Atomic and residue hydrophilicity in the context of folded protein structures

Water-protein interactions drive protein folding, stabilize the folded structure, and influence molecular recognition and catalysis. We analyzed the closest protein contacts of 10,837 water molecules in crystallographic structures to define a specific hydrophilicity scale reflecting specific rather than bulk solvent interactions. The tendencies of different atom and residue types to be the nearest protein neighbors of bound water molecules correlated with other hydrophobicity scales, verified the relevance of crystallographically determined water positions, and provided a direct experimental measure of water affinity in the context of the folded protein. This specific hydrophilicity was highly correlated with hydrogen-bonding capacity, and correlated better with experimental than computationally derived measures of partitioning between aqueous and organic phases. Atoms with related chemistry clustered with respect to the number of bound water molecules. Neutral and negatively charged oxygen atoms were the most hydrophilic, followed by positively-charged then neutral nitrogen atoms, followed by carbon and sulfur atoms. Agreement between observed side-chain specific hydrophilicity values and values derived from the atomic hydrophilicity scale showed that hydrophilicity values can be synthesized for different functional groups, such as unusual side or main chains, discontinuous epitopes, and drug molecules. Two methods of atomic hydrophilicity analysis provided a measure of complementarity in the interfaces of trypsin:pancreatic trypsin inhibitor and HIV protease:U-75875 inhibitor complexes. © 1995 Wiley-Liss, Inc.     

The SEA module: a new extracellular domain associated with O-glycosylation.

Using a variety of homology search methods and multiple alignments, a new extracellular module was identified in (1) agrin, (2) enterokinase, (3) a 63-kDa sea urchin sperm protein, (4) perlecan, (5) the breast cancer marker MUCI (episialin), (6) the cell surface antigen 114/A10, and (7/8) two functionally uncharacterized, probably extracellular, Caenorhabditis elegans proteins. Despite the functional diversity of these adhesive proteins, a common denominator seems to be their existence in heavily glycosylated environments. In addition, the better characterized proteins mentioned above contain all O-glycosidic-linked carbohydrates such as heparan sulfate that contribute considerably to their molecular masses. The common module might regulate or assist binding to neighboring carbohydrate moieties.     

The distribution of alpha-helix propensity along the polypeptide chain is not conserved in proteins from the same family.

We address the question of whether the distribution of secondary structure propensities of the residues along the polypeptide chain (denominated here as secondary structure profiles) is conserved in proteins throughout evolution, for the particular case of alpha-helices. We have analyzed by CD the conformation of peptides corresponding to the five alpha-helices of two alpha/beta parallel proteins (ComA and Ara). The large alpha-helical population of peptide ComA-4 detected by CD in aqueous solution has been confirmed by NMR. These proteins are members of the CheY and P21-ras families, respectively, which have been studied previously in the same way (Muñoz V, Jiménez MA, Rico M, Serrano L, 1995, J Mol Biol 245:275-296). Comparison of the helical content of equivalent peptides reveals that protein alpha-helix propensity profiles are not conserved. Some equivalent peptides show very different helical populations in solution and this is especially evident in very divergent proteins (ComA and CheY). However, all the peptides analyzed so far adopted an important population of helical conformations in the presence of 30% trifluoroethanol, indicating that there could be a conserved minimal requirement for helical propensity.     

Mating type differentiation in tetrahymena thermophila: Characterization of the delayed refeeding effect and its implications concerning intranuclear coordination

