PREDICTION OF PROTEIN CONFORMATION FROM THE PRIMARY STRUCTURE

Secondary structure prediction of liver microsomal cytochrome P-450; proposed model of spatial arrangement in a membrane

The secondary structure of rabbit liver microsomal cytochrome P-450 LM2, rat liver microsomal cytochromes P-450b and P-450e (phenobarbital-inducible), and rat liver microsomal cytochromes P-450c, P-450d (3-methylcholanthrene-inducible) was predicted by a combination of methods (i) identifying the transmembrane parts of integral membrane proteins, and (ii) statistically predicting the secondary structure of globular proteins. The results are similar for all phenobarbital-inducible enzymes and make it possible to construct two structural models with seven or four transmembrane alpha-helices. The cytochromes of the second group obviously form a second structural family with four membrane-spanning alpha-helices. In both cases, a large ectodomain with several consecutive alpha-helices, which may provide the heme-binding pocket, is exposed out of the membrane.

A substitution in a nonconserved region of polyomavirus large T antigen which causes a thermosensitive mutation

The temperature-sensitive defect of the tsP155 mutant of polyomavirus (Py) maps in the large T antigen (LT) coding sequence of a viral DNA diverging markedly from that of extensively characterized wild-types (WTs) such as A2 and CSP. We have sequenced about 600 base pairs (bp) "early" DNA encompassing the mutated site in tsP155, as well as the corresponding DNA segment from a revertant virus (RtsP155). As expected, tsP155 was found to be more closely related to CSP than to A2. Out of 3 single bp differences between tsP155 and CSP, 2 were common to tsP155 and RtsP155. The only substitution exclusive to tsP155 was a G----C transversion at bp 2658 which canceled the HaeIII site at bp 2657. Heteroduplexes inclusive of tsP155 DNA and of a 312-bp-long fragment of RtsP155 DNA yielded recombinant viruses growing under restrictive conditions whose DNAs had all regained the HaeIII site at bp 2657. These findings clearly identify the ts mutation with the tranversion at bp 2658, which is expected to change Ala 701 for a Pro in LT. We discuss this substitution in relation to the phenotype of tsP155.

Secondary structure prediction and determination of proteins--a review

The rapid increase in sequence data in combination with a greater understanding of the forces regulating protein structure has been the impetus for an upsurge in the development of theoretical prediction methods. These methods have afforded protein chemists the ability to identify and quantify the various secondary structures along the protein chain. Concurrently, various physico-chemical techniques have been developed such as nuclear Overhauser enhancement n.m.r. and laser Raman spectroscopy. In addition, traditional methods such as infrared and circular dichroism spectroscopy have been refined. Although both predictive and physico-chemical techniques are limited in the types of secondary structure they are capable of determining, they have provided valuable information with regards to protein folding and topology in the absence of X-ray data, and have formed the basis for the development of improved methods for secondary structure determination. This paper reviews some of the predictive and physico-chemical methods presently used to determine protein secondary structure.

Molecular aspects, physiological function, and clinical significance of metallothioneins

Metallothioneins (MTs) are well-characterized low molecular weight, heat-stable cytosolic proteins with exceptional high content of cysteinyl sulfur and are known to bind heavy metals like cadmium (Cd), zinc (Zn), and copper (Cu). Since these proteins are induced on exposure to heavy metals, it is now accepted that they have a detoxifying role during heavy metal toxicity. It has also been suggested that the primary function of Mt is in the homeostasis of the essential metals Zn and Cu. Recently, a role MT in selenium metabolism in primates has been established. Further, MT has gained considerable importance in the clinical disorders related to trace metal metabolism.

A survey on cytosolic non-enzymic proteins involved in the metabolism of lipophilic compounds: from organic anion binders to new protein families

This review deals with recent advances in the research of cytosolic non-enzymic proteins involved in the metabolism of lipophilic compounds. Emphasis is given to the important contribution of structural data in the understanding of the functional properties of these proteins and in the emergence of new protein families. The possibility that many of the 'cytosolic' proteins might be structure-bound and structure-forming in the living cell is discussed, with references to so far available structural data and to recent investigations on the architecture and biochemical composition of the cytoplasm. The aim of this review is to present in a condensed form (227 references) the evolution in the study of cytosolic proteins binding and transferring lipophilic compounds and to enable interested investigators to become aware of current concepts and perspectives in this active and steadily growing area of research.

Amphiphilic growth hormone releasing factor (GRF) analogs: peptide design and biological activity in vivo

The first twenty-nine amino acids of human Growth Hormone Releasing Factor (hGRF) possess a distinct amphiphilic character. This is seen as twisted hydrophobic and hydrophilic bands in the helical net projection. Four amidated analogs were designed by optimizing amphiphilic and helical potentials of the native sequence. These designed analogs, with up to eight-amino acid changes, were tested in sheep via intravenous injection. The growth hormone-stimulating activities of the analogs were significantly higher when compared to bovine Growth Hormone Releasing Factor (bGRF44-NH2). This suggests that the amphiphilic conformation of GRF(1-29) is important to the receptor.

