Whole-Organism Analysis by Vibrational Spectroscopy

Vibrational spectroscopy has contributed to the understanding of biological materials for many years. As the technology has advanced, the technique has been brought to bear on the analysis of whole organisms. Here, we discuss advanced and recently developed infrared and Raman spectroscopic instrumentation to whole-organism analysis. We highlight many of the recent contributions made in this relatively new area of spectroscopy, particularly addressing organisms associated with disease with emphasis on diagnosis and treatment. The application of vibrational spectroscopic techniques to entire organisms is still in its infancy, but new developments in imaging and chemometric processing will likely expand in the field in the near future.

Prediction of Signal Peptides in Proteins from Malaria Parasites

Signal peptides are N-terminal presequences responsible for targeting proteins to the endomembrane system, and subsequent subcellular or extracellular compartments, and consequently condition their proper function. The significance of signal peptides stimulates development of new computational methods for their detection. These methods employ learning systems trained on datasets comprising signal peptides from different types of proteins and taxonomic groups. As a result, the accuracy of predictions are high in the case of signal peptides that are well-represented in databases, but might be low in other, atypical cases. Such atypical signal peptides are present in proteins found in apicomplexan parasites, causative agents of malaria and toxoplasmosis. Apicomplexan proteins have a unique amino acid composition due to their AT-biased genomes. Therefore, we designed a new, more flexible and universal probabilistic model for recognition of atypical eukaryotic signal peptides. Our approach called signalHsmm includes knowledge about the structure of signal peptides and physicochemical properties of amino acids. It is able to recognize signal peptides from the malaria parasites and related species more accurately than popular programs. Moreover, it is still universal enough to provide prediction of other signal peptides on par with the best preforming predictors.

Report: Unsupervised identification of malaria parasites using computer vision

Malaria in human is a serious and fatal tropical disease. This disease results from Anopheles mosquitoes that are infected by Plasmodium species. The clinical diagnosis of malaria based on the history, symptoms and clinical findings must always be confirmed by laboratory diagnosis. Laboratory diagnosis of malaria involves identification of malaria parasite or its antigen / products in the blood of the patient. Manual diagnosis of malaria parasite by the pathologists has proven to become cumbersome. Therefore, there is a need of automatic, efficient and accurate identification of malaria parasite. In this paper, we proposed a computer vision based approach to identify the malaria parasite from light microscopy images. This research deals with the challenges involved in the automatic detection of malaria parasite tissues. Our proposed method is based on the pixel-based approach. We used K-means clustering (unsupervised approach) for the segmentation to identify malaria parasite tissues.

Three-dimensional structures in the design of therapeutics targeting parasitic protozoa: reflections on the past, present and future

Parasitic protozoa cause a range of diseases which threaten billions of human beings. They are responsible for tremendous mortality and morbidity in the least-developed areas of the world. Presented here is an overview of the evolution over the last three to four decades of structure-guided design of inhibitors, leads and drug candidates aiming at targets from parasitic protozoa. Target selection is a crucial and multi-faceted aspect of structure-guided drug design. The major impact of advances in molecular biology, genome sequencing and high-throughput screening is touched upon. The most advanced crystallographic techniques, including XFEL, have already been applied to structure determinations of drug targets from parasitic protozoa. Even cryo-electron microscopy is contributing to our understanding of the mode of binding of inhibitors to parasite ribosomes. A number of projects have been selected to illustrate how structural information has assisted in arriving at promising compounds that are currently being evaluated by pharmacological, pharmacodynamic and safety tests to assess their suitability as pharmaceutical agents. Structure-guided approaches are also applied to incorporate properties into compounds such that they are less likely to become the victim of resistance mechanisms. A great increase in the number of novel antiparasitic compounds will be needed in the future. These should then be combined into various multi-compound therapeutics to circumvent the diverse resistance mechanisms that render single-compound, or even multi-compound, drugs ineffective. The future should also see (i) an increase in the number of projects with a tight integration of structural biology, medicinal chemistry, parasitology and pharmaceutical sciences; (ii) the education of more `medicinal structural biologists' who are familiar with the properties that compounds need to have for a high probability of success in the later steps of the drug-development process; and (iii) the expansion of drug-development capabilities in middle- and low-income countries.

A comparative proteomic analysis of the simple amino acid repeat distributions in Plasmodia reveals lineage specific amino acid selection

Background

Microsatellites have been used extensively in the field of comparative genomics. By studying microsatellites in coding regions we have a simple model of how genotypic changes undergo selection as they are directly expressed in the phenotype as altered proteins. The simplest of these tandem repeats in coding regions are the tri-nucleotide repeats which produce a repeat of a single amino acid when translated into proteins. Tri-nucleotide repeats are often disease associated, and are also known to be unstable to both expansion and contraction. This makes them sensitive markers for studying proteome evolution, in closely related species.

Results

The evolutionary history of the family of malarial causing parasites Plasmodia is complex because of the life-cycle of the organism, where it interacts with a number of different hosts and goes through a series of tissue specific stages. This study shows that the divergence between the primate and rodent malarial parasites has resulted in a lineage specific change in the simple amino acid repeat distribution that is correlated to A–T content. The paper also shows that this altered use of amino acids in SAARs is consistent with the repeat distributions being under selective pressure.

