluate a Tat-conjugated peptide for its ability to disrupt the PSD-95/NMDA receptor interaction in living cells.     

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.     

Contributions of F-BAR and SH2 Domains of Fes Protein Tyrosine Kinase for Coupling to the Fc?RI Pathway in Mast Cells

This study investigates the roles of Fer-CIP4 homology (FCH)-Bin/amphiphysin/Rvs (F-BAR) and SH2 domains of Fes protein tyrosine kinase in regulating its activation and signaling downstream of the high-affinity immunoglobulin G (IgE) receptor (FcɛRI) in mast cells. Homology modeling of the Fes F-BAR domain revealed conservation of some basic residues implicated in phosphoinositide binding (R113/K114). The Fes F-BAR can bind phosphoinositides and induce tubulation of liposomes in vitro. Mutation of R113/K114 to uncharged residues (RK/QQ) caused a significant reduction in phosphoinositide binding in vitro and a more diffuse cytoplasmic localization in transfected COS-7 cells. RBL-2H3 mast cells expressing full-length Fes carrying the RK/QQ mutation show defects in FcɛRI-induced Fes tyrosine phosphorylation and degranulation compared to cells expressing wild-type Fes. This correlated with reduced localization to Lyn kinase-containing membrane fractions for the RK/QQ mutant compared to wild-type Fes in mast cells. The Fes SH2 domain also contributes to Fes signaling in mast cells, via interactions with the phosphorylated FcɛRI β chain and the actin regulatory protein HS1. We show that Fes phosphorylates C-terminal tyrosine residues in HS1 implicated in actin stabilization. Thus, coordinated actions of the F-BAR and SH2 domains of Fes allow for coupling to FcɛRI signaling and potential regulation the actin reorganization in mast cells.Mast cells reside in connective and mucosal tissues and play a key protective role in the immune response to helminth infection (13, 21), sepsis (39), and snake or bee venoms (42). Mast cells express FcɛRI, which becomes sensitized to antigens or allergens upon immunoglobulin E (IgE) binding. Aggregation of FcɛRI by multivalent antigens causes the release of preformed mediators by degranulation and the de novo production of lipid mediators and cytokines (1, 52). Release of these mediators causes increased vascular permeability, leukocyte recruitment and activation, and inflammation (41). Aberrant mast cell activation is implicated in IgE-mediated type I hypersensitivity reactions including anaphylaxis, allergic rhinitis, and asthma (20). FcɛRI is a tetrameric receptor composed of an IgE-binding α chain and of β and γ chains containing immunoreceptor tyrosine-based activation motifs that become phosphorylated following multivalent antigen-mediated clustering of FcɛRI and activation of Src family protein tyrosine kinases (PTKs), primarily involving Lyn (51). Lyn phosphorylates and activates both positive effectors of FcɛRI signaling (e.g., Syk PTK) and key negative regulators (e.g., Shp-1 and SHIP) that serve to limit mast cell activation (28, 46, 69).Fes (the mammalian orthologue of the v-Fps and v-Fes oncoproteins from avian [57, 58] and feline [15, 56] retroviruses) and Fer are closely related PTKs that become activated following FcɛRI aggregation in mast cells (10). Surprisingly, FcɛRI-induced tyrosine phosphorylation of Fes and Fer does not require their kinase activities (55) and is almost entirely dependent on Lyn (67). Through the use of transgenic mouse models, evidence for both unique and redundant functions for Fes and Fer has been described in regulating hematopoiesis (55) and limiting the innate immune response (22, 40, 50, 72). In mast cells, we have shown that Fer promotes activation of p38 mitogen-activated protein kinase and chemotaxis of mast cells (10). We also found that Fer and Fes PTKs contribute to FcɛRI-evoked phosphorylation of platelet-endothelial cell adhesion molecule 1 (PECAM-1) (67).Each of the Fes and Fer PTKs is composed of an N-terminal regulatory domain containing a Fer-CIP4 homology (FCH) domain