Plasma protein map: an update by microsequencing.

The reference plasma protein map, obtained with immobilized pH gradients in the first dimension of two-dimensional electrophoresis, is presented. By microsequencing, more than 40 polypeptide chains were identified. The new polypeptides and previously known proteins are listed in a table and labeled on the protein map, thus providing an update of the human plasma two-dimensional gel database.     

Two-dimensional gel electrophoresis, protein electroblotting and microsequencing: a direct link between proteins and genes.

We have used two-dimensional gel electrophoresis as a general "preparative" method to purify proteins for microsequencing analysis. In the first experiments, proteins derived from a total extract of Nicotiana tabacum leaf tissue were directly blotted from the gel onto poly(4-vinyl-N-methylpyridinium iodide)-coated glass fiber sheets. The major spots were excised and subjected to NH2-terminal sequence analysis, which made it possible to identify five of the eight selected proteins, while two more were recognized by generated internal sequences. In a second set of experiments, proteins of human origin were separated on multiple two-dimensional gels and the Coomassie Brilliant Blue-stained spots were excised from the gels. The combined spots were re-eluted and concentrated in a new gel and blotted on Immobilon. They were fragmented by in situ proteolysis and the generated peptides were separated by reverse phase-high performance liquid chromatography and sequenced. At the average, the internal sequences that were obtained covered 35 residues per protein and allowed unambiguous identification of 13 of the 23 proteins analyzed so far. The sequence information obtained of the unidentified proteins is sufficient for further cloning. These results demonstrate that systematic sequence analysis of the major proteins seen in two-dimensional gels is within the reach of current technologies. This offers a unique opportunity to link information contained in protein databases with known or forthcoming DNA sequence data.     

Human liver protein map: a reference database established by microsequencing and gel comparison.

This publication establishes a reference human liver protein map obtained with immobilized pH gradients. By microsequencing, 57 spots or 42 polypeptide chains were identified. By protein map comparison and matching (liver, red blood cell and plasma sample maps), 8 additional proteins were identified. The new polypeptides and previously known proteins are listed in a table and/or labeled on the protein map, thus providing a human liver two-dimensional gel database. This reference map can be used to identify protein spots on other samples such as rectal cancer biopsies.     

Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase

The identification of hot spots, i.e., binding regions that contribute substantially to the free energy of ligand binding, is a critical step for structure-based drug design. Here we present the application of two fragment-based methods to the detection of hot spots for DJ-1 and glucocerebrosidase (GCase), targets for the development of therapeutics for Parkinson’s and Gaucher’s diseases, respectively. While the structures of these two proteins are known, binding information is lacking. In this study we employ the experimental multiple solvent crystal structures (MSCS) method and computational fragment mapping (FTMap) to identify regions suitable for the development of pharmacological chaperones for DJ-1 and GCase. Comparison of data derived via MSCS and FTMap also shows that FTMap, a computational method for the identification of fragment binding hot spots, is an accurate and robust alternative to the performance of expensive and difficult crystallographic experiments.     

2-carbethoxy-1,3-butadiene irontricarbonyl : chemical transformations and reactivity of the corresponding free dienes.

Chemical transformations on the 2-carbethoxy-1,3-butadiene irontricarbonyl complex were performed. The dienic and dienophilic reactivities of the corresponding free dienes are studied.     

Amino acids and peptides. XXXV. Synthesis of mouse metallothionein I. (2). Synthesis of a nonacosapeptide corresponding to N-terminal sequence 1-29 (beta-fragment) of mouse metallothionein I and related peptides and examination of their heavy metal-binding properties.

A nonacosapeptide corresponding to the N-terminal sequence 1-29 (beta-fragment) of mouse metallothionein I and related peptides were synthesized by the conventional solution method and their heavy metals (Cu2+, Cu+ and Cd2+)-binding properties were examined. The Cu(2+)- or Cu(+)-binding activities of various peptides were not greatly dependent on the peptide structure, so far as examined, as in the cases of N. crassa MT and A. bisporus MTs. On the contrary, the Cd(2+)-binding activities of these peptides were fairly structure-dependent.     

On the hypothetical protein F154 of the TTV1 virus/Thermoproteus Tenax. Part II: Synthesis of the trieicosapeptide,corresponding to the protein sequence 79–101

Summary For the identification of a protein predicted by DNA sequence analysis of the TTV1 virus from the archaebacteriumThermoproteus tenax, the trieicosapeptide H-Thr-Pro-Thr-Pro-Thr-Pro-Thr-Tyr-Asp-Ile-Thr-Tyr-Val-Val-Phe-Asp-Val-Thr-Pro-Ser-Pro-Thr-Pro-OH, corresponding to the protein fragment 79–101, was prepared by conventional methods of peptide synthesis. This sequence portion may possibly represent a suitable protein specific immunepitope.

