Biophysical chemistry articles within Nature Chemistry

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  • Article |

    Key molecular features that drive protein liquid–liquid phase separation (LLPS) for biomolecular condensate have been reported. A spectrum of additional interactions that influence protein LLPS and material properties have now been characterized. These interactions extend beyond a limited set of residue types and can be modulated by environmental factors such as temperature and salt concentration.

    • Shiv Rekhi
    • , Cristobal Garcia Garcia
    •  & Jeetain Mittal

  • News & Views |

    Liquid–liquid phase separation (LLPS) within cells is a captivating phenomenon known to aid the organization of cellular components; however, its complex kinetics have remained a puzzle. Now, a new study elucidates the crosstalk between the phase state of an encapsulating membrane and LLPS dynamics.

    • Rumiana Dimova

  • Article
    | Open Access

    Shifts in temperature alter the structure and dynamics of macromolecules. Now, infra-red laser-induced temperature jump is combined with X-ray crystallography to observe protein structural dynamics in real time. Using this method, motions related to the catalytic cycle of lysozyme, a model enzyme, are visualized at atomic resolution and across broad timescales.

    • Alexander M. Wolff
    • , Eriko Nango
    •  & Michael C. Thompson

  • Article |

    The design and improvement of enzymes based on physical principles remain challenging. Now, the vibrational Stark effect has been used to demonstrate how an electrostatic model can unify the catalytic effects of distinct chemical forces in a quantitative manner and guide the design of enzyme variants that outperform their natural counterpart.

    • Chu Zheng
    • , Zhe Ji
    •  & Steven G. Boxer

  • Research Briefing |

    A multimodal imaging approach is developed to interrogate microorganism–semiconductor biohybrids at the single-cell and single-molecule level for light-driven CO2 fixation. Application to lithoautotrophic bacterium Ralstonia eutropha biohybrids reveals the roles of two hydrogenases in electron transport and bioplastic formation, the magnitude of semiconductor-to-single-cell electron transport and the associated pathways.

  • Article |

    Understanding interfacial and cellular electron transport is essential for guiding efficiency optimization in microbe–semiconductor biohybrids for energy conversion. A multimodal imaging platform that combines optical imaging and photocurrent mapping can now interrogate such electron-transport pathways at the single-cell level, uncovering different roles of hydrogenases and a microbe’s large electron-uptake capacity.

    • Bing Fu
    • , Xianwen Mao
    •  & Peng Chen

  • Article |

    The kinetics of liquid–liquid phase separation (LLPS) in cell-like confinements remains poorly understood. Now it has been shown that it involves complex interplay between the incipient phases and the membrane boundary, which arrests phase coarsening, deforms the membrane and couples LLPS with lipid phase separation.

    • Wan-Chih Su
    • , James C. S. Ho
    •  & Atul N. Parikh

  • Article
    | Open Access

    Allostery produces concerted functions of protein complexes by orchestrating the cooperative work between the constituent subunits. By restoring functions of pseudo-active sites that have been lost through evolution, allosteric sites have now been designed into a rotary molecular motor, V1-ATPase, resulting in its rotation being boosted allosterically.

    • Takahiro Kosugi
    • , Tatsuya Iida
    •  & Nobuyasu Koga

  • News & Views |

    Genetic code expansion beyond α-amino acids is a major challenge, in which stitching together non-natural building blocks within the ribosome is a critical barrier. Now, the molecular determinants for the efficient incorporation of non-natural amino acids into the ribosome have been unlocked, accelerating ribosomal synthesis.

    • Souvik Sinha
    • , Mohd Ahsan
    •  & Giulia Palermo

  • Article |

    Incorporating polar residues into hydrophobic protein channel pores facilitates selective proton transport. Now, classical and multiscale reactive molecular dynamics simulations of designed channels reveal dynamic water wires within the channel lumen that are proton conductive according to structural and functional validation. These results provide some guiding principles for biological and engineered proton conduction.

    • Huong T. Kratochvil
    • , Laura C. Watkins
    •  & William F. DeGrado

  • Article |

    Generating aptamers for use as affinity reagents in analytical applications is important, but SELEX, the standard method for aptamer generation, is unable to select for pre-defined binding affinities. Now, by combining efficient particle display, high-performance microfluidic sorting and high-content bioinformatics, the method ‘Pro-SELEX’ can afford the quantitative generation of aptamers with programmable binding affinities.

    • Dingran Chang
    • , Zongjie Wang
    •  & Shana O. Kelley

  • Perspective |

    Bioresponsive hyperpolarized probes contain magnetic resonance signals that can be many orders of magnitude larger than those of common, thermally polarized probes. This Perspective discusses how bioresponsive hyperpolarized probes can be directly linked to biological events to give functional information, enabling the mapping of physiological processes and diseases in real time using magnetic resonance.

    • Goran Angelovski
    • , Ben J. Tickner
    •  & Gaoji Wang

  • Article |

    The advantages and disadvantages of building a nanosystem using one, two or more molecular components are poorly understood. Now, using structural and catalytic DNA-based nanosystems and theoretical simulations, it has been shown that the assembly of trimeric nanosystems displays much higher levels of programmability and functionality than the monomeric or dimeric counterparts.