followed by several predicted coiled-coils (CC), a central SH2 domain, and C-terminal PTK domain (19). It is worth noting that early studies pointed toward an important role for the N-terminal domain of v-Fps for its transforming activity and membrane localization (5, 63). Several recent studies have defined the FCH and first CC domain (amino acids 1 to 300) in Fer, CIP4, and other pombe Cdc15 homology (PCH) family adaptor proteins as an F-BAR domain (also termed extended FCH or EFC domain) (reviewed in references 3 and 9). The F-BAR domain was found to constitute a novel phosphoinositide-binding domain that can promote tubulation of liposomes in vitro and membranes in vivo (27, 33, 66). The crystal structures of F-BAR domains from several PCH adaptors were recently solved (27, 59). The F-BAR module was shown to consist of a triple helical bundle that forms a homodimer, with a concave surface rich in basic residues that have recently been shown to contact phospholipids in curved membranes (16). In vitro studies using the Fer F-BAR domain have shown that the F-BAR domain binds strongly to phosphatidylinositol-4,5-bisphosphate [PI(4,5)P₂]; however, the Fer F-BAR is relatively weak compared with the adaptor protein FBP17 at inducing membrane tubulation (66). Liposome sedimentation assays have identified several conserved basic residues required for F-BAR domain binding to PI(4,5)P₂(66). The substitution of R113/K114 to glutamines (RK/QQ) in FBP17 reduced phosphoinositide binding by 80% (66). A recent electron cryoelectron microscopy study provided insights into binding of F-BAR dimers to flat and curved membranes via different binding faces (16). This study also confirmed that R113/K114 residues (in CIP4) constitute a site of direct interaction with the liposomes. Interestingly, microdomains of the plasma membrane rich in PI(4,5)P₂ are sites of dynamic actin assembly (47) and endocytosis (4, 31). Previous studies have described Fes localization to a variety of subcellular structures, including endocytic vesicles (71), the trans-Golgi apparatus (71), microtubules (37), and focal adhesions (44). The rapid activation of Fes and Fer PTKs upon FcɛRI aggregation on mast cells (10) would suggest that there is a mechanism by which Fes localizes at or near the plasma membrane. Phosphoinositide-binding via the F-BAR domain of Fes and Fer PTKs may promote their recruitment to the plasma membrane prior to their activation by cell surface receptors such as FcɛRI. The potential colocalization with endocytosis and actin assembly regulators may allow for regulation of receptor endocytosis or chemotaxis of mast cells by Fes/Fer PTKs. A recent study implicates Rab5 GTPase and its exchange factor RabGEF1/Rabex-5 in promoting internalization of FcɛRI following clustering by antigens (34). It is worth noting that defects in internalization of Toll-like receptor 4 and transferrin receptor were observed in Fes-deficient macrophages (48), and there is a potential role for Fes in regulating internalization of mast cell receptors.In this study, we provide novel insights into the phospholipid binding and liposome tubulating properties of the Fes F-BAR domain. Mutation of two conserved basic residues within the Fes F-BAR domain (RK/QQ) reduced phospholipid binding in vitro, and membrane localization in vivo. In transfected RBL-2H3 mast cells, the Fes harboring the RK/QQ mutation (Fes^RK/QQ) displayed reduced FcɛRI-evoked tyrosine phosphorylation compared to wild-type Fes (Fes^WT), which correlated with reduced localization to Lyn-containing membranes in mast cells. The SH2 domain of Fes was found to interact with several phosphoproteins in mast cells, including FcɛRI and HS1, an actin regulator and cortactin homologue. We found that Fes contributes to HS1 phosphorylation at C-terminal residues implicated in actin branch stabilization, and we present a model for how F-BAR-containing adaptor proteins and PTKs may coordinate actin-driven endocytosis in mast cells.     

