Fluorescent carbazole-derived α-amino acids: structural mimics of tryptophan

Fluorescent tags are commonly used for imaging of proteins and peptides during biological events; however, the large size of dyes can disrupt protein structure and function, and typically require the use of a chemical spacer. Herein, we report the synthesis of a new class of fluorescent unnatural α-amino acid, containing carbazole side-chains designed to mimic l-tryptophan and thus, readily incorporated into peptides. The amino acids were constructed using a Negishi cross-coupling reaction as the key step and exhibited strong fluorescent emission, with high quantum yields in both organic solvents and water. Compatible with solid phase peptide synthesis, the carbazole amino acids were used to replace tryptophan in a β-hairpin model peptide and shown to be a close structural mimic with retention of conformation. They were also found to be effective fluorescent molecular reporters for biological events. Incorporation into a proline-rich ligand of the WW domain protein demonstrated that the fluorescent properties of a carbazole amino acid could be used to measure the protein-protein binding interaction of this important biological signalling process.

Sublithospheric diamond ages and the supercontinent cycle

Subduction related to the ancient supercontinent cycle is poorly constrained by mantle samples. Sublithospheric diamond crystallization records the release of melts from subducting oceanic lithosphere at 300-700 km depths1,2 and is especially suited to tracking the timing and effects of deep mantle processes on supercontinents. Here we show that four isotope systems (Rb-Sr, Sm-Nd, U-Pb and Re-Os) applied to Fe-sulfide and CaSiO3 inclusions within 13 sublithospheric diamonds from Juína (Brazil) and Kankan (Guinea) give broadly overlapping crystallization ages from around 450 to 650 million years ago. The intracratonic location of the diamond deposits on Gondwana and the ages, initial isotopic ratios, and trace element content of the inclusions indicate formation from a peri-Gondwanan subduction system. Preservation of these Neoproterozoic-Palaeozoic sublithospheric diamonds beneath Gondwana until its Cretaceous breakup, coupled with majorite geobarometry3,4, suggests that they accreted to and were retained in the lithospheric keel for more than 300 Myr during supercontinent migration. We propose that this process of lithosphere growth-with diamonds attached to the supercontinent keel by the diapiric uprise of depleted buoyant material and pieces of slab crust-could have enhanced supercontinent stability.

Near-Field Probing of Optical Superchirality with Plasmonic Circularly Polarized Luminescence for Enhanced Bio-Detection

Nanophotonic platforms in theory uniquely enable < femtomoles of chiral biological and pharmaceutical molecules to be detected, through the highly localized changes in the chiral asymmetries of the near fields that they induce. However, current chiral nanophotonic based strategies are intrinsically limited because they rely on far field optical measurements that are sensitive to a much larger near field volume, than that influenced by the chiral molecules. Consequently, they depend on detecting small changes in far field optical response restricting detection sensitivities. Here, we exploit an intriguing phenomenon, plasmonic circularly polarized luminescence (PCPL), which is an incisive local probe of near field chirality. This allows the chiral detection of monolayer quantities of a de novo designed peptide, which is not achieved with a far field response. Our work demonstrates that by leveraging the capabilities of nanophotonic platforms with the near field sensitivity of PCPL, optimal biomolecular detection performance can be achieved, opening new avenues for nanometrology.

Comment on "Discovery of davemaoite, CaSiO3-perovskite, as a mineral from the lower mantle"

Tschauner et al. (Reports, 11 November 2021, p. 891) present evidence that diamond GRR-1507 formed in the lower mantle. Instead, the data support a much shallower origin in cold, subcratonic lithospheric mantle. X-ray diffraction data are well matched to phases common in microinclusion-bearing lithospheric diamonds. The calculated bulk inclusion composition is too imprecise to uniquely confirm CaSiO3 stoichiometry and is equally consistent with inclusions observed in other lithospheric diamonds.

How Coiled-Coil Assemblies Accommodate Multiple Aromatic Residues

Rational protein design requires understanding the contribution of each amino acid to a targeted protein fold. For a subset of protein structures, namely, α-helical coiled coils (CCs), knowledge is sufficiently advanced to allow the rational de novo design of many structures, including entirely new protein folds. Current CC design rules center on using aliphatic hydrophobic residues predominantly to drive the folding and assembly of amphipathic α helices. The consequences of using aromatic residues-which would be useful for introducing structural probes, and binding and catalytic functionalities-into these interfaces are not understood. There are specific examples of designed CCs containing such aromatic residues, e.g., phenylalanine-rich sequences, and the use of polar aromatic residues to make buried hydrogen-bond networks. However, it is not known generally if sequences rich in tyrosine can form CCs, or what CC assemblies these would lead to. Here, we explore tyrosine-rich sequences in a general CC-forming background and resolve new CC structures. In one of these, an antiparallel tetramer, the tyrosine residues are solvent accessible and pack at the interface between the core and the surface. In another more complex structure, the residues are buried and form an extended hydrogen-bond network.

