Biochemistry articles within Nature Chemistry

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  • News & Views |

    Anfinsen's principle tells us that the folded structure of a protein is determined solely by its sequence. Now, it has been shown that the rate at which a polypeptide chain is synthesized in the cell can affect which of two alternative folded structures it adopts.

    • Elin M. Sivertsson
    •  & Laura S. Itzhaki

  • News & Views |

    Labelling of proteins with pairs of fluorophores enables their conformations to be studied; however, complete incorporation of labels in multiple, pre-defined locations is very difficult. Now, a combination of double unnatural amino acid mutagenesis and selective chemical modification offers a general method to achieve this.

    • E. James Petersson
    •  & John B. Warner

  • Article |

    The biosynthesis of lipid mediators has not previously been identified in mitochondria. Here, polyunsaturated cardiolipins are shown to be oxidized in the mitochondria by cytochrome c. Subsequent hydrolysis of these oxygenated species generates a variety of oxygenated fatty acids as well as non-oxygenated and oxygenated lyso-cardiolipins. These reactions represent a new biosynthetic pathway for the production of lipid mediators.

    • Yulia Y. Tyurina
    • , Samuel M. Poloyac
    •  & Valerian E. Kagan

  • News & Views |

    Amyloid fibrils are formed from polypeptide chains assembled into an organized fibrillar structure. Now, it has been shown that such fibrillar structures can also bind metal ions and catalyse chemical reactions.

    • Tobias Aumüller
    •  & Marcus Fändrich

  • Article |

    FeFe hydrogenases, the enzymes that oxidize or produce H2, are inactivated under oxidizing conditions. Here, it is shown that this inactivation results from H2 binding to coordination positions that are normally blocked by intrinsic CO ligands. This flexibility of the active site prevents irreversible oxidative damage.

    • Vincent Fourmond
    • , Claudio Greco
    •  & Christophe Léger

  • Article |

    Amyloid fibril formation is often catalysed by mature fibrils or other aggregates on the fibrillization pathway; however, fibrils cannot normally catalyse other chemical reactions. Here, small seven-residue peptides designed from first principles are shown to form amyloid fibrils that can efficiently catalyse ester hydrolysis.

    • Caroline M. Rufo
    • , Yurii S. Moroz
    •  & Ivan V. Korendovych

  • News & Views |

    ATP synthase is an important enzyme for the storage and release of energy in cells. Ion-mobility mass spectrometry has now been used to study its structure, revealing important mechanistic details about its operation and regulation.

    • Jianhua Zhao
    •  & John L. Rubinstein

  • Article |

    The extraction of uranium from seawater is limited by the high concentrations of carbonate and competing metal ions. Now, a highly selective uranyl-binding protein with femtomolar affinity has been developed. This protein can extract up to 60% uranium from synthetic seawater when immobilized on bacterial cell surfaces or amylose resin.

    • Lu Zhou
    • , Mike Bosscher
    •  & Chuan He

  • News & Views |

    Fluorine imparts many drugs with beneficial properties, however, the synthesis of fluorinated complex natural products is challenging. Biosynthetic strategies and recent experimental precedents have paved the way for bioengineered fluorinated polyketides.

    • Peter A. Jordan
    •  & Bradley S. Moore

  • News & Views |

    Replication of the HIV-1 viral genome can be inhibited by a protein known as APOBEC3G, via two seemingly contradictory mechanisms. Now, the molecular conundrum behind these two processes has been resolved.

    • Graeme A. King
    •  & Gijs J. L. Wuite

  • Article |

    Identification of glycosylation patterns is complicated by the lack of sensitive analytical techniques that can distinguish between epimeric carbohydrates. It has now been shown that ion-mobility tandem mass spectrometry of ions derived from glycopeptides and oligosaccharides enables glycan stereochemistry to be determined, highlighting the potential of this technique for sequencing complex carbohydrates on cell surfaces.

    • P. Both
    • , A. P. Green
    •  & C. E. Eyers

  • Article |

    HIV-1 replication is inhibited by the enzyme APOBEC3G via two separate mechanisms. A deamination mechanism requires rapid binding and release of single-stranded DNA (ssDNA), whereas a roadblock mechanism requires slow binding. Now APOBEC3G has been shown to initially bind ssDNA with rapid on–off rates. The enzyme subsequently converts via oligomerization to a slowly dissociating binding mode, which, it is proposed, inhibits reverse transcription.

    • Kathy R. Chaurasiya
    • , Micah J. McCauley
    •  & Mark C. Williams

  • News & Views |

    An RNA replicase ribozyme has long been sought by chemists interested in the origin of life. Now, a selection strategy employing a low-temperature water–ice mixture as the medium has led to discovery of a ribozyme that can catalyse polymerization of an RNA chain greater than its own length.