Mating type determination in Tetrahymena thermophila involves developmentally programmed, heritable alterations of the macronucleus, localized to the mtd locus. This determination can be predictably controlled by the environmental conditions during macronuclear development, eg, temperature and time of refeeding. In this article we have further characterized the effects of delayed refeeding on mating type determination, as revealed by the frequency of mating types among the progeny of a cross. Our results show that 1) the magnitude of this starvation effect decreases with temperature of conjugation and becomes undetectable at 18°C; 2) starvation during the interval 14 to 22 hr (after conjugation is induced at 30°C) is a necessary and sufficient condition for the induction of starvation effects; 3) relative mating type frequencies vary monotonically with nutrient concentration present during this critical period; and 4) sister macronuclei, developing under starvation conditions in the same cytoplasm, differentiate majority mating types characteristic of early or late refeeding; sister macronuclei show no apparent correlation with each other. On the basis of our observations on early and late refed cells, we propose that the composition of the newly developed macronucleus is the outcome of two key events: 1) mating type determination at the mtd locus and 2) differential molecular cloning of generally one or two autonomously replicating fragments (ARFs) of the macronuclear DNA bearing the mtd locus.     

Theoretical studies on the modes of binding of some of the derivatives of d-mannose to concanavalin A

The possible modes of binding for $\text{methyl}\text{-α-}\text{d}\text{-mannopyranoside}$, $\text{methyl}\text{-β-}\text{d}\text{-mannopyranoside}$, $\text{2-O-}\text{methyl}\text{-α-}\text{d}\text{-mannopyranoside}$, $\text{methyl-2-O-methyl}\text{-α-}\text{d}\text{-mannopyranoside}$ and $\text{methyl}\text{-α-}\text{d}\text{-N-}\text{acetylmannosamine}$ to concanavalin A have been investigated using theoretical methods. All these sugars, except $\text{methyl}\text{-α-}\text{d}\text{-N-}\text{acetylmannosamine}$, reach the active site of concanavalin A with a highly restricted number of binding orientations. Present investigations suggest that the failure of $\text{methyl}\text{-α-}\text{d}\text{-N-}\text{acetylmannosamine}$ to bind to concanavalin A is not so much due to steric factors as to repulsive electrostatic interactions. $\text{Methyl}\text{-2-O-}\text{methyl}\text{-α-}\text{d}\text{-mannopyranoside}$ can bind to concanavalin A in one mode whereas the other sugars can bind in more than one mode. The high potency of $\text{methyl}\text{-α-}\text{d}\text{-mannopyranoside}$ over $\text{methyl}\text{-β-}\text{d}\text{-mannopyranoside}$ is mainly due to the possibility of hydrophobic interactions of the α-methoxy group with Leu(99) or Tyr(100) and also due to the possibility of formation of better and more hydrogen bonds with the protein. A comparison of these data with those for the d-glucopyranosides suggests that the change of the hydroxyl at the C-2 atom from equatorial to axial orientation increases the stereochemically allowed region as well as the possible binding modes. From these studies it is also suggested that the overall shape of the oligosaccharides rather than the terminal or internal mannose alone affects the binding potency of saccharides to concanavalin A.     

Theoretical studies on the modes of binding of some of the derivatives of d-mannose to concanavalin A

The possible modes of binding for methyl-α-d-mannopyranoside, methyl-β-d-mannopyranoside, 2-O-methyl-α-d-mannopyranoside, methyl-2-O-methyl-α-d-mannopyranoside and methyl-α-d-N-acetylmannosamine to concanavalin A have been investigated using theoretical methods. All these sugars, except methyl-α-d-N-acetylmannosamine, reach the active site of concanavalin A with a highly restricted number of binding orientations. Present investigations suggest that the failure of methyl-α-d-N-acetylmannosamine to bind to concanavalin A is not so much due to steric factors as to repulsive electrostatic interactions. Methyl-2-O-methyl-α-d-mannopyranoside can bind to concanavalin A in one mode whereas the other sugars can bind in more than one mode. The high potency of methyl-α-d-mannopyranoside over methyl-β-d-mannopyranoside is mainly due to the possibility of hydrophobic interactions of the α-methoxy group with Leu(99) or Tyr(100) and also due to the possibility of formation of better and more hydrogen bonds with the protein. A comparison of these data with those for the d-glucopyranosides suggests that the change of the hydroxyl at the C-2 atom from equatorial to axial orientation increases the stereochemically allowed region as well as the possible binding modes. From these studies it is also suggested that the overall shape of the oligosaccharides rather than the terminal or internal mannose alone affects the binding potency of saccharides to concanavalin A.     