β-Turn Mimics by Chemical Ligation

We report a simple reductive amination protocol to ligate two peptides, while simultaneously installing a β-turn mimic at the ligation junction. This strategy uses commercially available materials, mild chemical conditions, and a chemoselective ligation reaction of unprotected peptide substrates accessed through standard solid phase methods. This system was implemented in a designed β-hairpin system, and biophysical analysis demonstrates effective mimicry of the β-turn.

Applying graph theory to protein structures: an Atlas of coiled coils

Motivation

To understand protein structure, folding and function fully and to design proteins de novo reliably, we must learn from natural protein structures that have been characterized experimentally. The number of protein structures available is large and growing exponentially, which makes this task challenging. Indeed, computational resources are becoming increasingly important for classifying and analyzing this resource. Here, we use tools from graph theory to define an Atlas classification scheme for automatically categorizing certain protein substructures.

Results

Focusing on the α-helical coiled coils, which are ubiquitous protein-structure and protein-protein interaction motifs, we present a suite of computational resources designed for analyzing these assemblies. iSOCKET enables interactive analysis of side-chain packing within proteins to identify coiled coils automatically and with considerable user control. Applying a graph theory-based Atlas classification scheme to structures identified by iSOCKET gives the Atlas of Coiled Coils, a fully automated, updated overview of extant coiled coils. The utility of this approach is illustrated with the first formal classification of an emerging subclass of coiled coils called α-helical barrels. Furthermore, in the Atlas, the known coiled-coil universe is presented alongside a partial enumeration of the 'dark matter' of coiled-coil structures; i.e. those coiled-coil architectures that are theoretically possible but have not been observed to date, and thus present defined targets for protein design.

Availability and implementation

iSOCKET is available as part of the open-source GitHub repository associated with this work (https://github.com/woolfson-group/isocket). This repository also contains all the data generated when classifying the protein graphs. The Atlas of Coiled Coils is available at: http://coiledcoils.chm.bris.ac.uk/atlas/app.

Navigating the Structural Landscape of De Novo α-Helical Bundles

The association of amphipathic α helices in water leads to α-helical-bundle protein structures. However, the driving force for this-the hydrophobic effect-is not specific and does not define the number or the orientation of helices in the associated state. Rather, this is achieved through deeper sequence-to-structure relationships, which are increasingly being discerned. For example, for one structurally extreme but nevertheless ubiquitous class of bundle-the α-helical coiled coils-relationships have been established that discriminate between all-parallel dimers, trimers, and tetramers. Association states above this are known, as are antiparallel and mixed arrangements of the helices. However, these alternative states are less well understood. Here, we describe a synthetic-peptide system that switches between parallel hexamers and various up-down-up-down tetramers in response to single-amino-acid changes and solution conditions. The main accessible states of each peptide variant are characterized fully in solution and, in most cases, to high resolution with X-ray crystal structures. Analysis and inspection of these structures helps rationalize the different states formed. This navigation of the structural landscape of α-helical coiled coils above the dimers and trimers that dominate in nature has allowed us to design rationally a well-defined and hyperstable antiparallel coiled-coil tetramer (apCC-Tet). This robust de novo protein provides another scaffold for further structural and functional designs in protein engineering and synthetic biology.

Hydra Mesoglea Proteome Identifies Thrombospondin as a Conserved Component Active in Head Organizer Restriction

Thrombospondins (TSPs) are multidomain glycoproteins with complex matricellular functions in tissue homeostasis and remodeling. We describe a novel role of TSP as a Wnt signaling target in the basal eumetazoan Hydra. Proteome analysis identified Hydra magnipapillata TSP (HmTSP) as a major component of the cnidarian mesoglea. In general, the domain organization of cnidarian TSPs is related to the pentameric TSPs of bilaterians, and in phylogenetic analyses cnidarian TSPs formed a separate clade of high sequence diversity. HmTSP expression in polyps was restricted to the hypostomal tip and tentacle bases that harbor Wnt-regulated organizer tissues. In the hypostome, HmTSP- and Wnt3-expressing cells were identical or in close vicinity to each other, and regions of ectopic tentacle formation induced by pharmacological β-Catenin activation (Alsterpaullone) corresponded to foci of HmTSP expression. Chromatin immunoprecipitation (ChIP) confirmed binding of Hydra TCF to conserved elements in the HmTSP promotor region. Accordingly, β-Catenin knockdown by siRNAs reduced normal HmTSP expression at the head organizer. In contrast, knockdown of HmTSP expression led to increased numbers of ectopic organizers in Alsterpaullone-treated animals, indicating a negative regulatory function. Our data suggest an unexpected role for HmTSP as a feedback inhibitor of Wnt signaling during Hydra body axis patterning and maintenance.

ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design

Motivation

The rational design of biomolecules is becoming a reality. However, further computational tools are needed to facilitate and accelerate this, and to make it accessible to more users.

Results

Here we introduce ISAMBARD, a tool for structural analysis, model building and rational design of biomolecules. ISAMBARD is open-source, modular, computationally scalable and intuitive to use. These features allow non-experts to explore biomolecular design in silico. ISAMBARD addresses a standing issue in protein design, namely, how to introduce backbone variability in a controlled manner. This is achieved through the generalization of tools for parametric modelling, describing the overall shape of proteins geometrically, and without input from experimentally determined structures. This will allow backbone conformations for entire folds and assemblies not observed in nature to be generated de novo, that is, to access the ‘dark matter of protein-fold space’. We anticipate that ISAMBARD will find broad applications in biomolecular design, biotechnology and synthetic biology.

Availability and implementation

A current stable build can be downloaded from the python package index (https://pypi.python.org/pypi/isambard/) with development builds available on GitHub (https://github.com/woolfson-group/) along with documentation, tutorial material and all the scripts used to generate the data described in this paper.

Supplementary information

Supplementary data are available at Bioinformatics online.

Membrane-spanning α-helical barrels as tractable protein-design targets

The rational (de novo) design of membrane-spanning proteins lags behind that for water-soluble globular proteins. This is due to gaps in our knowledge of membrane-protein structure, and experimental difficulties in studying such proteins compared to water-soluble counterparts. One limiting factor is the small number of experimentally determined three-dimensional structures for transmembrane proteins. By contrast, many tens of thousands of globular protein structures provide a rich source of 'scaffolds' for protein design, and the means to garner sequence-to-structure relationships to guide the design process. The α-helical coiled coil is a protein-structure element found in both globular and membrane proteins, where it cements a variety of helix-helix interactions and helical bundles. Our deep understanding of coiled coils has enabled a large number of successful de novo designs. For one class, the α-helical barrels-that is, symmetric bundles of five or more helices with central accessible channels-there are both water-soluble and membrane-spanning examples. Recent computational designs of water-soluble α-helical barrels with five to seven helices have advanced the design field considerably. Here we identify and classify analogous and more complicated membrane-spanning α-helical barrels from the Protein Data Bank. These provide tantalizing but tractable targets for protein engineering and de novo protein design.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.

The phase diagrams of KCaF3 and NaMgF3 by ab initio simulations

ABF3 compounds have been found to make valuable low-pressure analogues for high-pressure silicate phases that are present in the Earth's deep interior and that may also occur in the interiors of exoplanets. The phase diagrams of two of these materials, KCaF3 and NaMgF3, have been investigated in detail by static ab initio computer simulations based on density functional theory. Six ABF3 polymorphs were considered, as follows: the orthorhombic perovskite structure (GdFeO3-type; space group Pbnm); the orthorhombic CaIrO3 structure (Cmcm; commonly referred to as the "post-perovskite" structure); the orthorhombic Sb2S3 and La2S3 structures (both Pmcn); the hexagonal structure previously suggested in computer simulations of NaMgF3 (P63/mmc); the monoclinic structure found to be intermediate between the perovskite and CaIrO3 structures in CaRhO3 (P21/m). Volumetric and axial equations of state of all phases considered are presented. For KCaF3, as expected, the perovskite phase is shown to be the most thermodynamically stable at atmospheric pressure. With increasing pressure, the relative stability of the KCaF3 phases then follows the sequence: perovskite → La2S3 structure → Sb2S3 structure → P63/mmc structure; the CaIrO3 structure is never the most stable form. Above about 2.6 GPa, however, none of the KCaF3 polymorphs are stable with respect to dissociation into KF and CaF2. The possibility that high-pressure KCaF3 polymorphs might exist metastably at 300 K, or might be stabilised by chemical substitution so as to occur within the standard operating range of a multi-anvil press, is briefly discussed. For NaMgF3, the transitions to the high-pressure phases occur at pressures outside the normal range of a multi-anvil press. Two different sequences of transitions had previously been suggested from computer simulations. With increasing pressure, we find that the relative stability of the NaMgF3 phases follows the sequence: perovskite → CaIrO3 structure → Sb2S3 structure → P63/mmc structure. However, only the perovskite and CaIrO3 structures are stable with respect to dissociation into NaF and MgF2.