Conclusions

The study shows that simple amino acid repeat distributions can be used to group related species and to examine their phylogenetic relationships. This study also shows that an outgroup species with a similar A–T content can be distinguished based only on the amino acid usage in repeats, and suggest that this might be a useful feature for proteome clustering. The lineage specific use of amino acids in repeat regions suggests that comparative studies of SAAR distributions between proteomes gives an insight into the mechanisms of expansion and the selective pressures acting on the organism.

[Development of anti-malarial vaccines and need for clinical trials in accordance with international standards in South Africa]

In the 20th century malaria remains a major problem of public health in sub-Saharan Africa. This haemosporidium discovered in Africa by Laveran in 1880, kills one child every 30 seconds which amounts to three "tsunami" flowing each year into the African continent. The current international solidarity raises new hopes as regards the possibility to suppress the morbidity effects on the population's health condition. In order to be efficient, today's strategies (impregnated mosquito nets, intermittent preventive treatments, artemisinin based combination therapy) should reach at least 80% of the targeted population (pregnant women and children). By 2025, the uncontrolled urbanization of the African population and the social disorders will make a new population a target for malaria. The new data of functional genomics and proteonics open new avenues of research for new mechanisms, new therapeutics and vaccine targets and new tools of diagnosis and prognosis. The current candidate vaccines of the first generation have allowed the development of African competences in clinical trials of international standard. Although they represent scientific advances they will not resolve the problem of public health. Research on candidate vaccines of 2nd and 3rd generation remains a challenge for the international scientific community. Africa should play a determining role in this process. Scientific information on the field remains essential for these generations of new anti-malarial vaccines. The ethical aspects regarding those clinical trials and actions of public health and research remain an universal necessity Deontology and ethics are two complementary approaches for the good practice of medicine and research of a good practitioner. For the protection and advantages of the patient and/or volunteer of the research are the cornerstones of the ethical approach. The scientific quality of a research protocol submitted to an independent research ethics committee and the volunteer 's informed consent are universal ethical obligations. For the quality of ethics observance in a country reflects best the quality of the efficiency of its research system and its democracy.

Hemozoin and the human monocyte--a brief review of their interactions

In vitro, human monocytes avidly ingest hemozoin (HZ) that modifies a number of monocyte functions. Inhibitory effects: inhibition of: PMA-elicited respiratory burst, ability to killing and repeat phagocytosis, activity of NADPH-oxidase and PKC, expression of ICAM-1, integrin-CD11c, MHC-class-II (IFN-gamma-mediated), differentiation to functional, antigen-presenting dendritic cells. Stimulatory effects: increase in phagocytosis-related respiratory burst and accumulation of lipoperoxidation products; induction of metalloproteinase-9 and pro-inflammatory cytokines and chemokines. Mechanism of action: HZ generates by nonenzymatic catalysis large amounts of lipoperoxidation products, such as monohydroxy derivatives of arachidonic (HETE) and linoleic (HODE) acid, and 4-hydroxynonenal (HNE). Several HZ effects were reproduced by supplementation with plausible concentrations of HETE or HNE, the first most likely via interaction with PPAR-receptors, the second via adduct or crosslinks formation with critical targets.

Structural biology of plasmodial proteins

Malaria is a global disease infecting several million individuals annually. Malarial infection is particularly severe in the poorest parts of the world and is a major drain on their limited resources. Development of drug resistance and absence of a preventive vaccine have led to an immediate necessity for identifying new drug targets to combat malaria. Understanding the intricacies of parasite biology is essential to design novel intervention strategies that can prevent the growth of the parasite. The structural biology approach towards this goal involves the identification of key differences in the structures of the human and parasite enzymes and the determination of unique protein structures essential for parasite survival. This review covers the work on structural biology of plasmodial proteins carried out during the period of January 2006 to June 2007.

A rational strategy for a malarial vaccine development

Twenty years ago we reported the first synthetic peptide-based anti-malarial vaccine named SPf66, which conferred limited protective efficacy in large-scale human field-trials. Our efforts towards a second vaccine generation based on the rational selection of conserved high activity binding peptides (HABPs) whose critical binding residues have to be precisely replaced by others. Introducing peptide bond isosters on these HABPs' critical binding residues constitutes also an important approach. Our results suggest that knowing a parasite's immunologically active peptides, their 3D structure, and their interaction for properly stabilizing MHC-II peptide-TCR complexes constitutes the basis for rationally designing a fully effective, multi-component, multistage subunit-based anti-malarial vaccine.

Plasmodium cysteine repeat modular proteins 1-4: complex proteins with roles throughout the malaria parasite life cycle

The Cysteine Repeat Modular Proteins (PCRMP1-4) of Plasmodium, are encoded by a small gene family that is conserved in malaria and other Apicomplexan parasites. They are very large, predicted surface proteins with multipass transmembrane domains containing motifs that are conserved within families of cysteine-rich, predicted surface proteins in a range of unicellular eukaryotes, and a unique combination of protein-binding motifs, including a >100 kDa cysteine-rich modular region, an epidermal growth factor-like domain and a Kringle domain. PCRMP1 and 2 are expressed in life cycle stages in both the mosquito and vertebrate. They colocalize with PfEMP1 (P. falciparum Erythrocyte Membrane Antigen-1) during its export from P. falciparum blood-stage parasites and are exposed on the surface of haemolymph- and salivary gland-sporozoites in the mosquito, consistent with a role in host tissue targeting and invasion. Gene disruption of pcrmp1 and 2 in the rodent malaria model, P. berghei, demonstrated that both are essential for transmission of the parasite from the mosquito to the mouse and has established their discrete and important roles in sporozoite targeting to the mosquito salivary gland. The unprecedented expression pattern and structural features of the PCRMPs thus suggest a variety of roles mediating host-parasite interactions throughout the parasite life cycle.