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Zur Hypothese eines TTV1 Virus/Thermoproteus tenax F154-Proteins. Teil II: Synthese des Protein-fragments 79–101

Zusammenfassung Für den Nachweis der Expression des Proteins F154 — nach einer Sequenzanalyse des Genoms des TTV1 Virus im ArchaebakteriumThermoproteus tenax postuliert — wurde das Peptid H-Thr-Pro-Thr-Pro-Thr-Pro-Thr-Tyr-Asp-Ile-Thr-Tyr-Val-Val-Phe-Asp-Val-Thr-Pro-Ser-Pro-Thr-Pro-OH (Proteinfragment 79–101) mit Hilfe konventioneller Peptidsynthese hergestellt. Diese Peptidsequenz sollte ein geeignetes proteinspezifisches Immunepitop darstellen.

     

Conversion of a tyrosine kinase protein substrate to a high affinity ligand by ATP linkage

Protein kinases often show low affinity for their protein substrates, which makes it difficult to study kinase-substrate interactions. Here, we show using expressed protein ligation with the signaling protein Src that it is feasible to install a covalently linked ATP moiety into the tail of Src, generating a semisynthetic protein with a high affinity for its cognate tyrosine kinase, Csk. It is also established that this Src-ATP conjugate can be used to selectively pull down Csk from a complex protein mixture. This work outlines a general strategy for identifying an unknown kinase that is responsible for the phosphorylation of a protein substrate on a site of interest.     

Highly enantioselective oxidation of cis-cyclopropylmethanols to corresponding aldehydes catalyzed by chloroperoxidase.

Chloroperoxidase (CPO) catalyzes the enantioselective oxidation of cyclopropylmethanols, such as 2-methylcyclopropylmethanol, to cyclopropyl aldehydes using tert-butyl hydroperoxide as the terminal oxidant. In all cases, CPO oxidation of cis-cyclopropanes shows much higher enantioselectivity than with the trans isomers, although CPO gives similar catalytic activity on both isomers. This presents the first example for a heme enzyme that catalyzes the enantioselective oxidation of cyclopropylmethanols. This finding enables a novel route to the synthesis of optically active cyclopropane derivatives, which occur widely in natural products and compounds of pharmaceutical interest. In addition, chiral cyclopropane molecules may be useful model substrates to investigate reaction mechanisms of CPO and the related cytochromes P450.     

Mechanism for the reduction of ketones to the corresponding alcohols using supercritical 2-propanol

The mechanism for the reduction of ketones into the corresponding alcohols using supercritical 2-propanol under non-catalytic conditions was investigated. The studies of the kinetic-isotope effect and isotopic-labeling for the reduction of benzophenone and acetophenone were carried out using (CH₃)₂CD(OH), (CH₃)₂CH(OD), (CD₃)₂CH(OH), and (CD₃)₂CD(OD). It was clarified that the α- and hydroxyl hydrogens on 2-propanol, respectively, transfer to the carbonyl C and O in the rate-determining step. These isotope studies also suggested that this reaction proceeds via a six-membered cyclic transition state analogous to that of the Meerwein-Ponndorf-Verley reduction. The fact that Hammett's reaction constant for this reaction was low, i.e., ρ=0.33, and that the reduction of the prochiral ketones using optically active alcohols at supercritical or high temperature provided optically active products also supported the existence of a six-membered cyclic transition state.     

Binding free energy of several sterols to the N-terminal domain of Niemann-Pick C1-like 1 protein due to mutation: Molecular dynamics study

The membrane protein Niemann-Pick type C1-like 1 (NPC1L1) plays a central role in the absorption of cholesterol in the small intestine. Other sterols, notably vitamin E and vitamin K1 also utilize NPC1L1 as a membrane transporter even though other absorption paths exist. Many NPC1L1 mutations causing the disease due to poor transport of cholesterol are known. It is not clear at this moment if the same mutation can lead to reduced transport behavior with these vitamins. In this study, we have obtained the binding free energies of these two sterols using molecular dynamics simulation and compared these values with the cholesterol-binding free energy. The N-terminal domain (NTD) of the wild as well as the disease-causing two mutations, T61M and L110F, are used for this purpose. The result indicates that the mutations show reduced binding affinity compared to the wild except for the vitamin K1 in the T61M mutant, which has increased binding free energy. Also, we found the similarity of the key amino acids responsible for the change of free energy by mutation between T61M and L110F. At the same time, non-negligible differences exist also.