The FEBS JournalVolume 280, Issue 1 p. 319-319 Author indexFree Access Author index First published: 03 January 2013 https://doi.org/10.1111/j.1742-4658.2012.08759.xAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat No abstract is available for this article. Volume280, Issue1January 2013Pages 319-319 RelatedInformation

Lafora disease (LD) proteins laforin and malin assemble as a disruptor to breakdown polyglucosan synthesized by muscle glycogen synthase (GS1) for endoplasmic reticulum stress relief. The process requires laforin phosphatase and malin E3 ligase activities and their recruitment to polyglucosan. Deficiency in laforin increases malin polyubiquitination and polyglucosan bodies in brain neurons. These results imply a causative pathogenic mechanism underlying LD.

Prediction and understanding of the folding and stability of the 3D structure of proteins is still a challenge. The different atomic interactions, such as non polar contacts and hydrogen bonding, are known but their exact relative weights and roles when contributing to protein folding and stability are not identified. Initiated by a previous molecular dynamics simulation of fully ester-linked hen egg white lysozyme (HEWL), which showed a more compact fold of the ester-linked molecule compared to the native one, three variants of this protein are analyzed in the present study. These are 129-residue native HEWL, partly ester-linked HEWL, in which only 34 peptide linkages that are not involved in the helical or β-strand parts of native HEWL were replaced by ester linkages, and fully (126 residues) ester-linked HEWL. Native and partly ester-linked HEWL showed comparable behaviour, whereas fully ester-linked HEWL could not maintain the native secondary structure of HEWL in the simulation and adopted a more compact fold. The conformational changes were analyzed by comparing simulation averaged values of quantities that can be measured by NMR, such as (1)H-(15)N backbone order parameters, residual dipolar couplings, proton-proton NOE distances and (3)J-couplings with the corresponding values derived from experimental NMR data for native HEWL. The information content of the latter appeared to be insufficient to detect the local conformational rearrangements upon esterification of the loop regions of the protein. For fully ester-linked HEWL, a significantly reduced agreement was observed. Upon esterification, the backbone-side chain and side chain-side chain hydrogen-bonding pattern of HEWL changes to maintain its compactness and thus the structural stability of the ester-linked lysozymes.

The inhibition of phosphatases by adenosine 5'-phosphorothioate (AMPS) was first reported in the late 1960s; however, the structural basis for the inhibition has remained unknown. Here, it is shown that AMPS is a submicromolar inhibitor of class C acid phosphatases, a group of bacterial outer membrane enzymes belonging to the haloacid dehalogenase structural superfamily. Furthermore, the 1.35-Å resolution crystal structure of the inhibited recombinant Haemophilus influenzae class C acid phosphatase was determined; this is the first structure of a phosphatase complexed with AMPS. The conformation of AMPS is identical to that of the substrate 5'-AMP, except that steric factors force a rotation of the thiophosphoryl out of the normal phosphoryl-binding pocket. This conformation is catalytically nonproductive, because the P atom is not positioned optimally for nucleophilic attack by Asp64, and the O atom of the scissile O-P bond is too far from the Asp (Asp66) that protonates the leaving group. The structure of 5'-AMP complexed with the Asp64→Asn mutant enzyme was also determined at 1.35-Å resolution. This mutation induces the substrate to adopt the same nonproductive binding mode that is observed in the AMPS complex. In this case, electrostatic considerations, rather than steric factors, underlie the movement of the phosphoryl. The structures not only provide an explanation for the inhibition by AMPS, but also highlight the precise steric and electrostatic requirements of phosphoryl recognition by class C acid phosphatases. Moreover, the structure of the Asp64→Asn mutant illustrates how a seemingly innocuous mutation can cause an unexpected structural change.