Abundance of intrinsically unstructured proteins in P. falciparum and other apicomplexan parasite proteomes

Preliminary sequence analysis of Plasmodium falciparum has shown that the proteome of this organism is enriched in intrinsically unstructured proteins (IUPs), which are either completely disordered or contain large disordered regions. IUPs have been characterized as a unique class of proteins that plays an important role in biology and disease. In this study, the IUP contents in the proteomes of apicomplexan parasites, especially the proteome of P. falciparum and its various life cycle stages, have been evaluated with DisEMBL-1.4. Compared with other proteomes, apicomplexan species are extremely abundant in proteins containing long disordered regions, and the IUP contents in mammalian Plasmodium species are higher than in most other apicomplexan parasites. The proteome of the P. falciparum sporozoite appears to be distinct from the other life cycle stages in having an even higher content of disordered proteins. The abundance of IUPs in the P. falciparum proteome correlates with its enrichment in repetitive sequences. The structural plasticity of IUPs, which allows promiscuous binding interactions, may favour parasite survival both by inhibiting the generation of effective high affinity antibody responses and by facilitating the interactions with host molecules necessary for attachment and invasion of host cells.

Functional and immunological insights from the three-dimensional structures of Plasmodium surface proteins

Malaria is a major global health problem and is caused by the unicellular parasite Plasmodium. Plasmodial surface proteins have important roles in host cell invasion and are responsible for antigenic diversity in this organism. Knowledge of the three-dimensional structure of surface proteins can facilitate our understanding their biological function, and contribute to the development of therapeutic and vaccine strategies against malaria. Structural studies allow rational drug design when ligand- or receptor-binding sites are identified and characterized. Analysis of the three-dimensional distribution of protective antibody epitopes and polymorphic residues can facilitate vaccine candidate optimization. With this in mind, some Plasmodium surface-protein structures have determined by X-ray crystallography or nuclear magnetic resonance.

Plasmodium motility: actin not actin' like actin

Apicomplexan parasites such as Plasmodium and Toxoplasma display actomyosin-dependent motility in the absence of readily detectable actin polymers. Three recent studies indicate that parasite actin polymers, either harvested from parasites or formed from purified recombinant proteins, are exceptionally short ( approximately 100 nm). We propose that parasite motility could be directed by the transient formation of short actin filament scaffolds. Parasite actin polymers that support transmembrane receptors are pulled, by myosin interaction, backwards along the parasite periphery, resulting in forward movement.

Structure of the MTIP-MyoA complex, a key component of the malaria parasite invasion motor

The causative agents of malaria have developed a sophisticated machinery for entering multiple cell types in the human and insect hosts. In this machinery, a critical interaction occurs between the unusual myosin motor MyoA and the MyoA-tail Interacting Protein (MTIP). Here we present one crystal structure that shows three different conformations of Plasmodium MTIP, one of these in complex with the MyoA-tail, which reveal major conformational changes in the C-terminal domain of MTIP upon binding the MyoA-tail helix, thereby creating several hydrophobic pockets in MTIP that are the recipients of key hydrophobic side chains of MyoA. Because we also show that the MyoA helix is able to block parasite growth, this provides avenues for designing antimalarials.

New insights into myosin evolution and classification

Myosins are eukaryotic actin-dependent molecular motors important for a broad range of functions like muscle contraction, vision, hearing, cell motility, and host cell invasion of apicomplexan parasites. Myosin heavy chains consist of distinct head, neck, and tail domains and have previously been categorized into 18 different classes based on phylogenetic analysis of their conserved heads. Here we describe a comprehensive phylogenetic examination of many previously unclassified myosins, with particular emphasis on sequences from apicomplexan and other chromalveolate protists including the model organism Toxoplasma, the malaria parasite Plasmodium, and the ciliate Tetrahymena. Using different phylogenetic inference methods and taking protein domain architectures, specific amino acid polymorphisms, and organismal distribution into account, we demonstrate a hitherto unrecognized common origin for ciliate and apicomplexan class XIV myosins. Our data also suggest common origins for some apicomplexan myosins and class VI, for classes II and XVIII, for classes XII and XV, and for some microsporidian myosins and class V, thereby reconciling evolutionary history and myosin structure in several cases and corroborating the common coevolution of myosin head, neck, and tail domains. Six novel myosin classes are established to accommodate sequences from chordate metazoans (class XIX), insects (class XX), kinetoplastids (class XXI), and apicomplexans and diatom algae (classes XXII, XXIII, and XXIV). These myosin (sub)classes include sequences with protein domains (FYVE, WW, UBA, ATS1-like, and WD40) previously unknown to be associated with myosin motors. Regarding the apicomplexan "myosome," we significantly update class XIV classification, propose a systematic naming convention, and discuss possible functions in these parasites.

