Biophysical chemistry articles within Nature Chemistry

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  • Article |

    There is increasing evidence that highly dynamic, polydisperse peptide oligomers are the toxic species in amyloid-related diseases such as Alzheimer's and Parkinson's. Now, the secondary structure of individual amyloid oligomers has been analysed directly for the first time using a combination of ion-mobility spectrometry–mass spectrometry and gas-phase infrared spectroscopy.

    • Jongcheol Seo
    • , Waldemar Hoffmann
    •  & Kevin Pagel

  • News & Views |

    A quantitative understanding of the functional landscape of a biochemical circuit can reveal the design rules required to optimize the circuit. Now, a high-throughput droplet-based microfluidic platform has been developed which enables high-resolution mapping of bifurcation diagrams for two nonlinear DNA networks.

    • Fei Wang
    •  & Chunhai Fan

  • Article |

    Natural collagen contains triple helices that are approximately 1,000 residues in length and cannot be formed by chemical synthesis. Now, short collagen-mimetic peptides that self-assemble into three-stranded helices have been designed. These peptides are inspired by the mathematics of tessellations, and the triple helices formed via this approach match or exceed the length of those found in natural collagen.

    • I. Caglar Tanrikulu
    • , Audrey Forticaux
    •  & Ronald T. Raines

  • Article |

    A temperature-dependent kinetic study of ground-state proton transfer in the green fluorescent protein highlights the role of ‘deep tunnelling’ in proton wires. A potential mechanism for directional proton transport is proposed, where high-pKa amino acid residues act as ‘tunnel diodes’ and as stabilizing elements within protein water wires.

    • Bridget Salna
    • , Abdelkrim Benabbas
    •  & Paul M. Champion

  • News & Views |

    The low-complexity-protein, liquid phases of membraneless organelles have now been established to selectively partition biomolecules. The specialized microenvironment that they provide differs chemically from the surrounding medium and enables specific nucleic-acid remodelling reactions.

    • James Shorter

  • Article |

    Membraneless organelles form as liquid droplets inside cells. These bodies are effectively a separate organic phase, with unique biochemical properties. Now, the solvent interior of membraneless organelles has been shown to have a significant effect on the properties and structure of biomolecules. In addition to selectively partitioning and trafficking proteins, they can melt DNA without using ATP.

    • Timothy J. Nott
    • , Timothy D. Craggs
    •  & Andrew J. Baldwin

  • Article |

    Nature's speciality is to direct and control the reactivity of species, which are otherwise fatally destructive. However, the processes and design rules required to achieve such precise control are not clear. A de novo designed metalloprotein that stabilizes an otherwise unstable organic radical has now been developed to guide our understanding.

    • Gözde Ulas
    • , Thomas Lemmin
    •  & William F. DeGrado

  • Article |

    Proposed as the source of the light-dependent magnetic compass in migratory birds, the radical pair mechanism is thought to operate in flavoproteins in the retina. Now, it has been demonstrated that the primary magnetic field effect on flavin photoreactions can be chemically amplified by slow radical termination reactions under conditions of continuous photoexcitation.

    • Daniel R. Kattnig
    • , Emrys W. Evans
    •  & P. J. Hore

  • Article |

    Intracellular bodies called liquid organelles are rich in nucleic acids and proteins, and are thought to occur by liquid–liquid phase coexistence. Now, enzymatic control over the phosphorylation state of a simple cationic peptide, thereby altering its electrostatic interaction with RNA, has been shown to drive formation and dissolution of droplets that mimic these intracellular liquid bodies.

    • William M. Aumiller Jr
    •  & Christine D. Keating

  • Article |

    Uncertainty associated with solution-based electron-transfer studies of DNA–metal-complex systems has now been overcome by combining X-ray and time-resolved infrared data obtained for ruthenium polypyridyl–DNA crystals. Using these methods both the geometry of the reaction site and the kinetics of the reversible photo-induced one-electron oxidation of guanine have been determined.

