A ffinity-based proteomics reveal cancer-specific networks coordinated by Hsp90

Hsp90 is a house keeping protein that assists in folding and transloction of proteins. It is also shown to be up-regulated in cancer cells. In this paper, the authors show that the small molecule, PU-H71, binds to and inhibits a fraction of Hsp90 that is more abundant in cancer cells. They then take PU-H71, and use an affinity capture method to identify proteins that are up regulated in different cancer types.

Enzyme directed assembly and manipulation of organic nanomaterials

This article talks about taking advantage of the enzymatic reactions to make organic nanoscale materials. Three different approaches are described. First, Engineered enzymes are able to assemble and form aggregations or change morphology via polymeric precursors. Second, engineered enzymes, having the ability to aggregate, form hydrogel upon small molecule treatment. Third, phosphatase or a destabilizing switch element triggers a conformation change of a peptide leading to polymer aggregation and formation of nanofibrils. These advancements can lead future material with biological systems. 

Spontaneous Crowding of Ribosomes and Proteins inside Vesicles: A Possible Mechanism for the Origin of Cell Metabolism

In this article, the authors encapsulate macromolecules and cellular machinery to show how cellular metabolism may have spontaneously occurred. By monitoring the vesicles with cryo-TEM, they were able to quantify the contents to show that encapsulated molecules varied from the theoretical distribution of molecules. The researchers were also able to encapsulate cellular lysate and monitor the production of GFP in a vesicle. From these experiments, the authors were able to conclude that spontaneous formation of vesicles may have lead to simple cellular metabolism. I thought the article was interesting because it investigated basic cellular function and operation from a ground-up approach.

Learning from Nature's Drug Factories: Nonribosomal Synthesis of Macrocyclic Peptides

In Gavin's class we discussed the mechanism and promiscuity of the thioesterase domain from tyrocidine A biosynthesis. Chris suggested that only N-terminal D-Phe and Orn amino acid residues are important for cyclization activity of TycC because it might be that only these residues are accommodated into the active site of the TycC, with the rest of the polypeptide chain looping out of the enzyme. This review paper provides some insights into the mechanism of TE-catalized macrocyclization. Based on crystal structure solved for SrfTE, it has been determined that only two Leu residues were important for cyclization, with the rest of the peptide sequence less well coordinated. This agrees with what Chris suggested and explains the promiscuity of these NRPSs.

Expanded Click Conjugation of Recombinant Proteins with Ubiquitin-Like Modifiers Reveals Altered Substrate Preference of SUMO2-Modified Ubc9

This paper reports a new way to add a Ubiquitin-like modifier on a protein via click chemistry. Ubiquitin-like (Ubl) modifiers are important in the regulation of a lot of biological pathways and while the specific introduction of a Ubl modifier at a certain site of a protein would be interesting, it is really challenging to achieve. They developed a Ubl-modified enzyme using unnatural amino acid mutagenesis and click chemistry, they selectively introduced a small ubiquitin-like modifier at position 14 of Ubc9.

Enhancement of proteasome activity by a small-molecule inhibitor of USP14

In Alex's class we discussed ubiquitin labeling technologies which can degrade proteins. Naturally proteins are ubquitinated via the E1,E2, E3 pathway and broken down by the proteasome. The protein USP14 is in a class of ubquitin trimming enzymes that prevent degradation of a target protein. This paper describes the discovery and use of a small molecule that inhibits USP14, which results in a increase in proteasomal degradation.

A Small-Molecule Screening Strategy To Identify Suppressors of Statin Myopathy

Wagner and coworkers used myotube ATP levels to screen for induction or prevention of myopathy caused by statins. They found that statins decreased ATP levels, but addition of geranylgeranyl pyrophosphate (GGPP) restored ATP levels caused by statins, indicating a role for protein prenylation in causation of myopathy. Additionally, they found that inhibition of GGT-II decreased ATP levels, indicating that Rab prenylation is being blocked. They screened a library of compounds and found 4 that restored ATP levels when co-administered with statins. Inhhibition of GGII blocked the rescue caused by those four compounds. Finally, one of the compounds was tested with a statin in zebrafish and was found to reduce myopathy.

Exploration of Biarsenical Chemistry - Challenges in Protein Research

Here is a review article about a class of fluorophores, biarsenical probes, that be attached to a target protein containing (engineered to contain) a 4-cyseteine motif - CCXXCC- . While free molecules are virtually non-fluorescent, binding to this motif produces specific tagging with high fluoresence in-vivo. Cysteine makes a logical target because of its relative low abundance and high nucleophilicity. The authors suggest that this technology has the ability to be applied to many other techniques in biology, either for measurement -, FRET, Purification of proteins, electron microscopy or alteration of the system - such as Enzyme activity switching, or linking interacting proteins .

N-PEGylation of a Reverse Turn Is Stabilizing in Multiple Sequence Contexts, unlike N-GlcNAcylation

Protein stabilization is an important issue in Biology. Conjugation of poly(ethylene glycol) (PEG) oligomer onto a folded protein can improve shelf life and protein thermodynamic stability. In this article, allowing N-PEGylation to occur in various sequence contexts, PEGylation stabilizes native proteins compared to N-GlcNAcylation which is stabilized only in a particular sequence context.