The prediction of the conformation of membrane proteins from the sequence of amino acids

Conformation and stability of Sendai virus fusion protein

The conformation and stability of Sendai virus fusion (F) protein were studied by circular dichroism spectroscopy, and the protein predictive models of Chou and Fasman and Robson and Suzuki were used to elucidate the secondary structure of Sendai virus F protein. The F protein conformation is predicted to contain 33% alpha-helix, 53% beta-sheet and 15% beta-turn by the Chou and Fasman model, and 30% alpha-helix, 55% beta-sheet, 9% beta-turn and 7% random coil by the Robson and Suzuki model. C.d. studies of F protein purified in the presence of the non-ionic detergent, n-octylglucoside, indicated the presence of 49% alpha-helix and 31% beta-sheet at pH 7.0, 54% alpha-helix and 28% beta-sheet at pH 9.0 and 50% alpha-helix and 23% beta-sheet at pH 5.4. A small change in conformation of the protein occurred when the pH was titrated from 7.0 to 5.4 and from 7.0 to 9.0 and a more pronounced conformational change occurred when the pH was changed from 9.0 to 5.4. The F protein in 0.2% n-octylglucoside was resistant to denaturation by 4 M guanidine hydrochloride, the reducing agent 20 mM mercaptoethanol, and to increases in temperature from 5 to 80 degrees C. Monoclonal anti-F protein antibody showed an increased binding to whole virus when the pH was changed from 7.0 to 9.0. The antibody binding was decreased when the pH was shifted from 9.0 to 5.4 Maximum haemolytic activity was observed with virus that was preincubated at pH 8.0.(ABSTRACT TRUNCATED AT 250 WORDS)

Differentiated analysis of the secondary structure of hydrophilic and hydrophobic regions in alpha- and beta-subunits of Na+,K+-ATPase by Raman spectroscopy

Raman spectra of active Na+,K+-ATPase from pig kidney and membrane-bound products of its two-stage trypsinolysis, including alpha-subunit hydrophobic regions as well as the intact beta-subunit and hydrophobic regions of alpha- and beta-subunits, were measured to calculate the secondary structure of hydrophilic and hydrophobic regions of the enzyme. Consequent comparison demonstrated unambiguously that (i) membrane-bound hydrophobic parts of polypeptide chains of Na+,K+-ATPase subunits are in the alpha-helical conformation; (ii) essential contents of the alpha-helix as well as beta-sheet are estimated to form the hydrophilic (mainly cytoplasmic) domain of the Na+,K+-ATPase alpha-subunit; (iii) the exoplasmic hydrophilic domain of the beta-subunit is shown to include several antiparallel beta-pleated sheets and a small amount of the alpha-helix and unordered conformations. The model of the secondary structure organization of hydrophilic domains as well as 8 hydrophobic transmembrane segments of the enzyme molecule was proposed on the basis of experimental results and predictional calculations.

The sucrase-isomaltase complex: primary structure, membrane-orientation, and evolution of a stalked, intrinsic brush border protein

The complete primary structure (1827 amino acids) of rabbit intestinal pro-sucrase-isomaltase (pro-SI) was deduced from the sequence of a nearly full-length cDNA. Pro-SI is anchored in the membrane by a single 20 amino acid segment spanning the bilayer only once. The amino-terminal, cytoplasmic domain consists of 12 amino acids and is not preceded by a cleaved leader sequence. This suggests a dual role for the membrane-spanning segment as an uncleaved signal for membrane insertion. This is followed by a 22 residue serine/threonine-rich, probably glycosylated, stretch, presumably forming the stalk on which the globular, catalytic domains are directed into the intestinal lumen. Following this is a high degree of homology between the isomaltase and sucrase portions (41% amino acid identity), indicating that pro-SI evolved by partial gene duplication.

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.

Complete amino acid sequence and predicted membrane topology of phenobarbital-induced cytochrome P-450 (isozyme 2) from rabbit liver microsomes

The complete amino acid sequence of phenobarbital-induced isozyme 2 of rabbit liver microsomal cytochrome P-450 (P-450LM2) is presented. The polypeptide consists of 491 residues with a calculated Mr of 55,755. The rabbit isozyme is 77% identical to the corresponding rat cytochrome, P-450b, as deduced from cDNA, with 96% of the hydrophobic, 88% of the anionic, and 83% of the cationic positions conserved. The secondary structure of isozyme 2 was predicted and a model was developed for the membrane topology of this cytochrome. Of the two highly conserved cysteinyl peptides in P-450LM2, P-450b, and bacterial P-450cam, we favor, on the basis of our model, the one nearer the NH2 terminus (Cys-152 in P-450LM2) as the source of the thiolate ligand to the heme iron atom. The recently reported sequence of the apparently identical protein [Heinemann, F. S. & Ozols, J. (1983) J. Biol. Chem. 258, 4195-4201] has two fewer residues and differs in 14 other amino acid assignments.