Plasmodium permeomics: membrane transport proteins in the malaria parasite

Membrane transport proteins are integral membrane proteins that mediate the passage across the membrane bilayer of specific molecules and/or ions. Such proteins serve a diverse range of physiological roles, mediating the uptake of nutrients into cells, the removal of metabolic wastes and xenobiotics (including drugs), and the generation and maintenance of transmembrane electrochemical gradients. In this chapter we review the present state of knowledge of the membrane transport mechanisms underlying the cell physiology of the intraerythrocytic malaria parasite and its host cell, considering in particular physiological measurements on the parasite and parasitized erythrocyte, the annotation of transport proteins in the Plasmodium genome, and molecular methods used to analyze transport protein function.

Structural comparison of apical membrane antigen 1 orthologues and paralogues in apicomplexan parasites

Apical membrane antigen 1 (AMA1) is a membrane protein present in Plasmodium species and is probably common to all apicomplexan parasites. The recent crystal structure of the complete ectoplasmic region of AMA1 from Plasmodium vivax has shown that it comprises three structural domains and that the first two domains are based on the PAN folding motif. Here, we discuss the consequences of this analysis for the three-dimensional structure of AMA1 from other Plasmodium species and other apicomplexan parasites, and for the Plasmodium paralogue MAEBL. Many polar and apolar interactions observed in the PvAMA1 crystal structure are made by residues that are invariant or highly conserved throughout all Plasmodium orthologues; a subgroup of these residues is also present in other apicomplexan orthologues and in MAEBL. These interactions presumably play a key role in defining the protein fold. Previous studies have shown that the ectoplasmic region of AMA1 must be cleaved from the parasite surface for host-cell invasion to proceed. The cleavage site in the crystal structure is not readily accessible to proteases and we discuss possible consequences of this observation. The three-dimensional distribution of polymorphic sites in PfAMA1 shows that these are all on the surface and that their positions are significantly biased to one side of the ectoplasmic region. Of particular note, a flexible segment in domain II, comprising about 40 residues and devoid of polymorphism, carries an epitope recognized by an invasion-inhibitory monoclonal antibody and a T-cell epitope implicated in the human immune response to AMA1.

Proteome analysis of rhoptry-enriched fractions isolated from Plasmodium merozoites

The rhoptries of Plasmodium species participate in merozoite invasion and modification of the host erythrocyte. However, only a few rhoptry proteins have been identified using conventional gene identification protocols. To investigate the protein organization of this organelle and to identify new rhoptry proteins, merozoite rhoptries from three different Plasmodium rodent species were enriched by sucrose density gradient fractionation, and subjected to proteome analysis using multidimensional protein identification technology (MudPIT); 148 proteins were identified. To distinguish abundant cellular contaminants from bona fide organellar proteins, a differential analysis comparing the proteins in the rhoptry-enriched fractions to proteins identified from whole cell lysates of P. berghei mixed asexual blood stages was undertaken. In addition, the proteins detected were analyzed for the presence of transmembrane domains, secretory signal peptide, cell adhesion motifs, and/or rhoptry-specific tyrosine-sorting motifs. Combining the differential analysis and bioinformatic approaches, a set of 36 proteins was defined as being potentially located to the Plasmodium rhoptries. Among these potential rhoptry proteins were homologues of known rhoptry proteins, proteases, and enzymes involved in lipid metabolism. Molecular characterization and understanding of the supramolecular organization of these novel potential rhoptry proteins may assist in the identification of new intervention targets for the asexual blood stages of malaria.

The evolution of amino acid repeat arrays in Plasmodium and other organisms

Repeat arrays in protein-coding sequences were analyzed by a novel approach, based on analyzing the distribution of the pairwise proportion of nucleotide differences among units within a repeat array. The results showed that evidence of recent repeat array expansion was particularly characteristic of the repeat arrays of the malaria parasites (genus Plasmodium), supporting the hypothesis that Plasmodium is particularly prone to repeat array expansion by slipped-strand mispairing or a similar mechanism. Repeat arrays in Plasmodium asexual-stage antigens (which are exposed to the immune system of the vertebrate host) had unique characteristics with respect to the number of repeat units, as well as nucleotide and amino acid composition, suggesting that natural selection exerted by the host immune system has shaped features of these arrays.

Dithiol Proteins as Guardians of the Intracellular Redox Milieu in Parasites: Old and New Drug Targets in Trypanosomes and Malaria-Causing Plasmodia

Parasitic diseases such as sleeping sickness, Chagas' heart disease, and malaria are major health problems in poverty-stricken areas. Antiparasitic drugs that are not only active but also affordable and readily available are urgently required. One approach to finding new drugs and rediscovering old ones is based on enzyme inhibitors that paralyze antioxidant systems in the pathogens. These antioxidant ensembles are essential to the parasites as they are attacked in the human host by strong oxidants such as peroxynitrite, hypochlorite, and H2O2. The pathogen-protecting system consists of some 20 thiol and dithiol proteins, which buffer the intraparasitic redox milieu at a potential of -250 mV. In trypanosomes and leishmania the network is centered around the unique dithiol trypanothione (N1,N8-bis(glutathionyl)spermidine). In contrast, malaria parasites have a more conservative dual antioxidative system based on glutathione and thioredoxin. Inhibitors of antioxidant enzymes such as trypanothione reductase are, indeed, parasiticidal but they can also delay or prevent resistance against a number of other antiparasitic drugs.