Cartilage type IX collagen is cross-linked by hydroxypyridinium residues

Type IX collagen, a recently discovered, unusual protein of cartilage, has a segmented triple-helical structure containing interchain disulfides. Its polymeric form and function are unknown. When prepared by pepsin from bovine articular cartilage, type IX collagen was found to contain a high concentration of hydroxypyridinium cross-links, similar to that in type II collagen. Fluorescence spectroscopy located the hydroxylysyl pyridinoline and lysyl pyridinoline cross-linking residues exclusively in the high-molecular-weight collagen fraction, from which they were recovered predominantly in a single CNBr-derived peptide. The results point to a structural role for type IX collagen in cartilage matrix, possibly as an adhesion material to type II collagen fibrils.     

Purification to apparent homogeneity of a thymocyte specific growth factor from calf thymus

A thymic peptide previously found to recruit thymocytes from G1 into S phase has been purified from a crude thymic extract by subsequent steps of gel exclusion chromatography and reverse phase high performance liquid chromatography (HPLC). The purified material, which appeared homogeneous on thin-layer chromatography and HPLC, stimulated the DNA synthesis of cultured guinea pig thymocytes in a nanomolar concentration range. The amino acid composition revealed a high content of acidic amino acids and no apparent homology to previously defined growth factors and thymus differentiation hormones.     

Radiation inactivation of membrane proteins: Molecular weight estimates in situ and after Triton X-100 solubilization

Target size analysis by radiation inactivation is widely used for molecular weight determination of membrane enzymes and receptors in situ without the need for prior solubilization or purification. However, since most molecular weight data available in the literature on membrane proteins involve the use of detergents for solubilization, the target sizes of membrane proteins in situ and after solubilization by detergent treatment have been compared. Using data from the literature and personal results, three different types of behavior of membrane proteins in presence of detergents were found: (i) uncoupling of subunits (electric eel acetylcholinesterase, placental steroid sulfatase, and human nonspecific β-glucosidase); (ii) coupling of protein molecules (mouse liver neuraminidase, and rat liver insulin receptor regulatory component); and (iii) no major change in quaternary structure (rat liver insulin receptor, kidney γ-glutamyltransferase, asialoglycoprotein receptor, insulin degrading enzyme, and human leucocyte neuraminidase). For all these proteins, there is a statistically significant increase in target size of about 24% over the value obtained in situ without detergent. A relatively large body of literature data involving a variety of membrane proteins, membrane types, and irradiation conditions (electron accelerators or ⁶⁰Co sources, and proteins irradiated in lyophilized form or frozen solution) was examined, and it was concluded that target sizes of membrane proteins, irradiated in the presence of Triton X-100, should be diminished by a factor of about 24% to obtain the molecular weight value.     

Molecular and cytological characteristics of nuclear DNA and chromatin for angiosperm systematics: DNA diversification in the evolution of four orchids

The species- and genus-specific DNA content, average base composition of nuclear DNA, presence or absence of satellite DNA, the percentage of heterochromatin and other characteristics of nuclear DNA and nuclear structure allow to deduce the molecular changes which accompanied, or more probably caused, cladogenesis in the orchids studied. It is suggested that saltatory replication (generative amplification) of certain DNA sequenes, diversification of reiterated DNA sequences, and loss of DNA play an important role in the evolution of orchids.—The relationship between changes of genome composition and of nuclear structure and ultrastructure is discussed on the basis of cot curves, heterochromatin staining with Giemsa (C banding), electron microscopy of nuclei, and molecular hybridization in situ.Some aspects of this paper have been presented at the Helsinki Chromosome Conference, August 1977 (Nagl & Capesius 1977).