Protein folds and protein folding

The classification of protein folds is necessarily based on the structural elements that distinguish domains. Classification of protein domains consists of two problems: the partition of structures into domains and the classification of domains into sets of similar structures (or folds). Although similar topologies may arise by convergent evolution, the similarity of their respective folding pathways is unknown. The discovery and the characterization of the majority of protein folds will be followed by a similar enumeration of available protein folding pathways. Consequently, understanding the intricacies of structural domains is necessary to understanding their collective folding pathways. We review the current state of the art in the field of protein domain classification and discuss methods for the systematic and comprehensive study of protein folding across protein fold space via atomistic molecular dynamics simulation. Finally, we discuss our large-scale Dynameomics project, which includes simulations of representatives of all autonomous protein folds.     

Challenges in forming successful mixed matrix membranes with rigid polymeric materials

Mixed matrix materials comprised of molecular sieve domains embedded in processable polymer matrices have the potential to provide membranes with higher permselectivity and equivalent productivity compared to existing membrane materials. It has been shown that successful mixed matrix materials can be formed using relatively low glass transition (T_g) polymers that have a favorable interaction with the sieves. This article extends this earlier work to include the use of more practical rigid matrix polymers with high T_gs that can ultimately be used in forming high‐performance mixed matrix layers for composite membranes. Initial attempts to form mixed matrix materials based on high T_g polymers with a type 4A zeolite resulted in poor adhesion between the polymer and sieve. Correcting this problem was pursued in this study by forming the composite material close to the T_g of the polymer by addition of a plasticizer to match the matrix T_g with the solvent volatility. Forming the films at elevated temperatures presented substantial challenges, and this work discusses overcoming these challenges in detail. With some modifications in the film casting procedure, successful materials were achieved. Promising oxygen/nitrogen transport results are presented for these zeolite 4A–Matrimid®/plasticizer membranes, and this data compares favorably with predictions of the well‐known Maxwell model for composite systems. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 881–890, 2002     

Characterisation of a novel growth hormone variant comprising a thioether link between Cys182 and Cys189

A novel variant of recombinant human growth hormone (r-hGH), isolated from biopharmaceutical preparations produced in E. coli, was identified and characterised. This variant contains a nonreducible thioether bridge near the C terminus between Cys182 and Cys189 and was characterised using various analytical techniques. As previous work by Cunningham and Wells (1993) highlighted the involvement of several residues in this part of the sequence in the binding and affinity of the molecule to its receptor, the presence of this modified intramolecular link may have important implications with regard to the biological behaviour of the molecule. Furthermore, as the conversion of a disulfide into a thioether was previously reported for a therapeutic monoclonal antibody (Tous et al., 2005), this may imply that disulfide bridges located in this part of the molecule have a generic susceptibility to thioether formation. This in turn is relevant to the biopharmaceutical industry for monitoring the integrity of disulfide bridges near the protein C terminus. The present study exhibits a state of the art physicochemical investigation for the unequivocal elucidation of a novel structure involving peptide mapping with mass spectrometry and de novo peptide sequencing. Changes in the higher order structure of the molecule were highlighted by near UV circular dichroism and molecular modelling.     

Plant sterol-C24-methyl transferases: Different profiles of tobacco transformed with SMT1 or SMT2

Higher plant cells contain a mixture of 24-desmethyl, 24-methyl(ene), and 24-ethyl(idene) sterols in given proportions according to species but also to cell type. As a first step to investigate the function of such sterol compositions in the physiology of a plant, we have illustrated in the present work the coexistence of two distinct (S)-adenosyl-l-methionine sterol-C24-methyltransferases (SMT) in transgenic Nicotiana tabacum L. Indeed, modulation of the expression of the tobacco gene SMT1-1, which encodes a cycloartenol-C24-methyltransferase, results in variations of the proportion of cycloartenol and a concomitant effect on the proportion of 24-ethyl sterols. Overexpression in tobacco of the Arabidopsis thaliana (L.) Heynh. gene SMT2-1 which encodes a 24-methylene lophenol-C24¹-methyltransferase, results in a dramatic modification of the ratio of 24-methyl cholesterol to sitosterol associated with a reduced growth, a topic discussed in the present work. Based in part on a paper presented at the Steroid Symposium of the American Oil Chemists' Society Annual Meeting, Orlando, Florida, May 1999.     

Resurgence of Emerald Shiners Notropis atherinoides in Lake Huron's Main Basin

Emerald shiners Notropis atherinoides were formerly common in Lakes Huron and Michigan, but declined during the 1960s as the exotic alewife Alosa pseudoharengus proliferated. The Lake Huron emerald shiner population was chronically depressed through 2004; however, we detected resurgence in emerald shiner density and biomass in Lake Huron during acoustic and midwater trawl surveys conducted during 2004–2006. Emerald shiners were not found during 2004, but by 2006 main basin density exceeded 500 fish/ha, biomass estimates exceeded 0.5 kg/ha, and emerald shiners contributed more to pelagic biomass than alewives or rainbow smelt Osmerus mordax. Length frequency distributions suggested that increased density was the result of two consecutive strong year classes in 2005 and 2006. Emerald shiner distributions also expanded from a focus in western Lake Huron in 2005 to a lakewide distribution in 2006. Emerald shiners occurred offshore, but were nearly always associated with epilimnetic surface waters warmer than 19°C. Resurgence of emerald shiners was likely a consequence of reduced alewife abundance, as they declined concurrently with alewife proliferation during the early 1960s. Return of this species may benefit native nearshore piscivores; however, benefits to Pacific salmonids Oncorhynchus spp. are uncertain because emerald shiners are smaller and still less abundant than historically important prey species, and they may be thermally segregated from salmonines.     