Hydrogen-1 and carbon-13 nuclear magnetic resonance of the aromatic residues of fd coat protein

The aromatic residues of fd coat protein in sodium dodecyl sulfate micelles are characterized by 1H and 13C NMR. Resonances from both types of nuclei show structure-induced chemical shift dispersion and line widths indicative of a folded native structure for the protein. The two tyrosines were found to have pKas of 12.3 and 12.5 by 1H NMR and spectrophotometric titrations. 13C relaxation measurements show that two of the three Phe rings have significant internal mobility, the two Tyr rings have moderate internal mobility, and the Trp side chain is completely immobilized. Qualitative comparisons are made between the intact virus and the isolated coat protein.

Nuclear magnetic resonance of the filamentous bacteriophage fd

The filamentous bacteriophage fd and its major coat protein are being studied by nuclear magnetic resonance (NMR) spectroscopy. 31P NMR shows that the chemical shielding tensor of the DNA phosphates of fd in solution is only slightly reduced in magnitude by motional averaging, indicating that DNA-protein interactions substantially immobilize the DNA packaged in the virus. There is no evidence of chemical interactions between the DNA backbone and the coat protein, since experiments on solid virus show the 31P resonances to have the same principle elements of its chemical shielding tensor as DNA. 1H and 13C NMR spectra of fd virus in solution indicate that the coat proteins are held rigidly in the structure except for some aliphatic side chains that undergo relatively rapid rotations. The presence of limited mobility in the viral coat proteins is substantiated by finding large quadrupole splittings in 2H NMR of deuterium labeled virions. The structure of the coat protein in a lipid environment differs significantly from that found for the assembled virus. Data from 1H and 13C NMR chemical shifts, amide proton exchange rates, and 13C relaxation measurements show that the coat protein in sodium dodecyl sulfate micelles has a native folded structure that varies from that of a typical globular protein or the coat protein in the virus by having a partially flexible backbone and some rapidly rotating aromatic rings.

The dynamics of membrane structure

The membranes of living organisms are involved in many aspects of the life, growth and development of all cells. The predominant structural elements of these membranes are lipids and proteins and the basic strucvture of these molecules has been reviewed. The physical properties of the lipid constituents particularly their behavior in aqueous systems has led to the concepts of thermotropic and lyotropic mesomorphism; the interaction between different types of lipid molecules modulate this behavior. Interaction of phospholipids in aqueous systems with cholesterol, ions and drugs have been examined in this context. In addition a variety of model lipid-protein systems have been investigated and the implications of interactions between lipids and different proteins in biological membranes has been evaluated. This leads to a detailed consideration of the way lipids and proteins ae organized in cell membranes and contains an appraisal of the evidence supporting contemporary views of membrane structure. Particular attention has been devoted to the question of how mobile the components are within the structure. Particular attention has been devoted to the question of how mobile the components are within the structure. Finally the biosynthesis, turnover and modulation of the properties of interacting membrane constituents is critically reviewed and possible ways of controlling the behavior of cells and organisms by altering the structural parameters of different membranes has been considered.

Proposed knobs-into-holes packing for several membrane proteins

We investigated the possible side chain/side chain interactions of four potential transmembrane proteins. The basic assumptions are that the proteins are alpha-helical, and that the proteins aggregate with knobs-into-holes packing. It was found that these four proteins can be assembled into stereochemically feasible bundles of alpha-helices with hydrophobic exteriors and with hydrogen bonds between the side chains of one alpha-helix and the side chains of its knobs-into-holes packed neighbors.

Structural analysis of a membrane glycoprotein: glycophorin A

Glycophorin A is the major sialoglycoprotein of the human erythrocyte membrane. Structural studies indicate that this molecule is made up of 3 domains composed of 2 hydrophilic segments which are separated by a region of 22 nonpolar amino acids. The N-terminal half of the molecule contains all the carbohydrate associated with this protein. Glycophorin A forms high-molecular-weight complexes which can be dissociated only under certain conditions. The site of subunit interaction is located within the hydrophobic segment, which serves both to mediate protein-protein and protein-lipid interactions within the bilayer membrane. Glycophorin A spans the membrane presumably as a dimeric complex with the carboxyterminal ends extending into the cytoplasm of the red cell. The transmembrane nature of the polypeptide chains finds strong support from the use of specific antibody-ferritin conjugates applied to thin sections of fixed and frozen intact cells. Preliminary information on the analysis of human red cell variants which may lack some or all of the sialoglycopeptides are consistent with the presence in normal cells of a second sialoglycoprotein, provisionally labeled glycophorin B.