    • James P. Hall
    • , Fergus E. Poynton
    •  & Susan J. Quinn

  • Article |

    Labelling biomolecules to improve the sensitivity of analysis can perturb their interactions. Now, microfluidic and chemical tools have been used to allow simple, sensitive detection of a labelled system to reveal the behaviour of the native and physiologically relevant unlabelled system. The system was used to characterize the solution-phase behaviour of a clinically relevant protein–protein interaction.

    • Emma V. Yates
    • , Thomas Müller
    •  & Tuomas P. J. Knowles

  • Article |

    Protein PEGylation is routinely used to produce molecules with improved pharmacokinetic properties. However, despite their importance, the structure of PEGylated proteins has remained elusive. Now, the first crystal structure of a model β-sheet protein modified with a single PEG chain has been reported. NMR spectroscopy data indicates that the protein and PEG behave as independent domains.

    • Giada Cattani
    • , Lutz Vogeley
    •  & Peter B. Crowley

  • Article |

    The use of kinetic simulations to guide the design of competitive hybridization probe systems is shown to enable high selectivity for single-nucleotide variants. Using this approach across 44 cancer mutation/wild-type sequence pairs showed between a 200- and 3,000-fold higher binding affinity than the corresponding wild-type sequence. In combination with PCR amplification this method enabled the detection of a 1% concentration of variant alleles in human genomic DNA.

    • Juexiao Sherry Wang
    •  & David Yu Zhang

  • Article |

    Photoswitching of phytochromes is based on the isomerization of the tetrapyrrole chromophore, and eventually leads to the (de)activation of an enzymatic output module. Now it has been shown that both the structural changes associated with photoswitching and the thermal decay of the light-activated state are coupled to proton translocations in the chromophore pocket.

    • Francisco Velazquez Escobar
    • , Patrick Piwowarski
    •  & Peter Hildebrandt

  • Article |

    Charge transport in molecular systems is typically through coherent tunnelling over a short distance or incoherent hopping over a long distance. An intermediate regime between those two transport mechanisms has now been found for DNA systems with stacked guanine–cytosine sequences.

    • Limin Xiang
    • , Julio L. Palma
    •  & Nongjian Tao

  • Article |

    The adenine analogue 2-aminopurine has been considered as intrinsically fluorescent and is widely used in biochemical assays to probe DNA and RNA structure. It is now shown that the molecule alone is nearly non-fluorescent, however, its fluorescence is increased by up to 95 times through hydrogen bonding to a single water molecule.

    • Simon Lobsiger
    • , Susan Blaser
    •  & Samuel Leutwyler

  • Article |

    Magnetic resonance imaging of gene expression has been limited by the low molecular sensitivity of conventional 1H-MRI. To overcome this limitation, the first genetically encoded reporters for hyperpolarized xenon MRI have been developed. These expressible reporters, based on gas-filled protein nanostructures from buoyant microorganisms, are detectable at picomolar concentrations.

    • Mikhail G. Shapiro
    • , R. Matthew Ramirez
    •  & Vikram S. Bajaj

  • News & Views |

    Biological solar energy conversion requires the coordinated and rapid movement of protons and electrons through complex proteins, called reaction centres. Now, an artificial and structurally simple reaction centre has been synthesized that mimics an important, photosynthetic charge relay.

    • Bridgette A. Barry

  • Article |

    An artificial reaction centre has been designed that contains a benzimidazole–phenol model of the Tyr–His relay in photosystem II. It has been seen to mimic both the short internal hydrogen bond of the natural relay, and — using electron paramagnetic resonance —the relaxation behaviour that accompanies proton-coupled electron transfer in photosystem II.

    • Jackson D. Megiatto Jr
    • , Dalvin D. Méndez-Hernández
    •  & Ana L. 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 |

    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

  • 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 |

    Electrochemical sensing of the function of cell-membrane proteins has led to the identification of inhibitors that could provide a new approach to the identification of antimicrobial drugs.

