Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag

We are currently witnessing a major epidemic caused by the 2019 novel coronavirus (2019-nCoV). The evolution of 2019-nCoV remains elusive. We found 4 insertions in the spike glycoprotein (S) which are unique to the 2019-nCoV and are not present in other coronaviruses. Importantly, amino acid residues in all the 4 inserts have identity or similarity to those in the HIV-1 gp120 or HIV-1 Gag. Interestingly, despite the inserts being discontinuous on the primary amino acid sequence, 3D-modelling of the 2019-nCoV suggests that they converge to constitute the receptor binding site. The finding of 4 unique inserts in the 2019-nCoV, all of which have identity /similarity to amino acid residues in key structural proteins of HIV-1 is unlikely to be fortuitous in nature. This work provides yet unknown insights on 2019-nCoV and sheds light on the evolution and pathogenicity of this virus with important implications for diagnosis of this virus.

RF-GlutarySite: a random forest based predictor for glutarylation sites

Glutarylation, which is a newly identified posttranslational modification that occurs on lysine residues, has recently emerged as an important regulator of several metabolic and mitochondrial processes. Here, we describe the development of RF-GlutarySite, a random forest-based predictor designed to predict glutarylation sites based on protein primary amino acid sequence.

New Delhi metallo-β-lactamase (NDM)

Metallo-β-lactamases (MBLs) are a class of Zn(II)-containing enzymes that hydrolyse the β-lactam bond in β-lactam-containing antibiotics, resulting in products that no longer exhibit antibacterial activity. Currently, there are 29 known MBLs (not including variants), and these enzymes have been classified on the basis of primary amino acid sequence and functionality into three or four classes (see www.mbled.uni-stuttgart.de for an updated MBL database)1. MBLs in classes B1 and B3 are known for their ability to hydrolyse all β-lactam antibiotics, except monobactams, including penicillins, carbapenems and cephalosporins. The class B2 enzymes exhibit a narrower substrate preference and preferentially hydrolyse carbapenems2. The most clinically important MBLs belong to class B1, which contains VIM (Verona integrinencoded MBLs), IMP (imipenemase) and NDM (New Delhi MBL), and all of these enzymes have multiple clinical variants (VIM-1—VIM-46, IMP-1—IMP-51, and NDM-1—NDM-16) (www.lahey.org/Studies/). The presence of multiple variants poses a challenge to identify clinical inhibitors because the variants often exhibit different substrate specificities and are affected differently by known non-clinical inhibitors3.

Spider silk morphology for responsive materials

ABSTRACTThis study reveals that an “old” mechanism for shape memory in oriented polymers is in fact just one separate contribution for “supercontraction” in Nephila spider major ampulate silks. When Nephila spider silks are in contact with liquid water, they “super”-contract up to 28% of the original stretched length. However, we discovered that under glass transition conditions these silks only relax with a maximum shrinkage of 13%, and this phenomenon is defined as Tg-contraction. Structural components permanent order (PO), permanent disorder (PD), meta order (MO) and meta disorder (MD) were proposed from the primary amino-acid sequence of the silk protein to explain morphological changes in the two contraction phenomena: MD contributes 13% of the full supercontraction and contributes to Tg-contraction; whereas MO (the proline-containing motifs) contributes the rest for the full super-contraction and does not contribute to Tg-contraction. The morphology in Nephila spider silk structure suggests two separate mechanisms to generate the shape memory effect in synthetic polymers.

Expression of Atp8b3 in murine testis and its characterization as a testis specific P-type ATPase

Spermatogenesis is a complex process that produces haploid motile sperms from diploid spermatogonia through dramatic morphological and biochemical changes. P-type ATPases, which support a variety of cellular processes, have been shown to play a role in the functioning of sperm. In this study, we isolated one putative androgen-regulated gene, which is the previously reported sperm-specific aminophospholipid transporter (Atp8b3, previously known asSaplt), and explored its expression pattern in murine testis and its biochemical characteristics as a P-type ATPase.Atp8b3is exclusively expressed in the testis and its expression is developmentally regulated during testicular development. Immunohistochemistry of the testis reveals thatAtp8b3is expressed only in germ cells, especially haploid spermatids, and the protein is localized in developing acrosomes. As expected, from its primary amino acid sequence, ATP8B3 has an ATPase activity and is phosphorylated by an ATP-producing acylphosphate intermediate, which is a signature property of the P-Type ATPases. Together, ATP8B3 may play a role in acrosome development and/or in sperm function during fertilization.

Prions in control of cell glycosylation

Prion proteins that are normal cellular components or involved in pathology can vary little or not at all in primary amino acid sequence, but their glycosylation is different, e.g. in scrapie versus normal forms; in mouse strain-specific isolates; and in BSE (bovine spongiform encephalopathy) and variant CJD (Creutzfeldt–Jakob disease) versus classical CJD. The results of Nielsen et al. published in this issue of the Biochemical Journal show that changes in glycosylation are not restricted to the prion. The paper comprehensively characterizes a decrease in the glycosylation of the insulin receptor in scrapie-infected neuroblastoma cells, but no change in glycosylation of the insulin-like growth factor-1 receptor. Thus the scrapie prion can influence glycosylation, not only of itself, but also of other selected cell glycoproteins.

Role of the C-terminal YG repeats of the primer-dependent streptococcal glucosyltransferase, GtfJ, in binding to dextran and mutan

The recombinant primer-dependent glucosyltransferase GtfJ of Streptococcus salivarius possesses a C-terminal glucan-binding domain composed of eighteen 21 aa YG repeats. By engineering a series of C-terminal truncated proteins, the position at which truncation prevented further mutan synthesis was defined to a region of 43 aa, confirming that not all of the YG motifs were required for the formation of mutan by GtfJ. The role of the YG repeats in glucan binding was investigated in detail. Three proteins consisting of 3·8, 7·2 or 11·0 C-terminal YG repeats were expressed in Escherichia coli. Each of the three purified proteins bound to both the 1,6-α-linked glucose residues of dextran and the 1,3-α-linked glucose residues of mutan, indicating that a protein consisting of nothing but 3·8 YG repeats could attach to either substrate. Secondary structure predictions of the primary amino acid sequence suggested that 37% of the amino acids were capable of forming a structure such that five regions of β-sheet were separated by regions capable of forming β-turns and random coils. CD spectral analysis showed that the purified 3·8 YG protein possessed an unordered secondary structure with some evidence of possible β-sheet formation and that the protein maintained this relatively unordered structure on binding to dextran.