    • Niles Lehman

  • News & Views |

    Selection of an RNA catalyst that can use the vitamin thiamin to catalyse a key metabolic decarboxylation reaction has broad implications for understanding the role of RNA in the early stages of chemical evolution.

    • Cynthia J. Burrows

  • Article |

    Molecular self-replication through ribozyme-catalysed RNA synthesis could shed light on the origins of life. Here, a polymerase ribozyme capable of synthesizing an RNA sequence longer than itself is described, based on a cold-adapted ribozyme variant evolved in ice. This process demonstrates the potential for the emergence of novel ribozyme phenotypes in altered reaction environments.

    • James Attwater
    • , Aniela Wochner
    •  & Philipp Holliger

  • Article |

    Vitamins are thought to be relics of a primordial RNA World. A demonstration that catalytic RNAs are capable of harnessing vitamin cofactors would support the likely role of vitamins in early metabolic processes. Here, a ribozyme that uses vitamin B1 to aid decarboxylation of a pyruvate-like substrate is reported.

    • Paul Cernak
    •  & Dipankar Sen

  • Article |

    Structural analysis of the enzyme transketolase at sub-ångström resolution shows the existence of physically distorted covalent intermediates with elongated scissile substrate bonds. These observations highlight the ability of enzymes to enhance the reactivity of reaction intermediates leading to a more efficient process.

    • Stefan Lüdtke
    • , Piotr Neumann
    •  & Kai Tittmann

  • News & Views |

    The interactions between a virus capsid and its cargo are essential for viral infection as well as in the design of synthetic virus-like particles. Now a combination of analytical techniques has unravelled key steps in the transformation of a model virus and the release of its RNA cargo.

    • Masaki Uchida
    •  & Trevor Douglas

  • Article |

    Removing Mg2+ from RNA and replacing it with Fe2+ confers on some RNAs the ability to catalyse single-electron transfer. Here, it is hypothesized that Fe2+ was an RNA cofactor on the early Earth, when iron was benign and abundant, and was replaced by Mg2+ during a period known as the great oxidation, brought on by photosynthesis.

    • Chiaolong Hsiao
    • , I-Chun Chou
    •  & Loren Dean Williams

  • Article |

    The stability of the capsid of a virus is strongly affected by its genome. Here the interplay between capsid and genome is explored using native mass spectrometry and atomic force microscopy. A mechanism is proposed to explain how the genome of the Triatoma virus stabilizes the capsid at neutral pH, but triggers disassembly under alkaline conditions.

    • J. Snijder
    • , C. Uetrecht
    •  & W. H. Roos

  • Thesis |

    Michelle Francl argues we should embrace molecular models, not tuck them away in the closet.

    • Michelle Francl

  • News & Views |

    Overcoming drug resistance requires drug–protein interactions that persist in spite of mutations, but such interactions are difficult to characterize. Two-dimensional infrared spectroscopy can reveal the dynamics of how key molecular groups interact, allowing new insights into how some drugs overcome resistance.

    • Christopher M. Cheatum

  • News & Views |

    The direct observation and quantification of G-quadruplex structures formed from DNA in human cells during the cell cycle demonstrate the biological importance of these structures and point towards opportunities for targeting them with small-molecule drugs.

    • Adam Siddiqui-Jain
    •  & Laurence H. Hurley

  • Article |

    Time-resolved X-ray crystallography on photoactive yellow protein shows the existence of a short-lived, highly distorted intermediate whose reaction trajectory bifurcates along ‘bicycle-pedal’ and ‘hula-twist’ pathways. The bifurcating reaction pathways can be controlled by weakening the hydrogen bond between the chromophore and an adjacent residue, which switches off the bicycle-pedal pathway.

    • Yang Ouk Jung
    • , Jae Hyuk Lee
    •  & Hyotcherl Ihee

  • Article |

    A structure-specific antibody generated and employed to visualize DNA G-quadruplex structures in human cells shows that these structures are modulated during the cell cycle and can be stabilized by a small-molecule ligand. This provides substantive evidence for endogenous DNA G-quadruplex formation in mammalian cells.

    • Giulia Biffi
    • , David Tannahill
    •  & Shankar Balasubramanian

  • News & Views |

    The biosynthesis of peptidoglycan is an important step in bacterial cell division and cell-wall maturation. Now it has been shown that fluorescent D-amino acids can be used to label the peptidoglycan cell wall of living bacteria, providing a new tool to study this important process.

