Focus on chemical systems biology

In this issue - pv

doi:10.1038/nchembio1108-v

Full Text - In this issue | PDF (215 KB) - In this issue

Focus on chemical systems biology

Networking chemical biology - p633

doi:10.1038/nchembio1108-633

Closer interactions between chemical biology and systems biology have the potential to provide a more integrated understanding of how biology functions.

Full Text - Networking chemical biology | PDF (118 KB) - Networking chemical biology

Focus on chemical systems biology

Chemical biology and the limits of reductionism - pp635 - 638

Randall T Peterson

doi:10.1038/nchembio1108-635

Chemical biology and systems biology have grown and evolved in parallel during the past decade, but the mindsets of the two disciplines remain quite different. As the inevitable intersections between the disciplines become more frequent, chemical biology has an opportunity to assimilate the most powerful ideas from systems biology. Can the integrationist mindset of systems biology liberate chemical biology from the compulsion to reduce everything to individual small molecule–target pairings?

Full Text - Chemical biology and the limits of reductionism | PDF (414 KB) - Chemical biology and the limits of reductionism

Focus on chemical systems biology

Challenges for the 'chemical-systems' biologist - pp639 - 642

Gabriel M Simon & Benjamin F Cravatt

doi:10.1038/nchembio1108-639

As the field of chemical biology matures, its practitioners are tackling ever more sophisticated biological problems. Chemical approaches, both synthetic and analytical, provide researchers with powerful new technologies to perturb, dissect and even reconstruct complex biological systems. Here we discuss the special challenges and opportunities confronted at the burgeoning interface of chemical and systems biology.

Full Text - Challenges for the 'chemical-systems' biologist | PDF (333 KB) - Challenges for the 'chemical-systems' biologist

Focus on chemical systems biology

Reverse engineering intracellular biochemical networks - pp643 - 647

Eli Zamir & Philippe I H Bastiaens

doi:10.1038/nchembio1108-643

Although much is known about the molecular components of cellular signaling pathways, very little is known about how these multicomponent biochemical machineries process complex extracellular signals to generate a consolidated cellular response. A newly developed theoretical approach for reverse engineering network structure—analyzing how perturbations propagate in a network—can be combined with chemical perturbations and quantitative detection approaches to reveal the causal connections within protein networks in cells. This information indicates the dynamic capabilities of a network and thereby its potential function.

Full Text - Reverse engineering intracellular biochemical networks | PDF (382 KB) - Reverse engineering intracellular biochemical networks

Killing two kinase families with one stone - pp648 - 649

Benoit Bilanges, Neil Torbett & Bart Vanhaesebroeck

doi:10.1038/nchembio1108-648

Multitargeted protein kinase inhibitors have shown great promise in cancer therapy, but the selectivity profiles of these compounds have largely relied on serendipity or 'off-target' activities rather than rational drug design. Purposefully designed compounds with activity against multiple target kinases bring us a step closer to personalized medicine.

Full Text - Killing two kinase families with one stone | PDF (423 KB) - Killing two kinase families with one stone

See also: Article by Apsel et al.

To dislodge an enzyme from an ion channel, try steroids - pp650 - 651

Susy C Kohout & Ehud Y Isacoff

doi:10.1038/nchembio1108-650

Voltage-gated K⁺ channels assemble into complexes with Kvs, a group of aldoketoreductases. The Kvs regulate channel gating and localization, and voltage-dependent changes in the channel regulate AKR activity. Pan and colleagues now propose a new type of modulation of this complex. Cortisone disrupts the complex and relieves channel inactivation—which should reduce neuronal excitability.

Full Text - To dislodge an enzyme from an ion channel, try steroids | PDF (949 KB) - To dislodge an enzyme from an ion channel, try steroids

See also: Article by Pan et al.

Proteolytic needles in the cellular haystack - pp651 - 652

Mari Enoksson & Guy S Salvesen

doi:10.1038/nchembio1108-651

The execution phase of cell death is driven by specific proteolytic signaling through cleavage of proteins by caspases. Within the mix of hundreds of newly identified caspase substrates lie the crucial proteolytic events whose sum defines the unique morphology known as apoptosis.

Full Text - Proteolytic needles in the cellular haystack | PDF (296 KB) - Proteolytic needles in the cellular haystack

Community organizers and (bio)filmmaking - pp653 - 654

Bruce Demple

doi:10.1038/nchembio1108-653

Bacteria produce and excrete toxic compounds classically categorized as waste products or chemical weapons. New work indicates a role for phenazines and SoxR, a transcription factor known for its role in defense against oxidative stress, in coordinating bacterial community growth.

Full Text - Community organizers and (bio)filmmaking | PDF (799 KB) - Community organizers and (bio)filmmaking

An autocatalytic network for ribozyme self-construction - pp654 - 655

Burckhard Seelig

doi:10.1038/nchembio1108-654

The emergence of a primordial RNA world would have required the formation of RNA polymers of sufficient length to possess catalytic activities, which are difficult to obtain by spontaneous polymerization. An analysis of an autocatalytic assembly pathway that can self-construct a functioning ribozyme from smaller oligonucleotide building blocks describes a potential route for RNA extension.

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Research highlights - p657

doi:10.1038/nchembio1108-657

Full Text - Research highlights | PDF (139 KB) - Research highlights

Focus on chemical systems biology

Learning biological networks: from modules to dynamics - pp658 - 664

Richard Bonneau

doi:10.1038/nchembio.122

Abstract - Learning biological networks: from modules to dynamics | Full Text - Learning biological networks: from modules to dynamics | PDF (1,041 KB) - Learning biological networks: from modules to dynamics

Focus on chemical systems biology

Targeting and tinkering with interaction networks - pp666 - 673

Robert B Russell & Patrick Aloy

doi:10.1038/nchembio.119

Abstract - Targeting and tinkering with interaction networks | Full Text - Targeting and tinkering with interaction networks | PDF (433 KB) - Targeting and tinkering with interaction networks

Focus on chemical systems biology

Combination chemical genetics - pp674 - 681

Joseph Lehár, Brent R Stockwell, Guri Giaever & Corey Nislow

doi:10.1038/nchembio.120

Abstract - Combination chemical genetics | Full Text - Combination chemical genetics | PDF (823 KB) - Combination chemical genetics

Focus on chemical systems biology

Network pharmacology: the next paradigm in drug discovery - pp682 - 690

Andrew L Hopkins

doi:10.1038/nchembio.118

Abstract - Network pharmacology: the next paradigm in drug discovery | Full Text - Network pharmacology: the next paradigm in drug discovery | PDF (674 KB) - Network pharmacology: the next paradigm in drug discovery