Friday, February 16, 2018

Nature Chemical Biology Contents: March 2018, Volume 14 No 3 pp 187 - 325

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Nature Chemical Biology

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March 2018 Volume 14, Issue 3

Research Highlights
News and Views
Brief Communication

Nature Catalysis is an online-only journal that publishes research, review and comment across all areas of catalysis. 


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Altering form for function   p187
Elucidating the mechanisms by which biomolecules are chemically modified and how these alterations regulate biological pathways represents a leading frontier in chemical biology.



The ABCs of PTMs   pp188 - 192
Karl W Barber and Jesse Rinehart
Post-translational modifications (PTMs) are ubiquitous in all forms of life and often modulate critical protein functions. Recent chemical and biological advances have finally enabled scientists to precisely modify proteins at physiologically relevant positions, ushering in a new era of protein studies.

Covalent modifications of polysaccharides in mycobacteria   pp193 - 198
Shiva k Angala, Zuzana Palcekova, Juan M Belardinelli and Mary Jackson
Mycobacteria produce carbohydrates of exceptional structures that are covalently modified by unique substituents, whose functional characterization could expand our understanding of how mycobacteria adapt to their environment.

Research Highlights


Lipids: Picturing palmitoylation | Viruses: Capsids under pressure | Glycosylation: Gluing on glycans | Ubiquitination: Trashing the CIA

News and Views


RNA structure: A LASER-focused view into cells   pp200 - 201
Philip C Bevilacqua and Sarah M Assmann
RNA structure is irrevocably linked to function. A new method, termed 'LASER', utilizes a light-activated chemical probe to query RNA tertiary structure and illuminate RNA-protein interactions in the living cell.

See also: Article by Feng et al.

GPCR: Lock and key become flexible   pp201 - 202
Marc Baldus
G-protein-coupled receptors (GPCRs) are critically involved in signal transduction. Structural views of several GPCRs have recently been obtained, but the structural principles determining subtype selectivity are still mostly elusive. Now, a combined solid-state NMR and molecular-modeling approach reveals how bradykinin GPCRs distinguish between closely related peptide ligands.

See also: Article by Joedicke et al.

Protein evolution: Hacking an enzyme   pp202 - 204
Kristoffer E Johansson and Jakob R Winther
Early stages of protein evolution are inherently difficult to study. Genetic selection in Escherichia coli has now identified a life-sustaining de novo enzyme arising from a simple scaffold that is completely different from the native enzyme.

See also: Brief Communication by Donnelly et al.

Synthetic biology: Reframing cell therapy for cancer   pp204 - 205
Taylor B Dolberg, Patrick S Donahue and Joshua N Leonard
Technologies for engineering immune cells to recognize features on cancer cells are transforming oncology. Synthetic biologists now expand this approach by conferring therapeutic functions to nonimmune cells and by programming cells to sense and respond to a new class of physiological cues.

See also: Article by Chang et al.

Nature Chemical Biology
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How many human proteoforms are there?   pp206 - 214
Ruedi Aebersold, Jeffrey N Agar, I Jonathan Amster, Mark S Baker, Carolyn R Bertozzi et al.

Distinguishing RNA modifications from noise in epitranscriptome maps   pp215 - 225
Anya V Grozhik and Samie R Jaffrey



Structural and evolutionary insights into ribosomal RNA methylation   pp226 - 235
Petr V Sergiev, Nikolay A Aleksashin, Anastasia A Chugunova, Yury S Polikanov and Olga A Dontsova

Insights into the biogenesis, function, and regulation of ADP-ribosylation   pp236 - 243
Michael S Cohen and Paul Chang

Features and regulation of non-enzymatic post-translational modifications   pp244 - 252
Robert Harmel and Dorothea Fiedler

Brief Communication


A de novo enzyme catalyzes a life-sustaining reaction in Escherichia coli   pp253 - 255
Ann E Donnelly, Grant S Murphy, Katherine M Digianantonio and Michael H Hecht

A de novo-designed protein, Syn-F4, hydrolyzes the siderophore ferric enterobactin both in vitro and in Escherichia coli cells, enabling a bacterial strain lacking the essential natural enterobactin esterase to grow in iron-limited medium.

See also: News and Views by Johansson & Winther

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Employing a biochemical protecting group for a sustainable indigo dyeing strategy   pp256 - 261
Tammy M Hsu, Ditte H Welner, Zachary N Russ, Bernardo Cervantes, Ramya L Prathuri et al.

An environmentally friendly approach to indigo production is facilitated by the characterization of a plant indoxyl glucosyltransferase, which converts the unstable indoxyl precursor into indican by addition of a glucose protecting group.