Sodium–Calcium Exchangers of the SLC8 Family in Oligodendrocytes: Functional Properties in Health and Disease

Neurochemical Research - The solute carrier 8 (SLC8) family of sodium–calcium exchangers (NCXs) functions as an essential regulatory system that couples opposite fluxes of sodium and calcium...     

Accumulation of Knowledge and Changes in Red List Classifications within the Family Galliformes1980–2004

The IUCN Red List classification scheme has, for many years, aided the prioritisation of conservation action by identifying taxa most at risk of extinction. This is a study of the accumulation of knowledge concerning extinction risk in gamebirds over the last 25 years (the Red Lists published in 1981, 1988, 1994, 2000 and 2004). The change from the rather subjective assessment criteria of the 1980s to the more quantitative scheme of 1994 was marked by a sharp increase in the proportion of species classed as threatened. Between 1994 and 2000, 17% of threatened species moved threat category (21 upgraded and 28 downgraded) while between 2000 and 2004 just 7% of species shifted category. The main threat criteria (those associated with ‘declining population’, ‘small range’ and ‘small population’) were used in similar proportions in 1994 and 2000, suggesting no real change in the ways that classifications are arrived at. Decision tree analysis showed that species moving between threat categories between 1994 and 2004 tended to be polytypic and have large global ranges, suggesting that such species are amongst those most difficult to classify. Considering actual direction of change between 1994 and 2004, geographic region and taxonomic group were important, with pheasants, and partridges and their allies (species of the Palearctic and Oriental regions), tending to be downgraded, and the grouse, megapodes and cracids of the New World and Australasia tending to be upgraded. While there are now few movements in threat category between assessments, we caution that this certainly does not mean that we have accumulated adequate knowledge to properly support the classifications for most species.     

A Gene of the β3-Glycosyltransferase Family Encodes N-Acetylglucosaminyltransferase II Function in Trypanosoma brucei

The bloodstream form of the human pathogen Trypanosoma brucei expresses oligomannose, paucimannose, and complex N-linked glycans, including some exceptionally large poly-N-acetyllactosamine-containing structures. Despite the presence of complex N-glycans in this organism, no homologues of the canonical N-acetylglucosaminyltransferase I or II genes can be found in the T. brucei genome. These genes encode the activities that initiate the elaboration of the Manα1–3 and Manα1–6 arms, respectively, of the conserved trimannosyl-N-acetylchitobiosyl core of N-linked glycans. Previously, we identified a highly divergent T. brucei N-acetylglucosaminyltransferase I (TbGnTI) among a set of putative T. brucei glycosyltransferase genes belonging to the β3-glycosyltransferase superfamily (Damerow, M., Rodrigues, J. A., Wu, D., Güther, M. L., Mehlert, A., and Ferguson, M. A. (2014) J. Biol. Chem. 289, 9328–9339). Here, we demonstrate that TbGT15, another member of the same β3-glycosyltransferase family, encodes an equally divergent N-acetylglucosaminyltransferase II (TbGnTII) activity. In contrast to multicellular organisms, where GnTII activity is essential, TbGnTII null mutants of T. brucei grow in culture and are still infectious to animals. Characterization of the large poly-N-acetyllactosamine containing N-glycans of the TbGnTII null mutants by methylation linkage analysis suggests that, in wild-type parasites, the Manα1–6 arm of the conserved trimannosyl core may carry predominantly linear poly-N-acetyllactosamine chains, whereas the Manα1–3 arm may carry predominantly branched poly-N-acetyllactosamine chains. These results provide further detail on the structure and biosynthesis of complex N-glycans in an important human pathogen and provide a second example of the adaptation by trypanosomes of β3-glycosyltransferase family members to catalyze β1–2 glycosidic linkages.     

Ligand entry pathways in the ligand binding domain of PPARγ receptor

To address the question of ligand entry process, we report targeted molecular dynamics simulations of the entry of the flexible ionic ligand GW0072 in the ligand binding domain of the nuclear receptor PPARγ. Starting with the ligand outside the receptor the simulations led to a ligand docked inside the binding pocket resulting in a structure very close to the holo-form of the complex. The results showed that entry process is guided by hydrophobic interactions and that entry pathways are very similar to exit pathways. We suggest that TMD method may help in discriminating between ligands generated by in silico docking.     

BRAIN-DAMAGED CHILDREN—The Problem of Relations in the Family Group

Children with minimal brain damage show a characteristic pattern of behavior.Often there are no physical signs of abnormality, but the diagnosis can be made from the history, electroencephalographic tracings, psychologic tests and repeated observations.The behavior is a composite of the effects of the brain damage and the response of the child to his environment. The behavior of the brain-damaged child is frequently so frustrating to parents that attitudes of rejection, withdrawal or excessive punitive measures occur.In the present study, when drugs were given and the child''s behavior improved, the parents were better able to understand the needs of the child and create a better home environment in which there was less frustration and emotional pressure.