Targeting Malaria Virulence and Remodeling Proteins to the Host Erythrocyte

To establish infection in the host, malaria parasites export remodeling and virulence proteins into the erythrocyte. These proteins can traverse a series of membranes, including the parasite membrane, the parasitophorous vacuole membrane, and the erythrocyte membrane. We show that a conserved pentameric sequence plays a central role in protein export into the host cell and predict the exported proteome in Plasmodium falciparum. We identified 400 putative erythrocyte-targeted proteins corresponding to approximately 8% of all predicted genes, with 225 virulence proteins and a further 160 proteins likely to be involved in remodeling of the host erythrocyte. The conservation of this signal across Plasmodium species has implications for the development of new antimalarials.

Merozoite surface protein 4/5 provides protection against lethal challenge with a heterologous malaria parasite strain

Immunization with merozoite surface protein 4/5 (MSP4/5), the murine malaria homologue of Plasmodium falciparum MSP4 and MSP5, has been shown to protect mice against challenge by parasites expressing the homologous form of the protein. The gene encoding MSP4/5 was sequenced from a number of Plasmodium yoelii isolates in order to assess the level of polymorphism in the protein. The gene was found to be highly conserved among the 13 P. yoelii isolates sequenced, even though many of the same isolates showed pronounced variability in their MSP1(19) sequences. Nonsynonymous mutations were detected only for the isolates Plasmodium yoelii nigeriensis N67 and Plasmodium yoelii killicki 193L and 194ZZ. Immunization and challenge of BALB/c mice showed that the heterologous MSP4/5 proteins were able to confer a level of protection against lethal Plasmodium yoelii yoelii YM challenge infection similar to that induced by immunization with the homologous MSP4/5 protein. To explore the limits of heterologous protection, mice were immunized with recombinant MSP4/5 protein from Plasmodium berghei ANKA and Plasmodium chabaudi adami DS and challenged with P. y. yoelii YM. Interestingly, significant protection was afforded by P. berghei ANKA MSP4/5, which shows 81% sequence identity with P. y. yoelii YM MSP4/5, but it was abolished upon reduction and alkylation. Significant protection was not observed for mice immunized with recombinant P. c. adami DS MSP4/5, which shows 55.7% sequence identity with P. y. yoelii YM MSP4/5. This study demonstrates the robustness of MSP4/5 in conferring protection against variant forms of the protein in a murine challenge system, in contrast to the situation found for other asexual-stage proteins, such as MSP1(19) and AMA1.

Hemozoin- and 4-hydroxynonenal-mediated inhibition of erythropoiesis. Possible role in malarial dyserythropoiesis and anemia

Malarial anemia involves destruction of parasitized and non-parasitized red blood cells and dyserythropoiesis. Malarial pigment, hemozoin (HZ), is possibly implicated in dyserythropoiesis. We show that supernatants of HZ and HZ-fed-monocytes, and 4-hydroxynonenal generated by them, inhibited progenitor growth.

The shape and size of hemozoin crystals distinguishes diverse Plasmodium species

All Plasmodium species produce a brown birefringent crystal known as malarial pigment or hemozoin. This work compares the morphology of hemozoin from P. falciparum, P. vivax, P. ovale, P. malariae, P. knowlesi, P. brasilianum, P. yoelii and P. gallinaceum. The human, primate and mouse hemozoins have a regular, flat-faced cuboidal morphology with modest size differences in contrast to the larger, regularly irregular barrel shape with a waffle surface of the avian, P. gallinaceum, pigment. Hydrogen peroxide (H2O2), as a biochemical test reagent, can distinguish the hemozoins by different concentrations to degrade half of the crystals. A surface area to volume ratio explains both the appearance and susceptibility to H2O2 degradation. The hemozoin from each species is able to be a template for hemozoin extension inhibitable by the quinolines. P. gallinaceum hemozoin more closely resembles the hemozoin from another avian apicomplexan, Haemoproteus, rather than the hemozoin from the mammalian malaria species. These distinct morphological characteristics between mammalian and avian crystals suggest different biochemical environments that affect morphology.

Shotgun proteomics: integrating technologies to answer biological questions

Proteomics is providing us with a variety of exciting new strategies to address biological questions. These strategies must integrate a series of seperative and analytical technologies to deal with the immense complexity involved. At some point in the process, the proteins are usually digested with a proteolytic enzyme to generate shorter peptides that are more easily analyzed by mass spectrometry. Shotgun proteomics relies on separation after this digestion step and takes advantage of tandem mass spectrometry to infer the amino acid sequence of individual peptides. Advances in quantitation, and the ability to find sites of post-translational modification are expanding the scope of questions that can be asked. The ultimate success of any proteomic experiment is dictated not only by an appropriate choice of seperative and analytical techniques, but also by making certain that the biological aspects of the experiment are focused and well designed.

Phase homogeneity and crystal morphology of the malaria pigment beta-hematin

Hemoglobin digestion in the intraerythrocytic trophozoite stages of the malaria parasite releases large quantities of heme, which is then detoxified by crystallization into regular crystallites, which are subsequently secreted into the host vascular network as malaria pigment. This crystalline product is isostructural with the synthetic phase b-hematin, and its structure, solved from its powder diffraction pattern, (Pagola et al., 2000), corresponds to a hydrogen bonded chain of propionate linked dimers, Figure 1. This is an example where the crystalline phase is the macromolecule of direct biological interest, particularly in light of the currently accepted hypothesis for the quinoline antimalarial drug action being the inhibition of b-hematin formation and biosynthesis. A surprisingly array of spectroscopically similar closely related phases can also form during the reactions which are used to synthesize b-hematin. Scanning electron microscopy and X-ray powder diffraction have been used to characterize these materials. Taken together these results indicate that infrared spectroscopy, in itself, is insufficient to identify synthetic analogs to malaria pigment and that a combination of electronmicroscopy and powder diffraction are required to unambiguously characterize these heme aggregates.