Construction of a Chassis for a Tripartite Protein-Based Molecular Motor

Improving our understanding of biological motors, both to fully comprehend their activities in vital processes, and to exploit their impressive abilities for use in bionanotechnology, is highly desirable. One means of understanding these systems is through the production of synthetic molecular motors. We demonstrate the use of orthogonal coiled-coil dimers (including both parallel and antiparallel coiled coils) as a hub for linking other components of a previously described synthetic molecular motor, the Tumbleweed. We use circular dichroism, analytical ultracentrifugation, dynamic light scattering, and disulfide rearrangement studies to demonstrate the ability of this six-peptide set to form the structure designed for the Tumbleweed motor. The successful formation of a suitable hub structure is both a test of the transferability of design rules for protein folding as well as an important step in the production of a synthetic protein-based molecular motor.

A monodisperse transmembrane α-helical peptide barrel

The fabrication of monodisperse transmembrane barrels formed from short synthetic peptides has not been demonstrated previously. This is in part because of the complexity of the interactions between peptides and lipids within the hydrophobic environment of a membrane. Here we report the formation of a transmembrane pore through the self-assembly of 35 amino acid α-helical peptides. The design of the peptides is based on the C-terminal D4 domain of the Escherichia coli polysaccharide transporter Wza. By using single-channel current recording, we define discrete assembly intermediates and show that the pore is most probably a helix barrel that contains eight D4 peptides arranged in parallel. We also show that the peptide pore is functional and capable of conducting ions and binding blockers. Such α-helix barrels engineered from peptides could find applications in nanopore technologies such as single-molecule sensing and nucleic-acid sequencing.

Controlling the Assembly of Coiled-Coil Peptide Nanotubes

An ability to control the assembly of peptide nanotubes (PNTs) would provide biomaterials for applications in nanotechnology and synthetic biology. Recently, we presented a modular design for PNTs using α-helical barrels with tunable internal cavities as building blocks. These first-generation designs thicken beyond single PNTs. Herein we describe strategies for controlling this lateral association, and also for the longitudinal assembly. We show that PNT thickening is pH sensitive, and can be reversed under acidic conditions. Based on this, repulsive charge interactions are engineered into the building blocks leading to the assembly of single PNTs at neutral pH. The building blocks are modified further to produce covalently linked PNTs via native chemical ligation, rendering ca. 100 nm-long nanotubes. Finally, we show that small molecules can be sequestered within the interior lumens of single PNTs.

The equation of state of the Pmmn phase of NiSi

The room-temperature equations of state of NiSi with Pmmn symmetry and Ni₅₃Si₄₇ in the B20 structure have been determined to 50 GPa using a diamond anvil cell. The equations of state are compared with existing experimental data and ab initio simulations.

The equation of state of the orthorhombic phase of NiSi with Pmmn symmetry has been determined at room temperature from synchrotron-based X-ray diffraction measurements of its lattice parameters, made in a diamond anvil cell. Measurements were performed up to 44 GPa, using Ne as the pressure medium and Au as the pressure standard. The resulting pressure–volume (P–V) data have been fitted with a Birch–Murnaghan equation of state of third order to yield V₀ = 11.650 (7) ų atom⁻¹, K₀ = 162 (3) GPa and K₀′ = 4.6 (2). In addition, P–V data have been collected on Ni₅₃Si₄₇ in the B20 structure using both Ne and He as the pressure media and Cu and Au as the pressure standards, also to 44 GPa. A fit using the same Birch–Murnaghan equation of state of third order yields V₀ = 11.364 (6) ų atom⁻¹, K₀ = 171 (4) GPa and K₀′ = 5.5 (3).