Na+-mimicking ligands stabilize the inactive state of leukotriene B4 receptor BLT1   pp262 - 269
Tetsuya Hori, Toshiaki Okuno, Kunio Hirata, Keitaro Yamashita, Yoshiaki Kawano et al.

A structure of leukotriene B4 receptor BLT1 bound with a benzamidine-containing compound, BIIL260, reveals an inverse-agonist mechanism involving ligand binding in the sodium ion-centered water cluster adjacent to the conserved orthosteric site of class A GPCRs.

Mechanism of intersubunit ketosynthase-dehydratase interaction in polyketide synthases   pp270 - 275
Matthew Jenner, Simone Kosol, Daniel Griffiths, Panward Prasongpholchai, Lucio Manzi et al.

A combination of biochemical and structural techniques allows the characterization of a novel docking domain in polyketide synthases, which is structurally disordered and facilitates association of subunits at ketosynthase-dehydratase junctions.

Light-activated chemical probing of nucleobase solvent accessibility inside cells   pp276 - 283
Chao Feng, Dalen Chan, Jojo Joseph, Mikko Muuronen, William H Coldren et al.

A method called Light Activated Structural Examination of RNA (LASER) enables monitoring of the solvent accessibility of purine nucleobases and identifies rapid structural changes of cellular RNA-protein interactions and intracellular RNA structures.
Chemical compounds
See also: News and Views by Bevilacqua & Assmann

The molecular basis of subtype selectivity of human kinin G-protein-coupled receptors   pp284 - 290
Lisa Joedicke, Jiafei Mao, Georg Kuenze, Christoph Reinhart, Tejaswi Kalavacherla et al.

NMR to resolve the subtype specificity of two peptide ligands for human bradykinin receptors B1R and B2R shows different presentations of the peptide termini toward the receptor and interactions with nonconserved receptor binding-pocket residues.

See also: News and Views by Baldus

A whole-animal platform to advance a clinical kinase inhibitor into new disease space   pp291 - 298
Masahiro Sonoshita, Alex P Scopton, Peter M U Ung, Matthew A Murray, Lisa Silber et al.

Combining Drosophila genetics with chemistry and computation led to the development of novel kinase inhibitors based on the RAF-targeting drug sorafenib that reveal the RET oncogene as an enhancer of drug action and improve the therapeutic window in medullary thyroid carcinoma models.
Chemical compounds

Chemical hijacking of auxin signaling with an engineered auxin-TIR1 pair   pp299 - 305
Naoyuki Uchida, Koji Takahashi, Rie Iwasaki, Ryotaro Yamada, Masahiko Yoshimura et al.

A synthetic, orthogonal pair of the plant hormone auxin and its receptor TIR1 was engineered to hijack auxin signaling without interfering with the endogenous system. The synthetic system conclusively demonstrates the role for TIR1 in auxin-induced acid growth.
Chemical compounds

Lytic xylan oxidases from wood-decay fungi unlock biomass degradation   pp306 - 310
Marie Couturier, Simon Ladeveze, Gerlind Sulzenbacher, Luisa Ciano, Mathieu Fanuel et al.

A new type of fungal lytic polysaccharide monooxygenase (LPMO) catalyzes the oxidative degradation of xylan components of cellulosic biomass and offers potential in wood biorefining.

Partial DNA-guided Cas9 enables genome editing with reduced off-target activity   pp311 - 316
Hao Yin, Chun-Qing Song, Sneha Suresh, Suet-Yan Kwan, Qiongqiong Wu et al.

Partial substitution of CRISPR RNAs with DNA nucleotides retains CRISPR-Cas9 genome editing activity while enhancing efficiency and specificity within cells, suggesting that DNA-RNA hybrids may be economical reagents for targeted genome editing.

Rewiring T-cell responses to soluble factors with chimeric antigen receptors   pp317 - 324
ZeNan L Chang, Michael H Lorenzini, Ximin Chen, Uyen Tran, Nathanael J Bangayan et al.

Chimeric antigen receptor (CAR)-expressing T cells were engineered to recognize soluble protein ligands that, by inducing CAR dimerization, mechanically couple ligand binding and receptor signaling to produce immune effector molecules.

See also: News and Views by Dolberg et al.

Animation on CRISPR: Gene editing and beyond

The CRISPR-Cas9 system has revolutionised gene editing, but cutting DNA isn't all it can do.

This Animation, from Nature Methods, explores where CRISPR might be headed next. 

Watch the Animation >> 

Produced with support from: 



Light-activated chemical probing of nucleobase solvent accessibility inside cells   p325
Chao Feng, Dalen Chan, Jojo Joseph, Mikko Muuronen, William H Coldren et al.

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