A comparison of two rapid field immunochromatographic tests to expert microscopy in the diagnosis of malaria

In Myanmar, we tested two rapid malaria immunochromatographic kits: the OptiMAL assay for the detection of parasite lactate dehydrogenase (pLDH), and the ICT Malaria P.f./P.v. test for histidine-rich protein 2 (PfHRP2) and panmalarial antigens. A total of 229 patients were examined, of whom 133 were found to be malaria positive by Giemsa microscopy. Both OptiMAL and ICT gave lower sensitivities than previously reported. ICT sensitivity for Plasmodium falciparum and non-falciparum parasites were 86.2 and 2.9%, respectively; specificity was 76.9 and 100%, respectively. OptiMAL sensitivity for P. falciparum and non-falciparum parasites were 42.6 and 47.1%, respectively; specificity was 97.0 and 96.9%, respectively. The sensitivity of both tests for the detection of both P. falciparum and non-falciparum parasites increased with parasite density. Several explanations for these results are explored. Our results raise particular concern over batch quality variations of malaria rapid diagnostic devices (MRDDs).

Evidence for different mechanisms of chloroquine resistance in 2 Plasmodium species that cause human malaria

Chloroquine (CQ)-resistant Plasmodium vivax malaria was first reported 12 years ago, nearly 30 years after the recognition of CQ-resistant P. falciparum. Loss of CQ efficacy now poses a severe problem for the prevention and treatment of both diseases. Mutations in a digestive vacuole protein encoded by a 13-exon gene, pfcrt, were shown recently to have a central role in the CQ resistance (CQR) of P. falciparum. Whether mutations in pfcrt orthologues of other Plasmodium species are involved in CQR remains an open question. This report describes pfcrt homologues from P. vivax, P. knowlesi, P. berghei, and Dictyostelium discoideum. Synteny between the P. falciparum and P. vivax genes is demonstrated. However, a survey of patient isolates and monkey-adapted lines has shown no association between in vivo CQR and codon mutations in the P. vivax gene. This is evidence that the molecular events underlying P. vivax CQR differ from those in P. falciparum.

The Toxoplasma homolog of Plasmodium apical membrane antigen-1 (AMA-1) is a microneme protein secreted in response to elevated intracellular calcium levels

A monoclonal antibody (MAb) has been generated against a novel 63 kDa surface/apical antigen of Toxoplasma gondii tachyzoites which is identified here as TgAMA-1, the Toxoplasma homolog of Plasmodium apical membrane antigen-1 (AMA-1). Sequence analysis, phase partitioning in Triton X-114, and labeling of TgAMA-1 with iodonaphthalene azide all suggest that TgAMA-1 is a type I transmembrane protein. There is a high degree of sequence similarity between TgAMA-1 and Plasmodium AMA-1, most notably in the position of conserved cysteine residues within the protein's predicted extracellular domain. In contrast to full length Plasmodium AMA-1, which has previously been localized to the rhoptries, it is shown here by immunofluorescence and immunoelectron microscopy that intracellular TgAMA-1 is found in the micronemes. A 53 kDa N-terminal proteolytic fragment of TgAMA-1 is constitutively secreted from the parasite at 37 degrees C. As is the case with other microneme proteins, the proteolytic processing and secretion of TgAMA-1 is dramatically enhanced in response to treatments which increase intracellular calcium levels.

The structure of malaria pigment beta-haematin

Despite the worldwide public health impact of malaria, neither the mechanism by which the Plasmodium parasite detoxifies and sequesters haem, nor the action of current antimalarial drugs is well understood. The haem groups released from the digestion of the haemoglobin of infected red blood cells are aggregated into an insoluble material called haemozoin or malaria pigment. Synthetic beta-haematin (FeIII-protoporphyrin-IX)2 is chemically, spectroscopically and crystallographically identical to haemozoin and is believed to consist of strands of FeIII-porphyrin units, linked into a polymer by propionate oxygen-iron bonds. Here we report the crystal structure of beta-haematin determined using simulated annealing techniques to analyse powder diffraction data obtained with synchrotron radiation. The molecules are linked into dimers through reciprocal iron-carboxylate bonds to one of the propionic side chains of each porphyrin, and the dimers form chains linked by hydrogen bonds in the crystal. This result has implications for understanding the action of current antimalarial drugs and possibly for the design of new therapeutic agents.