Investigations on the insertion of the mitochondrial precursor protein apocytochrome c into model membranes

Different aspects of the interaction of apocytochrome c and model membranes composed of negatively charged lipids, were studied in order to get insight into the nature of this interaction. The effect of the protein on the lipid packing properties are revealed by DSC, ESR and monolayer techniques. These experiments clearly demonstrate that upon electrostatic interaction with the negatively charged phospholipids, apocytochrome c is able to penetrate into the hydrophobic region of the model membrane. In the case of 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol, this results in a perturbation of 160 lipid molecules per apocytochrome c molecule. Most likely, apocytochrome c disrupts the formation of the gel phase and restricts the lipid chain motion above the gel to liquid-crystalline phase transition. Tryptophan fluorescence measurements confirm that at least a part of the protein penetrates into the bilayer, and suggest that after this penetration, the tryptophan (residue no. 59) is located in the glycerol backbone region of the phospholipids. Although the secondary structure of apocytochrome c is predicted to contain about 35% of alpha-helical structure, the CD pattern of an aqueous solution of the protein is featureless. However, negatively charged lipids are able to express this alpha-helical potency in the apocytochrome c, which might be important for the insertion of the protein into lipid membranes.

Effects of various amino acid replacements on the conformational stability of G-actin

Circular dichroic spectra of native, EDTA-treated and heat-denatured G-actin from chicken gizzard smooth muscle are virtually the same as those of rabbit skeletal muscle actin. The rates of changes produced by EDTA or heat in the secondary structure are, however, higher in the case of gizzard actin. Similar differences were found in the rates of inactivation as measured by loss of polymerizability during incubation with EDTA or Dowex 50. The results are explicable in terms of local differences in the conformation at specific site(s) important for maintaining the native state of actin monomer. Involvement of the ATP binding site was shown by measuring the equilibrium constant for the binding of ATP to the two actins. Difference in the conformation of some additional site(s) is indicated by a higher rate constant of inactivation of nucleotide-free actin observed for gizzard actin. No significant difference was found in the equilibrium constant for the binding of Ca2+ at the single high-affinity site in gizzard and skeletal muscle actin. Comparison of inactivation kinetics of actin from chicken gizzard, rabbit skeletal, bovine aorta, and bovine cardiac muscle suggests that the amino acid replacements Val-17----Cys-17 and/or Thr-89----Ser-89 have a destabilizing effect on the native conformation of G-actin. The results indicate that deletion of the acidic residue at position 1 of the amino acid sequence has no effect on the conformation of the ATP binding site and the high-affinity site for divalent cation as well.

Synthesis, conformational studies and biological activities of VIP and related fragments

VIP and related fragments were prepared by the solid-phase method. The peptides were assembled on a benzhydrylamine resin and couplings of the Boc-amino acids were carried out by the symmetrical anhydride method. Cleavage was achieved by treatment with liquid HF and purification was accomplished by successive steps of cation exchange, partition and semi-preparative high pressure liquid chromatography. The biological activities were evaluated in vitro in the rabbit perfused heart and in vivo on the rat blood pressure. Structural studies were performed by high resolution (400 MHz) 1H-NMR spectroscopy and circular dichroism. The results show that among all the fragments tested, only VIP2-28 retains significant biological activity. The fragments 1-14 and 15-28, which are devoid of activity, were found to be inactive as antagonists. VIP and some of the fragments tend to adopt the helical structure, as demonstrated by spectroscopic techniques.

Complete nucleotide sequence of phoE, the structural gene for the phosphate limitation inducible outer membrane pore protein of Escherichia coli K12

The complete nucleotide sequence of the gene phoE, which codes for the phosphate limitation inducible outer membrane pore protein of Escherichia coli K12 was established. The results show that PhoE protein is synthesized in a precursor form with a 21 amino acid residue amino-terminal extension. This peptide has the general characteristics of a signal sequence. The promoter region of phoE has no homology with the consensus sequence of E. coli promoter regions, but homologous sequences with the promoter region of phoA, the structural gene for alkaline phosphatase, were observed. The deduced amino acid sequence showed that the mature PhoE protein is composed of 330 amino acid residues with a calculated molecular weight of 36,782. A number of 81 charged amino acids was found scattered throughout the protein while no large stretches of hydrophobic amino acids were observed. Hydrophobicity and hydration profiles of PhoE protein showed five pronounced hydrophilic maxima which are all located in the region from the amino terminus to residue 212. When the deduced amino acid sequence of PhoE protein was compared with the established sequence of the OmpF pore protein, a number of 210 identical residues was found. Some aspects of the structure-function relationship of PhoE protein are discussed in view of the hydrophobicity and hydration profiles, and the homology between PhoE protein and OmpF protein.

Prediction of secondary structural elements in the phosphatidylcholine-transfer protein from bovine liver

Secondary structural elements of the phosphatidylcholine-transfer protein from bovine liver have been predicted from its primary structure with the aid of two computerized methods. The predicted alpha-helix and beta-strand content have been compared with the values derived from circular dichroism spectra. The hydrophobicity profile (Rose plot) of the protein indicated that the supposed lipid-binding site occurs in the most hydrophobic region. The predicted secondary structural elements have been folded in a tentative model of the protein molecule according to its hydrophobicity profile.