Functionalized α-Helical Peptide Hydrogels for Neural Tissue Engineering

Trauma to the central and peripheral nervous systems often lead to serious morbidity. Current surgical methods for repairing or replacing such damage have limitations. Tissue engineering offers a potential alternative. Here we show that functionalized α-helical-peptide hydrogels can be used to induce attachment, migration, proliferation and differentiation of murine embryonic neural stem cells (NSCs). Specifically, compared with undecorated gels, those functionalized with Arg-Gly-Asp-Ser (RGDS) peptides increase the proliferative activity of NSCs; promote their directional migration; induce differentiation, with increased expression of microtubule-associated protein-2, and a low expression of glial fibrillary acidic protein; and lead to the formation of larger neurospheres. Electrophysiological measurements from NSCs grown in RGDS-decorated gels indicate developmental progress toward mature neuron-like behavior. Our data indicate that these functional peptide hydrogels may go some way toward overcoming the limitations of current approaches to nerve-tissue repair.

The ubiquitin C-terminal hydrolase L1 (UCH-L1) C terminus plays a key role in protein stability, but its farnesylation is not required for membrane association in primary neurons

Ubiquitin C-terminal hydrolase L1 (UCH-L1) is a deubiquitinating enzyme that is highly expressed in neurons. A possible role for UCH-L1 in neurodegeneration has been highlighted because of its presence in Lewy bodies associated with Parkinson disease and neurofibrillary tangles observed in Alzheimer disease. UCH-L1 exists in two forms in neurons, a soluble cytoplasmic form (UCH-L1(C)) and a membrane-associated form (UCH-L1(M)). Alzheimer brains show reduced levels of soluble UCH-L1(C) correlating with the formation of UCH-L1-immunoreactive tau tangles, whereas UCH-L1(M) has been implicated in α-synuclein dysfunction. Given these reports of divergent roles, we investigated the properties of UCH-L1 membrane association. Surprisingly, our results indicate that UCH-L1 does not partition to the membrane in the cultured cell lines we tested. Furthermore, in primary cultured neurons, a proportion of UCH-L1(M) does partition to the membrane, but, contrary to a previous report, this does not require farnesylation. Deletion of the four C-terminal residues caused the loss of protein solubility, abrogation of substrate binding, increased cell death, and an abnormal intracellular distribution, consistent with protein dysfunction and aggregation. These data indicate that UCH-L1 is differently processed in neurons compared with clonal cell lines and that farnesylation does not account for the membrane association in neurons.

Assessing cellular response to functionalized α-helical peptide hydrogels

α-Helical peptide hydrogels are decorated with a cell-binding peptide motif (RGDS), which is shown to promote adhesion, proliferation, and differentiation of PC12 cells. Gel structure and integrity are maintained after functionalization. This opens possibilities for the bottom-up design and engineering of complex functional scaffolds for 2D and 3D cell cultures.

CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies

Motivation: The ability to accurately model protein structures at the atomistic level underpins efforts to understand protein folding, to engineer natural proteins predictably and to design proteins de novo. Homology-based methods are well established and produce impressive results. However, these are limited to structures presented by and resolved for natural proteins. Addressing this problem more widely and deriving truly ab initio models requires mathematical descriptions for protein folds; the means to decorate these with natural, engineered or de novo sequences; and methods to score the resulting models.

Results: We present CCBuilder, a web-based application that tackles the problem for a defined but large class of protein structure, the α-helical coiled coils. CCBuilder generates coiled-coil backbones, builds side chains onto these frameworks and provides a range of metrics to measure the quality of the models. Its straightforward graphical user interface provides broad functionality that allows users to build and assess models, in which helix geometry, coiled-coil architecture and topology and protein sequence can be varied rapidly. We demonstrate the utility of CCBuilder by assembling models for 653 coiled-coil structures from the PDB, which cover >96% of the known coiled-coil types, and by generating models for rarer and de novo coiled-coil structures.

Availability and implementation: CCBuilder is freely available, without registration, at http://coiledcoils.chm.bris.ac.uk/app/cc_builder/

Contact:D.N.Woolfson@bristol.ac.uk or Chris.Wood@bristol.ac.uk

A basis set of de novo coiled-coil peptide oligomers for rational protein design and synthetic biology

