Severe liver disease caused by chronic hepatitis C virus is the major indication for liver transplantation. Despite recent advances in antiviral therapy, drug toxicity and unwanted side effects ...render effective treatment in liver‐transplanted patients a challenging task. Virus‐specific therapeutic antibodies are generally safe and well‐tolerated, but their potential in preventing and treating hepatitis C virus (HCV) infection has not yet been realized due to a variety of issues, not least high production costs and virus variability. Heavy‐chain antibodies or nanobodies, produced by camelids, represent an exciting antiviral approach; they can target novel highly conserved epitopes that are inaccessible to normal antibodies, and they are also easy to manipulate and produce. We isolated four distinct nanobodies from a phage‐display library generated from an alpaca immunized with HCV E2 glycoprotein. One of them, nanobody D03, recognized a novel epitope overlapping with the epitopes of several broadly neutralizing human monoclonal antibodies. Its crystal structure revealed a long complementarity determining region (CD3) folding over part of the framework that, in conventional antibodies, forms the interface between heavy and light chain. D03 neutralized a panel of retroviral particles pseudotyped with HCV glycoproteins from six genotypes and authentic cell culture–derived particles by interfering with the E2‐CD81 interaction. In contrast to some of the most broadly neutralizing human anti‐E2 monoclonal antibodies, D03 efficiently inhibited HCV cell‐to‐cell transmission. Conclusion: This is the first description of a potent and broadly neutralizing HCV‐specific nanobody representing a significant advance that will lead to future development of novel entry inhibitors for the treatment and prevention of HCV infection and help our understanding of HCV cell‐to‐cell transmission. (Hepatology 2013;53:932–939)
Hantaviruses are zoonotic viruses transmitted to humans by persistently infected rodents, giving rise to serious outbreaks of hemorrhagic fever with renal syndrome (HFRS) or of hantavirus pulmonary ...syndrome (HPS), depending on the virus, which are associated with high case fatality rates. There is only limited knowledge about the organization of the viral particles and in particular, about the hantavirus membrane fusion glycoprotein Gc, the function of which is essential for virus entry. We describe here the X-ray structures of Gc from Hantaan virus, the type species hantavirus and responsible for HFRS, both in its neutral pH, monomeric pre-fusion conformation, and in its acidic pH, trimeric post-fusion form. The structures confirm the prediction that Gc is a class II fusion protein, containing the characteristic β-sheet rich domains termed I, II and III as initially identified in the fusion proteins of arboviruses such as alpha- and flaviviruses. The structures also show a number of features of Gc that are distinct from arbovirus class II proteins. In particular, hantavirus Gc inserts residues from three different loops into the target membrane to drive fusion, as confirmed functionally by structure-guided mutagenesis on the HPS-inducing Andes virus, instead of having a single "fusion loop". We further show that the membrane interacting region of Gc becomes structured only at acidic pH via a set of polar and electrostatic interactions. Furthermore, the structure reveals that hantavirus Gc has an additional N-terminal "tail" that is crucial in stabilizing the post-fusion trimer, accompanying the swapping of domain III in the quaternary arrangement of the trimer as compared to the standard class II fusion proteins. The mechanistic understandings derived from these data are likely to provide a unique handle for devising treatments against these human pathogens.
Plastic pollution in the world's ocean is one of the major environmental challenges that affects the society today, due to their persistence at sea, adverse consequences to marine life and being ...potentially harmful to human health. Rivers are now widely recognized as being the major input source of land-based plastic waste into the seas. Despite their key role in plastic transportation, riverine plastic pollution research is still in its infancy and plastic sources, hot-spots and degradation processes in riverine systems are to date poorly understood. In this contribution, we introduce a novel concept of following the aging of polypropylene based post-consumer goods placed in known trapping and mobility zones of macroplastics on a fluvial point bar, which was determined through repeated field surveys of macroplastic densities on this bar. As a proof-of-concept, we followed the degradation of 5 identical plastic butter tubs in 5 different locations on a riverbank and significant differences in the aging of the tubs were observed. The degree of aging of the tubs can to some extent be correlated to their proximity to the main river channel, exposure to natural conditions, such as solar radiation, and its storage time on land.
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•Novel concept of monitoring aging of plastic waste in riverine systems is proposed.•Macroplastic storage capacity depends on distance from river and riparian structure.•Aging of plastic is measured by following changes in polymer properties.•Unusual aging behavior of polypropylene based plastic is observed.•Degradation rate of plastic depends on location of the waste in riverine sink.
Why is the genetic code the way it is? Concepts from fields as diverse as molecular evolution, classical chemistry, biochemistry and metabolism have been used to define selection pressures most ...likely to be involved in the shaping of the genetic code.
Here minimization of kinetic energy disturbances during protein evolution by mutation allows an optimization of the genetic code to be highlighted. The quadratic forms corresponding to the kinetic energy term are considered over the field of rational numbers. Arguments are given to support the introduction of notions from basic number theory within this context. The observations found to be consistent with this minimization are statistically significant. The genetic code may well have been optimized according to energetic criteria so as to improve folding and dynamic properties of polypeptide chains.
This review focusses on the isolation of proteins from genomic or cDNA expression products libraries displayed on phage. The use of phage display is highlighted for the characterization of binding ...proteins with diverse biological functions. Phage display is compared with another strategy, the yeast two-hybrid method. The combination of both strategies is especially powerful to eliminate false positives and to get information on the biochemical functions of proteins.
Running in reverse: A set of enzymes selected according to their RNA‐dependent DNA polymerase activity from a library of more than 107 mutant enzymes has been characterized. The product was ...specifically bound to catalytically active proteins displayed on filamentous bacteriophage. The selected variants have a catalytic efficiency for reverse transcription that is two orders of magnitude higher.
The first symmetry by base substitutions of degeneracy in the genetic code was described by
Rumer (1966) and the other symmetries were identified later by
Jestin (2006) and
Jestin and Soulé (2007). ...Here, a rationale accounting for these symmetries is reported. The number of non-synonymous substitutions over the replicated coding sequence is written as a function of the substitution matrix, whose elements are the number of substitutions from any codon to any other codon. The
p-adic distance used as a similarity measure and applied to this matrix is shown to be biologically relevant. The rationale indicates that symmetries by base substitutions of degeneracy in the genetic code are symmetries of the measures of the number of non-synonymous substitutions for sets of synonymous codons.
A general strategy for the isolation of catalysts for given chemical reactions was designed. A FIRST LINK BETWEEN GENES AND THEIR CORRESPONDING PROTEINS WAS ESTABLISHED BY PHAGE DISPLAY: using ...Darwin's principles on evolution based on selection and amplification, rare protein molecules can then be selected for function from a large repertoire prior to their characterization by sequencing of their genes. A second link was created between enzymes and their products. By making use of the chelate effect and of Inovirus particles as a chemical, affinity chromatography for the reaction product is then sufficient to isolate among 10(6) to 10(11) proteins and their genes, the rare ones coding for catalysts of interest. The strategy for the parallel processing of information on the catalytic activity of variants from a large protein repertoire is highlighted in this review.
This letter reports complete sets of two-fold symmetries between partitions of the universal genetic code. By substituting bases at each position of the codons according to a fixed rule, it happens ...that properties of the degeneracy pattern or of tRNA aminoacylation specificity are exchanged.
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