Monkeys of the rainforest in French Guiana are natural reservoirs for P. brasilianum/P. malariae malaria

Monkey blood samples were collected from 214 monkeys relocated as part of the wildlife rescue organized in French Guiana during the filling of the Petit Saut Dam on the Sinnamary River. These samples were tested for malaria parasites by microscopy of thick blood filsm and by nested PCR for small subunit rRNA genes (SSUrRNA). Parasitic blood forms similar to Plasmodium brasilianum were detected in 4 monkey species: Alouatta seniculus macconnelli, Saguinus midas midas, Pithecia pithecia and Ateles paniscus paniscus, with the highest prevalence in Alouatta monkeys. PCR was more sensitive than the conventional method for detecting low-grade parasitaemia in positive monkeys. The examination of blood films indicated that 5.6% of the animals carried parasites whereas the nested PCR for ribosomal DNA indicated a prevalence of 11.3%. The P. brasilianum SSUrRNA gene sequence was analysed and aligned with those from P. malariae, P. falciparum and P. vivax. This suggested that P. brasilianum and P. malariae are very closely related. Similar results were obtained from analysis of the sequences in P. malariae and P. brasilianum isolates of a polymorphic gene fragment analogous to the merozoite surface protein-1 (MSP-1) gene of P. falciparum. The P. brasilianum/P. malariae sequences were more similar to those of P. vivax than to those of P. falciparum, at least in the gene region examined. The high degree of DNA homology in the sequences of the SSUrRNA and msp1-like genes is consistent with other characterizations demonstrating a taxonomic relationship between P. brasilianum and P. malariae species. Our results provide further evidence that P. brasilianum and P. malariae are virtually identical and should probably be considered to be a single malaria species. This raises the question as to whether monkeys living in the rainforest are natural reservoirs for both simian and human malaria. These results have implications for the interpretation of the current epidemiological situation in French Guiana.

Modeling three-dimensional protein structures for amino acid sequences of the CASP3 experiment using sequence-derived predictions

Homology or comparative modeling is aimed at modeling the three-dimensional structure of a target sequence of unknown structure using the framework of an already known fold. Traditionally, homology modeling has been applied to targets with clear sequence similarity to proteins of known structure. Because methods to identify increasingly distant relationships have been developed, homology models can now be built for a wider range of targets. The first challenge in homology modeling is to obtain an initial, accurate, sequence-structure alignment with the most compatible fold. In CASP3, the abilities of fold-recognition methods to fulfill this challenge were evaluated with a number of target sequences of unknown structure. Sequence-structure alignments for 33 of the CASP3 targets using the fold-recognition method SDP were submitted (Fischer and Eisenberg, Protein Sci 1996; 5:947-955). After the three-dimensional structures of the sequences were subsequently released, the quality of the predictions were evaluated. Here I describe three of the predictions for targets with little sequence similarity to proteins of known structure that were judged by the assessors to be of higher quality. For two of these predictions, the sequence-structure alignment corresponded perfectly to the structural alignment (zero average shift), and for the third, the average shift was 0.1. This alignment accuracy entails an ideal starting point for homology modeling.

[Cytoskeletal actin and its associated proteins. Some examples in Protista]

Many processes, cell motility being an example, require cells to remodel the actin cytoskeleton in response to both intracellular and extracellular signals. Reorganization of the actin cytoskeleton involves the rapid disassembly and reassembly of actin filaments, a phenomenon regulated by the action of particular actin-binding proteins. In recent years, an interest in studying actin regulation in unicellular organisms has arisen. Parasitic protozoan are among these organisms and studies of the cytoskeleton functions of these protozoan are relevant related to either cell biology or pathogenicity. To discuss recent data in this field, a symposium concerning "Actin and actin-binding proteins in protists" was held on May 8-11 in Paris, France, during the XXXV meeting of the French Society of Protistology. As a brief summary of the symposium we report here findings concerning the in vitro actin dynamic assembly, as well as the characterization of several actin-binding proteins from the parasitic protozoan Entamoeba histolytica, Trichomonas vaginalis and Plasmodium knowlesi. In addition, localization of actin in non-pathogen protists such as Prorocentrum micans and Crypthecodinium cohnii is also presented. The data show that some actin-binding proteins facilitate organization of filaments into higher order structures as pseudopods, while others have regulatory functions, indicating very particular roles for actin-binding proteins. One of the proteins discussed during the symposium, the actin depolymerizing factor ADF, was shown to enhance the treadmilling rate of actin filaments. In vitro, ADF binds to the ADP-bound forms of G-actin and F-actin, thereby participating in and changing the rate of actin assembly. Biochemical approaches allowed the identification of a protein complex formed by HSP/C70-cap32-34 which might also be involved in depolymerization of F-actin in P. knowlesi. Molecular and cellular approaches were used to identify proteins such as ABP-120 and myosin IB at the leading edge of E. histolytica. ABP-120 organizes F-actin in a network and myosin IB participates in the pseudopod formation. Similar approaches using T. vaginalis resulted in the discovery of an actin-binding protein that participate in the F-actin reorganization during adhesion of parasites to target cells. This protein is homologous to alpha-actinin from other eukaryotic cells. Finally, by using cell biology approaches, F-actin was observed in the cytoplasm as well as in the nucleus of Dinoflagellates. The recent developments in the molecular genetics of protozoa will provide new insights to understand the roles of actin-binding proteins during cytoskeleton activities.

Synthetic peptides corresponding to a repetitive sequence of malarial histidine rich protein bind haem and inhibit haemozoin formation in vitro

Synthetic peptides containing a repetitive hexapeptide sequence (Ala-His-His-Ala-Ala-Asp) of malarial histidine-rich protein II were evaluated for binding with haem in vitro. The pattern of haem binding suggested that each repeat unit of this sequence provides one binding site for haem. Chloroquine inhibited the haem-peptide complex formation with preferential formation of a haem chloroquine complex. In vitro studies on haem polymerisation showed that none of the peptides could initiate haemozoin formation. However, they could inhibit haemozoin formation promoted by a malarial parasite extract, possibly by competitively binding free haem. These results indicate this hexapeptide sequence represents the haem binding site of the malarial histidine-rich protein and possibly the site of nucleation for haem polymerisation.