Protein engineering, chemical biology, and synthetic biology would benefit from toolkits of peptide and protein components that could be exchanged reliably between systems while maintaining their structural and functional integrity. Ideally, such components should be highly defined and predictable in all respects of sequence, structure, stability, interactions, and function. To establish one such toolkit, here we present a basis set of de novo designed α-helical coiled-coil peptides that adopt defined and well-characterized parallel dimeric, trimeric, and tetrameric states. The designs are based on sequence-to-structure relationships both from the literature and analysis of a database of known coiled-coil X-ray crystal structures. These give foreground sequences to specify the targeted oligomer state. A key feature of the design process is that sequence positions outside of these sites are considered non-essential for structural specificity; as such, they are referred to as the background, are kept non-descript, and are available for mutation as required later. Synthetic peptides were characterized in solution by circular-dichroism spectroscopy and analytical ultracentrifugation, and their structures were determined by X-ray crystallography. Intriguingly, a hitherto widely used empirical rule-of-thumb for coiled-coil dimer specification does not hold in the designed system. However, the desired oligomeric state is achieved by database-informed redesign of that particular foreground and confirmed experimentally. We envisage that the basis set will be of use in directing and controlling protein assembly, with potential applications in chemical and synthetic biology. To help with such endeavors, we introduce Pcomp, an on-line registry of peptide components for protein-design and synthetic-biology applications.

A de novo peptide hexamer with a mutable channel

The design of new proteins that expand the repertoire of natural protein structures represents a formidable challenge. Success in this area would increase understanding of protein structure, and present new scaffolds that could be exploited in biotechnology and synthetic biology. Here we describe the design, characterisation and X-ray crystal structure of a new coiled-coil protein. The de novo sequence forms a stand-alone, parallel, 6-helix bundle with a channel running through it. Although lined exclusively by hydrophobic leucine and isoleucine side chains, the 6 Å channel is permeable to water. One layer of leucine residues within the channel is mutable accepting polar aspartic acid (Asp) and histidine (His) side chains, and leading to subdivision and organization of solvent within the lumen. Moreover, these mutants can be combined to form a stable and unique (Asp-His)₃ heterohexamer. These new structures provide a basis for engineering de novo proteins with new functions.

Dissection of the DNA mimicry of the bacteriophage T7 Ocr protein using chemical modification

The homodimeric Ocr (overcome classical restriction) protein of bacteriophage T7 is a molecular mimic of double-stranded DNA and a highly effective competitive inhibitor of the bacterial type I restriction/modification system. The surface of Ocr is replete with acidic residues that mimic the phosphate backbone of DNA. In addition, Ocr also mimics the overall dimensions of a bent 24-bp DNA molecule. In this study, we attempted to delineate these two mechanisms of DNA mimicry by chemically modifying the negative charges on the Ocr surface. Our analysis reveals that removal of about 46% of the carboxylate groups per Ocr monomer results in an approximately 50-fold reduction in binding affinity for a methyltransferase from a model type I restriction/modification system. The reduced affinity between Ocr with this degree of modification and the methyltransferase is comparable with the affinity of DNA for the methyltransferase. Additional modification to remove approximately 86% of the carboxylate groups further reduces its binding affinity, although the modified Ocr still binds to the methyltransferase via a mechanism attributable to the shape mimicry of a bent DNA molecule. Our results show that the electrostatic mimicry of Ocr increases the binding affinity for its target enzyme by up to approximately 800-fold.

Getting harder: cobalt(III)-template synthesis of catenanes and rotaxanes

The synthesis of catenanes and rotaxanes using the hard trivalent transition metal ion cobalt(III) as a template is reported. Tridentate dianionic pyridine-2,6-dicarboxamido ligands, each with two terminal alkene groups, coordinate Co(III) in a mutually orthogonal arrangement such that entwined or interlocked molecular architectures are produced by ring-closing olefin metathesis. Double macrocyclization of two such ligands bound to Co(III) afford a non-interlocked "figure-of-eight" complex in 42% yield, the structure determined by X-ray crystallography. Preforming one macrocycle and carrying out a single macrocyclization of the second bis-olefin with both ligands attached to the Co(III) template led to the isomeric [2]catenate in 69% yield. The mechanically interlocked structure was confirmed by X-ray crystallography of both the Co(III) catenate and the metal-free catenand. A Co(III)-template [2]rotaxane was assembled in 61% yield by macrocyclization of the bis-olefin ligand about an appropriate dianionic thread. For both catenanes and rotaxanes, removal of the metal ion via reduction under acidic conditions to the more labile Co(II) gave neutral interlocked molecules with well-defined co-conformations stabilized by intercomponent hydrogen bonding.

Designed alpha-helical tectons for constructing multicomponent synthetic biological systems

One possible route to develop new synthetic-biological systems is to assemble discrete nanoscale objects from programmed peptide-based building blocks. We describe an algorithm to design such blocks based on the coiled-coil protein-folding motif. The success of the algorithm is demonstrated by the production of six peptides that form three target parallel, blunted-ended heterodimers in preference to any of the other promiscuous pairings and alternate configurations, for example, homodimers, sticky-ended assemblies, and antiparallel arrangements. The peptides were linked to promote the assembly of larger, defined nanoscale rods, thus demonstrating that targeted peptide-peptide interactions can be specified in complex mixtures.