    • Timothy D. H. Bugg

  • Article |

    RNA compartmentalization is essential for cellular functions and may have played a pivotal role in the emergence of life. However, the consequences of compartmentalization on RNA catalysis have been largely unexplored. Here, partitioning of catalytic RNA in a two-phase aqueous polymer solution increased local RNA concentration, enhancing ribozyme kinetics.

    • Christopher A. Strulson
    • , Rosalynn C. Molden
    •  & Philip C. Bevilacqua

  • Article |

    A demonstration of simple sugar synthesis from single carbon feedstocks would provide significant support for the involvement of RNA in the origin of life. Here, hydrogen cyanide is shown to feed a cyanocuprate photoredox cycle that ultimately provides both the starting material and the reducing power necessary for a Killiani–Fischer-type sugar synthesis.

    • Dougal Ritson
    •  & John D. Sutherland

  • News & Views |

    Nucleic acid aptamers have been employed to shield small molecules so that one among many similar reactive functional groups can be modified. This provides access to new chemical entities with potentially interesting properties while avoiding the use of covalent protecting groups.

    • Scott K. Silverman

  • Article |

    Representing the first successful rational reprogramming of function in a de novo protein, the reactivity of a designed di-iron carboxylate protein from the Due Ferri family was altered from hydroquinone oxidation to arylamine N-hydroxylation through the introduction of a critical third histidine ligand in the active site.

    • Amanda J. Reig
    • , Marcos M. Pires
    •  & William F. DeGrado

  • Article |

    A family of robust β-sheet macrocycles that can display a variety of heptapeptide sequences from different amyloid proteins is introduced. These amyloid β-sheet mimics can be tailored to antagonize aggregation of the proteins, thereby reducing the toxicity associated with diseases such as Alzheimer's.

    • Pin-Nan Cheng
    • , Cong Liu
    •  & James S. Nowick

  • Article |

    Rapid diagnostic methods that can be applied in resource-limited settings are important in the fight against tuberculosis. Here, fluorogenic probes are described that are activated by BlaC — an enzyme secreted by tubercle bacilli. The probes have enabled detection in unprocessed human sputum of live pathogen in less than 10 min.

    • Hexin Xie
    • , Joseph Mire
    •  & Jianghong Rao

  • Article |

    Many biological processes involve the binding of proteins to cell membrane receptors, making these proteins valuable disease biomarkers and therapeutic targets. A label-free plasmonic microscopy method has now been devised to determine the distribution and local binding kinetics of these ‘membrane proteins’, on the surface of single living cells rather than ex situ.

    • Wei Wang
    • , Yunze Yang
    •  & Nongjian Tao

  • News & Views |

    Hydrogen bonds play a key role in defining the folding of proteins and the maintenance of their structure. A high-pressure NMR study of ubiquitin now provides unprecedented detail on the temperature and pressure dependence of its hydrogen-bond network.

    • Gerd Nielsen
    •  & Harald Schwalbe

  • Article |

    Selective carbohydrate binding is a difficult task, usually accomplished by proteins (lectins) or complex synthetic analogues. It has now been achieved by a remarkably simple compound, accessible in just five steps from commercially available materials. This new receptor is highly selective for all-equatorial carbohydrates, and may be used to sense glucose through changes in anthracene fluorescence.

    • Chenfeng Ke
    • , Harry Destecroix
    •  & Anthony P. Davis

  • Editorial |

    Structure by structure, more information is steadily being gathered on how small molecules bind to DNA. A better understanding of the interactions involved in such processes will be crucial for the successful design of compounds for specific diagnostic and therapeutic purposes.

  • Interview |

    Claudia Turro from The Ohio State University talks Nature Chemistry through the different binding modes small metal complexes can adopt when interacting with DNA — and why elucidating them in detail matters.

    • Anne Pichon

  • News & Views |

    The interactions between ruthenium complexes and DNA duplexes, elucidated in detail in three different crystal structures, have been found to occur through the minor groove — an unexpected binding mode, but perhaps not such a strange one.

    • Stephen Neidle

  • News & Views |

    Supramolecular ligands are promising tools for interacting with proteins, but how exactly they bind together has so far been difficult to characterize. An unambiguous picture of the interaction between a synthetic ligand and the surface of cyctochrome c has now been obtained in solution and in the solid state.

    • Thomas Schrader

  • News & Views |

    The behaviour of di-selenol enzyme mimics indicates that a halogen bond between selenium and iodine, and a chalcogen interaction between the two selenium atoms, play an important role in the activation of thyroid hormones.

    • Pierangelo Metrangolo
    •  & Giuseppe Resnati

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