Structural similarities among malaria toxins insulin second messengers, and bacterial endotoxin

Malaria toxin causes hypoglycemia and induction of tumor necrosis factor. Extracts of parasitized erythrocytes which were coeluted and copurified with one of the two subtypes of mammalian insulin-mimetic inositolphosphoglycans similarly induced fibroblast proliferation in the absence of serum. In addition, induction of tumor necrosis factor in macrophages by malaria toxin and by lipopolysaccharide from Escherichia coli was enhanced by pretreatment of these toxins with alpha-galactosidase. Thus, parasitized erythrocytes contain both soluble inositolphosphoglycan-like insulin second messengers and endotoxin-like lipidic molecules.

The blood-stages of Plasmodium georgesi, P. gonderi and P. petersi: course of untreated infection in their natural hosts and additional morphological distinctive features

In the blood of a Cercocebus albigena and of a C. galeritus agilis monkey, the infection with Plasmodium gonderi was found to follow its well-known chronic course; P. georgesi seemed to occur as a relapsing type of malaria parasite; P. petersi was found for only a few days and at a low level in C. albigena (end of an attack?). As shown by using polarized light, the pigment granules appeared mostly as fine dots in P. georgesi, short rods in P. gonderi and long needles in P. petersi. The three species can be distinguished by the morphological appearance of the nucleus of the young trophozoites, and also by the measurement of its surface area (Sa): small round nucleus (Sa = 0.81 +/- 0.06 microns 2) in P. gonderi, large 2-coloured nucleus (Sa = 1.43 +/- 0.21 microns 2) in P. petersi, and long crescent-shaped nucleus (Sa = 2.18 +/- 0.25 microns 2) in P. georgesi. The first colour illustrations of the blood-stages of P. georgesi are presented. The dynamics of single and mixed blood infections in primate malaria parasites are discussed, with a proposal to classify them into 3 types.

The red cell membrane and invasion by malarial parasites

The red cell membrane with its bilipid layer, integral membrane proteins (especially the GPs and band 3), and the red cell skeleton pose a formidable barrier for the malarial parasite to overcome during invasion. Invasion is an ordered and sequential process, indicating a highly complex and specific process involving numerous molecular interactions. For P. vivax and P. knowlesi infections the Duffy glycoprotein seems to be a specific requirement in invasion. For P. falciparum the GPs, and especially the N-acetyl neuraminic acid linked in an alpha 2-3 configuration on them, appear to act as specific ligands although some strains of P. falciparum may use alternate ligands for invasion. The parasite enters the red cells within an invagination continuous with the red cell bilipid layer, the parasitophorous vacuole membrane, and recent evidence would indicate that this membrane is largely of parasite origin. The numerous occasions in which the red cell needs to deform during invasion indicates that membrane deformability could be an important factor in determining invasion, but the dissociation of invasion and deformability as induced by a number of reagents would not support this contention. Instead it is suggested that reagents which modify invasion may be acting via alterations in red cell or parasite protein phosphorylation or dephosphorylation.

Binding of malarial circumsporozoite protein to sulfatides [Gal(3-SO4)beta 1-Cer] and cholesterol-3-sulfate and its dependence on disulfide bond formation between cysteines in region II

Region II of the malaria circumsporozoite (CS) protein is highly conserved between the CS proteins of different species of malaria. Amino acid sequences homologous to that of region II are found in thrombospondin, properdin, von Willebrand factor and a few other proteins. We show here that the native CS protein from the rodent parasite Plasmodium berghei, and recombinant Plasmodium vivax and Plasmodium falciparum CS proteins containing region II, but not recombinant proteins lacking region II, specifically bind to sulfatides and cholesterol-3-sulfate. The binding is abolished following reduction and alkylation of the proteins. Region II contains 2 cysteines separated by only 3 amino acids, S(N), V, T, and these are the only cysteines present in our recombinant proteins. Therefore, our findings strongly suggest that the region II cysteines are linked by a disulfide bond forming a small peptide loop. We also present evidence that the recognition of sulfatides, cholesterol-3-sulfate, or other cross-reactive sulfated macromolecules by region II may be required during sporozoite invasion of liver cells. Antibodies to a peptide representing region II react with live sporozoites and with sporozoites fixed with glutaraldehyde, indicating that this region is exposed on the surface of the parasites. Furthermore, we have found that the sulfatide and cholesterol-3-sulfate recognition by the CS proteins, and the invasion of hepatocytes by P. berghei sporozoites, are specifically inhibited by dextran sulfate.

Repeat regions of malaria parasite proteins: a review of structure and possible role in the biology of the parasite

Tandemly repeated amino acid sequences are characteristic of many malaria parasite proteins that have been sequenced to date. Strong selective pressures must exist to maintain the repeat regions and also to diversify them in the case proteins containing strain-variant repeats. Repeats have been suggested to function in immune-evasion and in binding to host receptors. This article focuses on the structural characteristics of the repeats in relation to their postulated function.