How much of protein sequence space has been explored by life on Earth?

We suggest that the vastness of protein sequence space is actually completely explorable during the populating of the Earth by life by considering upper and lower limits for the number of organisms, genome size, mutation rate and the number of functionally distinct classes of amino acids. We conclude that rather than life having explored only an infinitesimally small part of sequence space in the last 4 Gyr, it is instead quite plausible for all of functional protein sequence space to have been explored and that furthermore, at the molecular level, there is no role for contingency.

Switchable Dual Binding Mode Molecular Shuttle

[Structure: see text] Protonation controls the location of a dual binding mode macrocycle in a [2]rotaxane. In the neutral form, amide-amide hydrogen bonds hold the macrocycle over a dipeptide residue; when the thread is protonated, polyether-ammonium cation interactions dominate and the macrocycle changes position.

Rotaxanes of cyclic peptides

The synthesis of rotaxanes derived from the synthetic peptide macrocycles cyclo(l-ProGly)4 and cyclo(l-ProGly)5 and diammonium threads is described. [2]Rotaxanes are formed in good yields (56-63%), despite the disruption of internal amide-amide hydrogen bonding in the macrocycles.

A comparison of the sensitivity of APTT reagents to the effects of enoxaparin, a low-molecular weight heparin

Low-molecular weight heparin (LMWH) is the product of enzymatic or chemical degradation of unfractionated heparin (UFH). It has been found to have better bio-availibility, more predictable dose response and can be used as an alternative to UFH for prophylaxis and treatment of thrombotic disorders. It is claimed that no laboratory monitoring is necessary for LMWH therapy; however, for the aged, renal impaired, obese or grossly underweight, monitoring of dose effect with anti-Xa assay is recommended. The activated partial thromboplastin time (APTT), which is the test of choice for UFH monitoring, is believed to be insensitive to the effect of LMWH. The sensitivity of the APTT to heparin lies in the APTT reagent used. In this study, eight different APTT reagents were used to compare the APTT with anti-Xa activity in ex vivo plasma from patients who were on enoxaparin (LMWH, Clexane) therapy. It was found that, as with UFH, APTT reagents show variable sensitivity to LMWH. The APTTs from all eight reagents were found to have a linear relationship to anti-Xa activity. The APTT results using three of the reagents gave an indication of the use of LMWH therapy. It was also found that patients who were lupus anticoagulant (LA)-positive had much more prolonged APTTs when on LMWH therapy; however, a linear correlation between APTT and anti-Xa was not present in these patients.

Effect of blood donation on the establishment of normal ranges of lymphocyte subsets

BACKGROUND

Absolute counts of CD4+ T-lymphocytes are used in the management of patients with human immunodeficiency virus infection. Low absolute counts of CD3+CD4+ cells have also been observed in healthy people--a phenomenon called idiopathic CD4 lymphocytopenia. It is common practice for normal ranges for lymphocyte subsets to be derived from samples taken from blood donors.

STUDY DESIGN AND METHODS

A sample of EDTA blood was taken through the donation line tubing, after donation from 565 blood donors in Sydney, Australia, who were selected from a range of age groups. An additional 12 donors provided a predonation sample as well as a postdonation sample. Hematologic assays were performed on two analyzers. Samples were stained for CD3, CD4, CD8, CD19, and CD56 and analyzed on a flow cytometer.

RESULTS

Three donors were found to have absolute CD3+CD4+ counts < 300 cells per microL. The percentage of CD3+CD4+ cells was found to increase with age. Both the percentage and the absolute count of CD3+CD8+ cells decreased with age, which resulted in an increased CD4:CD8 ratio with age. Men had consistently higher absolute counts of CD3-CD56+ cells than women. The 12 additional donors all had greater percentages of CD3+CD4+ cells and lower absolute counts for CD3+, CD3+CD4+, CD3+CD8+, CD19+ and CD3-CD56+ cells after donation than they had before donation (p < 0.001).

CONCLUSION

It is not satisfactory to base normal ranges for lymphocyte subsets on donor blood, from which the blood sample has been obtained after donation.

