Substrate specificity and affinity of a protein modulated by bound water molecules

Water molecules influence molecular interactions in all biological systems, yet it is extremely difficult to understand their effects in precise atomic detail. Here we present evidence, based on highly refined atomic structures of the complexes of the L-arabinose-binding protein with L-arabinose, D-fucose and D-galactose, that bound water molecules, coupled with localized conformational changes, can govern substrate specificity and affinity. The atoms common to the three sugars are identically positioned in the binding site and the same nine strong hydrogen bonds are formed in all three complexes. Two hydrogen-bonded water molecules in the site contribute further to tight binding of L-arabinose but create an unfavourable interaction with the methyl group of D-fucose. Equally tight binding of D-galactose is attained by the replacement of one of the hydrogen-bonded water molecules by its--CH2OH group, coordinated with localized structural changes which include a shift and redirection of the hydrogen-bonding interactions of the other water molecule. These observations illustrate how ordered water molecules can contribute directly to the properties of proteins by influencing their interaction with ligands.     

Structure of tumour necrosis factor

Tumour necrosis factor is a trimeric molecule, each subunit of which consists of an antiparallel beta-sandwich. Individual subunits from the trimer by a novel edge-to-face packing of beta-sheets. A comparison of the subunit fold with that of other proteins reveals a remarkable similarity to the 'jelly-roll' structural motif characteristic of viral coat proteins.     

Substitution at residue 227 of H-2 class I molecules abrogates recognition by CD8-dependent, but not CD8-independent, cytotoxic T lymphocytes

The CD8 (Lyt 2) molecule is a phenotypic marker for T lymphocytes that recognize and react with major histocompatibility complex (MHC) class I molecules. Antibody blocking experiments and gene transfection studies indicate that CD8 binds to a determinant on MHC class I molecules on the target cells, facilitating interaction between effector T lymphocytes and the target cell. The CD8 molecule may also be involved in transmembrane signalling during T-cell activation. The existence of CD8- cytotoxic T lymphocytes (CTL) and class I-reactive CTL that are not inhibited by antibody to CD8 suggests that at least some CTL do not require the CD8 molecule to interact with and lyse target cells. We have recently demonstrated that cells transfected with an H-2Dd gene that carries a mutation at residue 227 are not killed by primary CTL8. Here we show that although this mutation abrogates recognition by primary CTL, it does not affect recognition by CD8-independent CTL, suggesting that residue 227 of class I molecules might contribute to a determinant that is the ligand of the CD8 molecule.     

碳酸盐建造天然储层及其在地质历史中的演化

流体分布特征及其在储层中的运移取决于岩石的储集性和层序内部结构。块状储层一般是礁或浮游生物建造,部分属地台底栖生物建造,其中流体可进行垂向和横向运移;层状储层是典型的底栖生物建造,具不同渗透性的岩层成互层状,以横向运移为主;岩性圈闭储层产于未补偿拗陷的沥青质-硅质、粘土-碳酸盐建造。层状储层遍及整个显生宙,但其相型、孔隙空间的组成及特征均有所改变。礁块储层的意义在地质历史中随其厚度及非均质性的增加均有所增长。在中生代末的浮游生物建造中常有块状储层。岩性圈闭储层自泥盆纪以来零星出现于较年轻的沉积中。     

The C. elegans genome sequencing project: a beginning.

The long-term goal of this project is the elucidation of the complete sequence of the Caenorhabditis elegans genome. During the first year methods have been developed and a strategy implemented that is amenable to large-scale sequencing. The three cosmids sequenced in this initial phase are surprisingly rich in genes, many of which have mammalian homologues.     

Selective inhibition of the anchorage-independent growth of myc-transfected fibroblasts by retinoic acid

Fischer rat 3T3 (FR3T3) fibroblasts transfected with a cellular myc gene can be induced to grow and form colonies in soft agar by treatment either with epidermal growth factor (EGF) alone or with the combination of platelet-derived growth factor (PDGF) and type-beta transforming growth factor (TGF-beta). We now show that induction of anchorage-independent growth by each of these sets of growth factors involves different cellular pathways which can be distinguished by their sensitivity to retinoic acid. Colony formation induced by the combined action of PDGF and TGF-beta is 100-fold more sensitive to inhibition by retinoic acid than is colony formation induced by treatment of the myc-transfected cells with EGF. Moreover, retinoic acid (10(-8) M) is inhibitory for colony growth whenever TGF-beta is present, regardless of whether the effects of TGF-beta are stimulatory, as occurs in the presence of PDGF, or inhibitory, as found in the presence of EGF.     

Amino-acid sequence of a Ca2+ + Mg2+-dependent ATPase from rabbit muscle sarcoplasmic reticulum, deduced from its complementary DNA sequence

We have cloned and sequenced complementary DNA encoding a Ca2+-ATPase of rabbit muscle sarcoplasmic reticulum. We propose a model of the protein which has 3 cytoplasmic domains joined to a set of 10 transmembrane helices by a narrow, penta-helical stalk. In this model, ATP bound to one cytoplasmic domain would phosphorylate an aspartate in an adjoining cytoplasmic domain, inducing translocation of Ca2+ from binding sites on the stalk.     

Selective activation of Lyt 2+ precursor T cells by ligation of the antigen receptor

Resting T lymphocytes may be activated either physiologically, by the specific recognition of antigen in association with molecules encoded by the major histocompatibility complex (MHC), or non-physiologically using mitogens such as concanavalin A (Con A). The former activation process is difficult to analyse because resting precursor T cells specific for a particular antigen-MHC combination can only be isolated in the presence of a large excess of bystander cells of irrelevant specificity; clonal populations of uniform specificity are not useful for studying the activation of naive T cells because there is no reason to believe that such cloned cells ever return to the state of resting precursors. Mitogens may activate a large fraction of resting T cells, but analysis is again complicated because the target molecule(s) of most mitogens is unknown and the relationship of this kind of activation to physiological induction by antigen plus MHC molecules remains unclear. By using a monoclonal antibody specific for the antigen receptors on approximately 25% of all T cells of both Lyt 2+ and Lyt 2- subsets, we have studied the induction of lymphokine responsiveness in resting normal T cells. This antibody, immobilized on Sepharose beads, is sufficient to activate Lyt 2+ T cells, but not Lyt 2- T cells, to clonal expansion in the presence of a mixture of lymphokines (10% rat spleen Con A supernatant). We report here that clonal growth of the T cells obeys single-hit kinetics in limiting-dilution microcultures, suggesting that a single cell type is limiting. We conclude that cytotoxic T-lymphocyte (Tc) precursors require only ligation of the antigen receptor before they become responsive to lymphokines, whereas helper T-lymphocyte (Th) precursors require additional signals.