Minimalistic System Research Articles

Interfacial Proton Diffusion

Lateral diffusion along the membrane represents the most efficient pathway for proton transport between membrane proteins. The recent observation that protons do not jump between ionizable residues but travel along interfacial water molecules (A. Springer et al., PNAS, 2011) suggested that membrane lipids are not required and that lateral proton diffusion may be observed adjacent to any hydrophobic surface. To test that prediction we measured surface proton diffusion in a minimalistic system at the water-decane interface. Although the interface did not offer any proton binding sites, lateral proton diffusion occurred. Fitting a mathematical model to the proton density in the observation spot suggested that proton diffusion was decoupled from bulk at low buffer capacity. At higher aqueous buffer concentrations and in heavy water, proton bulk diffusion became more important. This proves that the retarded proton surface to bulk release is (i) a fundamental property of the boundary between hydrophobic and hydrophilic phases, and (ii) independent on the presence of specific lipids or amino acids.

Testing the Structural Mechanism of Transmembrane Translocation using De-Novo Designed Soft-Metal Transporters with Inverted Dual Topology

Recent crystallographic discoveries show that surprisingly diverse transmembrane transporters share a very similar topology composed of pseudo-symmetric inverted dual subunits. So, a common structural mechanism may govern the divers translocation. For instance, alternate frustration of the pseudo-symmetry can thought to be the underlying principle that governs the structural interconversion that results in alternate access of substrates. Here, to test the generation of transport function by a universal mechanism, we have employed a de-novo design approach to achieve a soft metal translocation function in a minimalist system. An anti-parallel homo-tetrameric bundle of 25-residue transmembrane helices was designed to adopt soft metal chelation in a pseudo inverted symmetry context. Vesicle-reconstituted de-novo peptide shows transport activity specific for soft metal ion Zn2+. Also, the protein structure and chelation, as well as its tetrameric arrangement, gazed by UV-Vis, circular dichroism, analytical ultra-centrifugation, NMR and x-ray diffraction in a micellar context is consistent with the design. Together, these results are in agreement with transport via alternate frustration of internal symmetry.View Large Image | View Hi-Res Image | Download PowerPoint Slide

Sustainable community waste collection in Karachi, Pakistan

Low-income communities residing in squatter settlements usually develop their own services through self-help efforts. Such schemes include solid waste disposal, with the aim of placing household and other kinds of waste outside the locality from where it can be removed by municipal authorities. This minimalist system ensures cleanliness and basic upkeep in the community area. The system normally utilises a sweeper and basic waste-collection tools such as a wheelbarrow improvised for waste collection, hand tools and collection bins used by households for routine collection. A community mobilisation effort is required for the efficient working of such a system. In two low-income communities in Karachi, this approach was applied by a local non-government organisation (NGO), the Association for Protection of Environment (APE), in 1996. After providing continuous professional support for three years with the objective of acting as a catalyst, APE trained several members of the local community-based organisation (CBO) to manage and run the project on an independent basis. This paper provides an account of the approach and the system that evolved from it. After withdrawal of the NGO in 2000, the project has been working successfully under the supervision of the local CBO and area youth. This paper presents the lessons learned from the process of empowering communities to develop their own internal service systems. It addresses the issues that are vital in ensuring the sustainability of such attempts in urban lower-income localities.

A novel horse α-defensin: gene transcription, recombinant expression and characterization of the structure and function

Defensins are a predominant class of antimicrobial peptides, which act as endogenous antibiotics. Defensins are classified into three distinct sub-families: theta-, beta-, and alpha-defensins. Synthesis of alpha-defensin has been confirmed only in primates and glires to date and is presumably unique for a few tissues, including neutrophils and Paneth cells of the small intestine. Antimicrobial activities of these peptides were shown against a wide variety of microbes including bacteria, fungi, viruses and protozoan parasites. In the present study, we report the characterization of the equine alpha-defensin DEFA (defensin alpha) 1. Transcription analysis revealed that the transcript of the gene is present in the small intestine only. An alignment with known alpha-defensins from primates and glires displayed a homology with Paneth-cell-specific alpha-defensins. DEFA1 was recombinantly expressed in Escherichia coli and subsequently analysed structurally by CD and molecular modelling. To examine the antimicrobial properties, a radial diffusion assay was performed with 12 different micro-organisms and the LD90 (lethal dose killing > or =90% of target organism) and MBC (minimal bactericidal concentration) values were examined. DEFA1 showed an antimicrobial activity against different Gram-positive and Gram-negative bacteria and against the yeast Candida albicans. Using viable bacteria in combination with a membrane-impermeable fluorescent dye, as well as depolarization of liposomes as a minimalistic system, it became evident that membrane permeabilization is at least an essential part of the peptide's mode of action.

A designed beta-hairpin peptide for molecular recognition of ATP in water.

A designed 12-residue beta-hairpin peptide with a diagonal tryptophan (Trp) pair was shown to bind ATP in water through a combination of aromatic and electrostatic interactions. The affinity for ATP was 5800 M-1 (DeltaG approximately -5.0 kcal/mol), a remarkable affinity for a short, structured peptide in water, consisting of entirely natural amino acid residues. Proton NMR measurements indicate that the adenine ring of the nucleotide is intercalated between the diagonal tryptophans in the bound state. Delineation of the contributions to ATP binding to the hairpin suggest that aromatic interactions contribute approximately -1.8 kcal/mol, while individual electrostatic interactions involving the ATP phosphates and positively charged side chains of the hairpin contribute approximately -1 kcal/mol each. The designed beta-hairpin receptor presents a novel minimalist system to investigate the energetic contributions to protein-nucleic acid recognition through the surface of a beta-sheet.

BRISK: a portable and flexible distributed instrumentation system

Researchers and practitioners in the area of parallel and distributed computing have been lacking a portable, flexible and robust distributed instrumentation system. This paper presents the reference implementation of Baseline Reduced Instrumentation System Kernel (BRISK). BRISK was developed as a part of a realtime system instrumentation and performance visualization project. The design is based on a simple distributed instrumentation system model for flexibility and extensibility. The basic implementation poses minimalistic system requirements and achieves high performance. The paper also shows evaluations of BRISK on both basic and advanced configurations. The first evaluation emphasizes local, simple performance metrics; and the second highlights aggregate performance, built-in clock synchronization and dynamic on-line sorting. Copyright © 2000 John Wiley & Sons, Ltd.