Monocyte isolation by flow cytometer-monitored centrifugal elutriation: a preparative tool for antibody-dependent cell-mediated cytotoxicity (ADCC) assays

The value of isolating monocytes by flow cytometer-monitored centrifugal elutriation (CE) after initial density gradient centrifugation (DGC) was investigated. A pooled cell suspension prepared by DGC+CE had a monocyte purity of 90% while a pool prepared by DGC alone had a monocyte purity of only 30%. Monocyte suspensions prepared from 15 separate blood donations demonstrated that, despite wide variation in initial monocyte purity following DGC (i.e. 13-32%), CE consistently increased the purity to 85-92%. Antibody-dependent cell-mediated cytotoxicity (ADCC) studies showed that the most sensitive and reproducible assays were those performed with the DGC+CE pool. At a monocyte concentration of 2 x 10(6)/ml the DGC+CE pool was almost twice as active as the DGC pool (60.2% lysis vs 31.2% lysis, respectively). Considerable variation in ADCC activity was seen when using monocytes from individual donors. We conclude that centrifugal elutriation is a valuable tool for preparing effector cells for use in monocyte driven ADCC assays.

Leukodepleted blood components

The use of leukodepleted blood components may reduce some adverse effects of transfusion in certain clinical situations. This review outlines the recognised effects of contaminating passenger leucocytes, the value of leukodepleted components in preventing some of these complications, methods of leukodepletion and the current recommendations for use of these components.

Guidelines for the use of fresh frozen plasma. British Committee for Standards in Haematology, Working Party of the Blood Transfusion Task Force

Fresh frozen plasma should only be used to treat bleeding episodes or prepare patients for surgery in certain defined situations. Definite indications for the use of FFP: 1. Replacement of single coagulation factor deficiencies, where a specific or combined factor concentrate is unavailable. 2. Immediate reversal or warfarin effect. 3. Acute disseminated intravascular coagulation (DIC). 4. Thrombotic thrombocytopenic purpura (TTP). Conditional uses: FFP only indicated in the presence of bleeding and disturbed coagulation: 1. Massive transfusion. 2. Liver disease. 3. cardiopulmonary bypass surgery. 4. Special paediatric indications. No justification for the use of FFP: 1. Hypovolaemia. 2. Plasma exchange procedures. 3. 'Formula' replacement. 4. Nutritional support. 5. Treatment of immunodeficiency states.

Comparative studies on mitochondrial respiration in four strains of rats (Rattus norvegicus)

Mitochondrial respiration and ATP synthesis were examined in young rats of the Sprague-Dawley, Wistar, BHE and Zucker strains. Both lean and obese Zucker rats were studied. Pyruvate-supported state 3 respiration was highest in mitochondria from Sprague-Dawley rats and least in mitochondria from obese Zucker rats. Succinate-supported state 3 respiration was highest in the Wistar group and least in the Sprague-Dawley rats. There appeared to be no relationship between oxygen consumption and the genetic tendency for hepatic hyperlipogenesis. ATP synthesis was greatest in the obese Zucker rats and least in the Sprague-Dawley rats. Differences in liver weights and mitochondrial yields may explain, in part, these observed strain differences in mitochondrial activity.

Brain adenosine 5'-triphosphate-creatine phosphotransferase

1. The purification of creatine kinase (ATP-creatine phosphotransferase, EC 2.7.3.2) from ox brain by a method that is quicker, simpler and gives much higher yields than other published procedures is described. 2. Stoicheiometric inhibition studies with iodoacetate showed that the enzyme, like that from muscle, has two reactive thiol groups that are essential for enzyme activity. 3. The amino acid sequence around the essential thiol groups was determined and found to be virtually identical with that in creatine kinases from rabbit and ox muscle, and very similar to that found in arginine kinase; the evolutionary significance of this is discussed. 4. The identification of DNS-amino acids on thin layers of silica gel was found to have, in many cases, distinct advantages over that on polyamide layers.

Preparation and properties of creatine kinase from the breast muscle of normal and dystrophic chicken (Gallus domesticus)

1. The purification of creatine kinase from normal and genetically dystrophic chicken breast muscle is described. Enzyme recovery was significantly lower from dystrophic muscle. 2. Both enzymes had the same number of reactive and total thiol groups and had similar specific activities and similar amino acid compositions. 3. No significant differences were observed in sedimentation, electrophoretic or kinetic properties. 4. Peptide ;maps' showed no significant differences, and electrophoresis of partial acid hydrolysates of the labelled enzymes suggested that corresponding amino acid sequences around all the thiol groups were very similar. 5. The enzymes showed identical temperature stabilities. 6. No significant differences between the enzymes from normal and dystrophic muscle were observed.