Finding the sweet spot
Article first published online: 23 NOV 2011
Copyright © 2011 Wiley Periodicals, Inc.
Volume 97, Issue 2, pages iii–iv, February 2012
How to Cite
(2012), Finding the sweet spot. Biopolymers, 97: iii–iv. doi: 10.1002/bip.22008
- Issue published online: 23 NOV 2011
- Article first published online: 23 NOV 2011
Finding the Sweet Spot
The outer envelope of the human immunodeficiency virus (HIV) is masked by a forest of glycans, and long-standing conventional wisdom has held that these sugars represent a near-impregnable shield against antibody recognition. More recent studies have put the lie to this notion, however, demonstrating that it is possible to elicit antibodies that bind strongly and specifically to glycosylated gp120 and that these might potentially achieve broad, cross-clade neutralization.
Pejchal et al. recently derived six such antibodies, and have now set about characterizing the manner in which two of these monoclonals, PG127 and PG128, interact with their viral target. Crystallographic analysis revealed that the antibodies simultaneously interact with three distinct sites on gp120. Two of these are glycans, attached to gp120 in close proximity to one another at Asn332 and Asn301, while the third binding site is part of the protein itself, on the highly-conserved V3 loop of gp120's outer domain. Strikingly, the Asn332 glycosylation is conserved across 73% of known HIV-1 isolates, and PG128 has likewise demonstrated the ability to neutralize 72% of viral subtypes.1
In a series of cell culture experiments, the researchers confirmed that both antibodies demonstrate strong affinity for gp120 trimers, and uncovered data indicating that GP127 and 128 may achieve enhanced potency in neutralizing viruses by cross-linking multiple gp120 ‘spikes’ together. Indeed, they determined that these antibodies can dramatically accelerate the rate at which viral infectivity declines over time. Collectively, these findings offer new hope for vaccine research efforts by demonstrating the feasibility of eliciting an effective immune counterattack that can recognize exposed epitopes that are shared across a majority of HIV-1 subtypes.—Michael Eisenstein
Pejchal, R. et al. Science, Published online 13 October 2011, doi: 10.1126/science.1213256.
Take it to the Limit
In order to understand why cells grow to a certain size or thrive at a particular temperature, one must understand the physical principles that constrain biological functions. This may seem like a daunting task, but Dill et al. have performed various mathematical analyses that probe the limits within which a given cell might successfully operate and thereby formulated a series of hypotheses regarding the evolutionary impacts of those strictures.
Remarkably, they conclude that the key parameter determining many of a protein's fundamental thermodynamic properties is its length. Following this determination, they find that many cells flourish at temperatures that are remarkably close to the point at which their proteomes would face a ‘denaturation catastrophe’, which suggests that they have evolved to operate at temperatures where metabolic processes run as rapidly as possible without crossing that terminal line.
Similar kinetic compromises appear to influence other key features of cells such as protein density, which must be neither so low that proteins need to travel great distances to encounter binding partners nor so high that intracellular transit is thwarted by constant collisions, as well as average size and replication rate.2
The standard 20 minute doubling time of Escherichia coli bacteria is remarkably close to the hypothetical maximum that these cells might achieve if they were operating with an ultra-minimal proteome, suggesting that the division process has been near-maximally streamlined over the course of evolution. On the other hand, this high division rate may keep such cells relatively small; the authors determine that the time required for protein diffusion across distances of >100 micrometers could introduce a rate-limiting bottleneck for replication. The fact that most cells are considerably smaller in diameter may therefore represent a compromise to enable faster replication.—Michael Eisenstein
Dill, K.A. et al. Proc. Natl. Acad. Sci. USA,108, 17876–17882 (2011).
A Piece of the Puzzle
Protein synthesis is a highly regulated process, in eukaryotic cells beginning with recognition of a 5'cap that is added to the mRNA and assembly of a complex of initiation factors. Some viruses, such as hepatitis C (a serious pathogen), circumvent this process by forming a structure in the mRNA that directly binds to ribosomes to initiate translation. By doing so they avoid efforts at down regulation of protein synthesis by the host cell. This special element of the mRNA is known as the ‘internal ribosome entry site’ (IRES), and is a rather complex folded RNA of ≈350 nucleotides. Determining structures of large RNAs remains very challenging, and so the approach taken by many groups to analyzing the IRES has been to divide it into more manageable pieces, solved their structures at high resolution, and then see where they may fit into lower resolution electron microscope images, the last process somewhat like fitting together pieces of a jigsaw puzzle. While many parts of the IRES have had structures reported, a key ‘linchpin’ piece at the center of the IRES puzzle remained unsolved until the report this month in Structure appeared. Berry et al.1 did extensive optimization of the ‘pseudoknot domain’, including engineering in tetraloop-receptor interactions to stabilize the molecules in the crystals. The structure they were then able to determine has a complex four-way junction (four different pieces of duplex RNA that come together at one point), with two loop elements folding back to form the pseudoknots (elements that look almost like knots in the RNA ‘string’). The structure has unusual tertiary structure elements that are key to positioning the start codon to interact with the ribosome. Determining a the molecular structure of this central piece of the IRES jigsaw puzzle provides better understanding of the overall structure derived from microscopy, and how it functions in starting translation. This work also serves as a reminder of how complex RNA folds can be, and such folds cannot yet be reliably predicted.—David Wemmer
Berry, K.E. et al., Structure,19, 1456–66 (2011).