For gene switching, chromatin must be manipulated, a process initiating at key cis-controlling elements, labelled operationally as DNaseI hypersensitive sites (DHS). This minireview series expands on how the remodelling of chromatin structure comes about and the consequences for gene activation and repression The conventional wisdom embodied (but not, in this age of rapid development, embalmed) in many textbooks has it that chromatin exists in cells either in a linker histone-containing condensed fibre of nucleosomes, diameter 30–40 nm, characteristic of heterochromatin, or as an open extended beads-on-a-string like structure, characteristic of all active genes. Even brief thought gives the lie to the second concept, since in very active tissues such as brain or stem cells in which, say, 40% of all genes are active, were they all fully extended throughout their transcribed length the nuclear volume could not possibly accommodate them. Since the chromatin of an active gene must be opened up at the moment of polymerase passage, it follows that continuous manipulation of chromatin structure must occur at active genes. Indeed, using the criterion of DNaseI accessibility we have recently shown that the overall state of certain active genes differs little from that of an immediately adjacent heterochromatin segment, experimentally demonstrated to be in the form of the 30 nm fibre. This time-averaged observation does not apply, however, to cis-controlling elements such as promoters and enhancers that, since the seminal observations of Hal Weintraub and Mark Groudine in 1976, have been shown to be locally hypersensitive to DNaseI digestion, i.e. in a more open conformation. Thus whereas the presence of bound histones, including the H1 linker, does not in general present a barrier to passage of the polymerase complex through an active gene, access to the DNA at cis elements requires a more open structure. It is worth emphasizing that DNaseI remains a valuable tool in studying local chromatin structure, not only for defining key control points as DNaseI hypersensitive sites, but also for locating the rare segments of open nucleosomal chromatin, i.e. genuine beads-on-a-string structures, sometimes found in the region of promoters or enhancers. This results from the fact that, whereas MNase digestion of nuclei always gives rise to conventional nucleosomal ladders, whether the underlying structure is the 30 nm fibre or open nucleosomal beads, DNaseI does not generate ladders from 30 nm chromatin fibres (the bulk of the chromatin) but it does from open beaded structures. Overall, the controlled manipulation of chromatin structure at such locations, in particular the displacement or even eviction of nucleosomes to permit the ordered recruitment of transcription factors, is a complex process requiring many interdependent components, in particular chromatin remodelling and histone modifying complexes. The following three minireviews address the problem of chromatin manipulation. The first, by Peter Cockerill, takes an overview of the chromatin structure at active genes and then illustrates this with the process of activating the human GM-CSF (granulocyte/macrophage colony stimulating factor) gene during T cell development, emphasizing how the binding of transcription factors is dependent on nucleosome displacement and is accompanied by the appearance of DNaseI hypersensitive sites. The paper by Gordon Hager and colleagues reviews how, following treatment of cells with steroid hormones, the chromatin structure of responsive genes changes in consequence of binding by the immediate hormone targets, the nuclear receptors. Finally, Stefan Dimitrov and his colleague Jan Bednar relate how the bare bone mechanics of chromatin manipulation could occur as nucleosomes and chromatin fibres are put under stress by pulling and tugging whilst held by optical and magnetic tweezers. In a field that can be confounded by the wide variation of experimental conditions, the authors very helpfully provide a summarizing table of published results.

Human β-defensin-2 (HBD-2) is an antimicrobial peptide produced by the epithelial cells that plays an important role in innate and adaptive immunity. Here we report that high mobility group protein N2 (HMGN2), a member of the high mobility group superfamily that affects chromatin function, modulates the expression of HBD-2 in A549 cells treated by lipopolysaccharide. Mechanistically, HMGN2 prolongs the retention time and enhances the accumulation of nuclear factor κB p65 in the nucleus, and promotes the acetylation of p65 through increasing histone acetyltransferase activity and enhancing p65-Ser536 phosphorylation. Additionally, chromatin immunoprecipitation reveals that HMGN2 and p65 synergistically promote their specific binding to HBD-2 promoter, thereby affecting the downstream transcription. Taken together, these results suggest that HMGN2 acts as a positive modulator of nuclear factor κB signalling to promote lipopolysaccharide-induced β-defensin expression.