Gold Nanoprisms as Optoacoustic Signal Nanoamplifiers for In Vivo Bioimaging of Gastrointestinal Cancers

Early detection of cancer greatly increases the chances of a simpler and more effective treatment. Traditional imaging techniques are often limited by shallow penetration, low sensitivity, low specificity, poor spatial resolution or the use of ionizing radiation. Hybrid modalities, like optoacoustic imaging, an emerging molecular imaging modality, contribute to improving most of these limitations. However, this imaging method is hindered by relatively low signal contrast. Here, gold nanoprisms (AuNPrs) are used as signal amplifiers in multispectral optoacoustic tomography (MSOT) to visualize gastrointestinal cancer. PEGylated AuNPrs are successfully internalized by HT‐29 gastrointestinal cancer cells in vitro. Moreover, the particles show good biocompatibility and exhibit a surface plasmon band centered at 830 nm, a suitable wavelength for optoacoustic imaging purposes. These findings extend well to an in vivo setting, in which mice are injected with PEGylated AuNPrs in order to visualize tumor angiogenesis in gastrointestinal cancer cells. Overall, both our in vitro and in vivo results show that PEGylated AuNPrs have the capacity to penetrate tumors and provide a high‐resolution signal amplifier for optoacoustic imaging. The combination of PEGylated AuNPrs and MSOT represents a significant advance for the in vivo imaging of cancers.     

Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations

The goal of Dynameomics is to perform atomistic molecular dynamics (MD) simulations of representative proteins from all known folds in explicit water in their native state and along their thermal unfolding pathways. Here we present 188-fold representatives and their native state simulations and analyses. These 188 targets represent 67% of all the structures in the Protein Data Bank. The behavior of several specific targets is highlighted to illustrate general properties in the full dataset and to demonstrate the role of MD in understanding protein function and stability. As an example of what can be learned from mining the Dynameomics database, we identified a protein fold with heightened localized dynamics. In one member of this fold family, the motion affects the exposure of its phosphorylation site and acts as an entropy sink to offset another portion of the protein that is relatively immobile in order to present a consistent interface for protein docking. In another member of this family, a polymorphism in the highly mobile region leads to a host of disease phenotypes. We have constructed a web site to provide access to a novel hybrid relational/multidimensional database (described in the succeeding two papers) to view and interrogate simulations of the top 30 targets: http://www.dynameomics.org. The Dynameomics database, currently the largest collection of protein simulations and protein structures in the world, should also be useful for determining the rules governing protein folding and kinetic stability, which should aid in deciphering genomic information and for protein engineering and design.     

MARE-1 in Milan: Status and Perspectives

The international project MARE (Microcalorimeter Array for a Rhenium Experiment) aims at the direct and calorimetric measurement of the electron neutrino mass with sub-eV sensitivity. Although the baseline of the MARE project consists in a large array of rhenium based thermal detectors, a different option for the isotope is also being considered. The different option is ¹⁶³Ho. The potential of using ¹⁸⁷Re for a calorimetric neutrino mass experiment has been already demonstrated. On the contrary, no calorimetric spectrum of ¹⁶³Ho has been so far measured with the precision required to set a useful limit on the neutrino mass. The first phase of the project (MARE-1) is a collection of activities with the aim of sorting out both the best isotope and the most suited detector technology to be used for the final experiment. One of the MARE-1 activities is carried out in Milan by the group of Milano–Bicocca in collaboration with NASA/GSFC and Wisconsin groups. The Milan MARE-1 arrays are based on semiconductor thermistors, provided by the NASA/GSFC group, with dielectric silver perrhenate absorbers, AgReO₄. The experiment, which is presently being assembled, is designed to host up to 8 arrays. With 288 detectors, a sensitivity of 3 eV at 90% CL on the neutrino mass can be reached within 3 years. This contribution gives an outlook for the MARE activities for the active isotope selection. In this contribution the status and the perspectives of the MARE-1 in Milan are also reported.     

Petroleum well drilling monitoring through cutting image analysis and artificial intelligence techniques

Petroleum well drilling monitoring has become an important tool for detecting and preventing problems during the well drilling process. In this paper, we propose to assist the drilling process by analyzing the cutting images at the vibrating shake shaker, in which different concentrations of cuttings can indicate possible problems, such as the collapse of the well borehole walls. In such a way, we present here an innovative computer vision system composed by a real time cutting volume estimator addressed by support vector regression. As far we know, we are the first to propose the petroleum well drilling monitoring by cutting image analysis. We also applied a collection of supervised classifiers for cutting volume classification.