    • Ellis C. O'Neill
    •  & Robert A. Field

  • News & Views |

    Accurately representing molecules with many coupled unpaired electrons is currently impossible using conventional electronic-structure theories. Now, using a recently developed approach, the near-exact quantum wavefunction of the highly complex Mn4CaO5 cluster of photosystem II has been calculated.

    • Jeremy N. Harvey

  • Article |

    Capsular polysaccharides (CPS) enclose many pathogenic strains of Escherichia coli, protecting the bacteria from the host. Here, an extracellular blocker of Wza, a pore-forming protein that transports CPS to the cell surface, has been discovered by single-channel electrical recording. Treatment with the blocker exposes the bacterial cell surface and thereby facilitates killing by the human immune system.

    • Lingbing Kong
    • , Leon Harrington
    •  & Hagan Bayley

  • Article |

    Many-electron quantum modelling of the metal clusters in metalloenzymes is a long-standing ambition for theoreticians. Here, using the density matrix renormalization group, the many-electron wavefunctions of the Mn4CaO5 cluster of photosystem II are computed, providing new insights into the electronic structure and reactivity at the level of many-particle quantum mechanics and entanglement.

    • Yuki Kurashige
    • , Garnet Kin-Lic Chan
    •  & Takeshi Yanai

  • Article |

    The influence of protein motions on the chemical step of enzyme reactions is a contentious issue. Now, by constructing free-energy surfaces using an explicit solvent coordinate, it is shown that, although some structural flexibility is required, protein motions can be described as equilibrium fluctuations.

    • Rafael García-Meseguer
    • , Sergio Martí
    •  & Iñaki Tuñón

  • 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 |

    Single-molecule experiments reveal substantial molecule-to-molecule variation in the Mg2+-induced isomerization dynamics of Holliday junctions (HJs). Effective ergodicity breaking of time trajectories results in the partitioning of HJ dynamics into multiple clusters. The observed dynamical heterogeneity is a consequence of various internal multiloop conformations that are frozen by Mg2+ ions.

    • Changbong Hyeon
    • , Jinwoo Lee
    •  & D. Thirumalai

  • Article |

    The pressure- and temperature-dependent changes of various hydrogen bonds within ubiquitin have been determined at very high resolution using NMR H-bond scalar couplings. The measured perturbations show a correlation with the sequence separation between donor and acceptor residues, and indicate that certain topologically crucial H-bonds are specifically stabilized.

    • Lydia Nisius
    •  & Stephan Grzesiek

  • News & Views |

    Activating caged reactive sites in proteins using mechanical force provides a powerful approach in the study of chemical reactions, and provides greater insight into which reactions are possible and their rates.

    • Chia-Ching Chou
    •  & Markus J. Buehler

  • Article |

    Multiple redox reaction pathways exist in proteins containing several cysteines. A technique termed mechanical uncaging is now demonstrated, allowing the release of a single reactive cysteine within a protein and the unequivocal observation of subsequent thiol/disulfide exchanges. Mechanical uncaging of reactive groups is useful for studying chemical kinetics in a synchronized manner.

    • Jorge Alegre-Cebollada
    • , Pallav Kosuri
    •  & Julio M. Fernández

  • News & Views |

    Mechanical unfolding of a single DNA G-quadruplex structure with and without a stabilizing ligand can be used to calculate the binding strength of the ligand and could help to identify drugs to target these important biological assemblies.

    • Micah J. McCauley
    •  & Mark C. Williams

  • Article |

    G-quadruplex structures in telomeric DNA inhibit the action of telomerase — an enzyme over-expressed in many cancer cells. Small molecules that stabilize the formation of G-quadruplex structures are therefore of interest as potential cancer treatments. Here, a platform is described that allows the interactions between small-molecule ligands and human telomeric G-quadruplexes to be measured at the single-molecule level.

    • Deepak Koirala
    • , Soma Dhakal
    •  & Hanbin Mao

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