    • D. Lauzon
    •  & A. Vallée-Bélisle

  • Article
    | Open Access

    Proteins rich in phenylalanine-glycine (FG) repeats can phase separate through FG–FG interactions. The molecular interactions of an important FG-repeat protein, nucleoporin 98, have now been studied in liquid-like transient and amyloid-like cohesive states. These interactions underlie the behaviour of FG-repeat proteins and their function in physiological and pathological cell activities.

    • Alain Ibáñez de Opakua
    • , James A. Geraets
    •  & Markus Zweckstetter

  • Article |

    The principal mid-visible light-harvesting system in cyanobacteria is the phycobilisome. Now, using broadband multidimensional spectroscopy, delocalized vibronic excitations and sub-picosecond excitation transfer pathways have been observed in the rods of intact phycobilisomes. An observed kinetic bottleneck in the phycobilisome’s core arises from the intramolecular charge-transfer character of the bilin chromophores, enabling photoregulatory processes to operate on the >10-ps timescale.

    • Sourav Sil
    • , Ryan W. Tilluck
    •  & Warren F. Beck

  • News & Views |

    How electric fields generated by enzyme active sites push and pull on substrates is important to their chemistry, but measuring them is difficult. Now, the electric field within an active site has been measured along two directions using a vibrational probe, revealing that the field effect in enzymes is different compared with that in bulk solvents.

    • Anuj Pennathur
    •  & Jahan Dawlaty

  • Article |

    A genetically encoded phototrigger based on a xanthone amino acid can expand the scope of time-resolved serial femtosecond crystallography beyond naturally photoactive proteins. This approach has been used to uncover metastable reaction intermediates that occur prior to C–H bond activation in a human liver fatty-acid-binding protein mutant.

    • Xiaohong Liu
    • , Pengcheng Liu
    •  & Jiangyun Wang

  • Article |

    The composition of toxic protein aggregates associated with neurodegenerative diseases is difficult to determine. Now, a method has been developed that can capture amyloid-containing aggregates in human biofluids using a structure-specific chemical dimer. This method—known as amyloid precipitation—enables unbiased determination of the molecular composition and structural features of the in vivo aggregates.

    • M. Rodrigues
    • , P. Bhattacharjee
    •  & D. Klenerman

  • Article |

    The biochemical roles and mechanisms of multiphase membraneless organelles are not yet well understood. Now, multiphase peptide droplets have been shown to sort RNA based on whether it is single- or double-stranded, as well as impact RNA duplexation through in-droplet thermodynamic equilibria. This work provides insight into possible primitive mechanisms for multicompartment intracellular condensates and can aid in the design of functional artificial membraneless organelles.

    • Saehyun Choi
    • , McCauley O. Meyer
    •  & Christine D. Keating

  • Article
    | Open Access

    Phase-separated compartments have long been proposed as precursors to cellular life. Now, it has been shown that RNA–peptide protocells are more robust when formed using shorter (rather than longer) peptides, and that peptide sequence determines the functional materials properties of these compartments.

    • Juan M. Iglesias-Artola
    • , Björn Drobot
    •  & Moritz Kreysing

  • Article |

    Histone H1 binds to nucleosomes with ultrahigh affinity, implying residence times incompatible with efficient biological regulation. Now it has been shown that the disordered regions of H1 retain their large-amplitude dynamics on the nucleosome, which enables a charged disordered histone chaperone to invade the H1–nucleosome complex and vastly accelerate H1 dissociation.

    • Pétur O. Heidarsson
    • , Davide Mercadante
    •  & Benjamin Schuler

  • Article
    | Open Access

    Complex coacervate microdroplets have been proposed as primordial cells, but their ability to evolve by fusion, growth and fission has not yet been demonstrated. Now, it has been shown that gas bubbles inside heated rock pores can drive the growth, fusion, division and selection of coacervate microdroplets.

    • Alan Ianeselli
    • , Damla Tetiker
    •  & T.-Y. Dora Tang

  • Article |

    Weakly hydrated anions solubilize macromolecules but cause small molecules that are made from identical chemical constituents to precipitate out of aqueous solutions. Now, this phenomenon has been understood by demonstrating that the binding of anions to polymers is regulated by molecular curvature and interfacial water structure.

    • Bradley A. Rogers
    • , Halil I. Okur
    •  & Paul S. Cremer

  • News & Views |

    Machine learning algorithms are fast surpassing human abilities in multiple tasks, from image recognition to medical diagnostics. Now, machine learning algorithms have been shown to be capable of accurately predicting the folded structures of proteins.

    • Cecilia Clementi

  • Thesis |

    Bruce C. Gibb reminds us that buffers are not necessarily innocent bystanders and that they can bind to biomacromolecules too.

    • Bruce C. Gibb

  • Article |

    Droplet interface bilayer measurements have now shown that membranes formed from chiral phospholipid bilayers are enantioselectively permeable to chiral amino acids. The results show that membrane stereochemistry is necessary and sufficient to drive such enantioselective transport, presenting a new potential route to homochirality. These findings could also have implications for pharmacokinetics and drug design.

    • Juan Hu
    • , Wesley G. Cochrane
    •  & Brian M. Paegel

  • Article |

    Analysis of the thermodynamics of protein–N-glycan interactions perturbed by mutations has revealed an enthalpy–entropy compensation that depends on the electronics of the interacting side chains. Machine-learned and statistical models showed that protein–N-glycan interactions highly correlate with stereoelectronic effects, and that a major part of protein–N-glycan interactions can be explained using the energetic rules of frontier molecular orbital interactions.

    • Maziar S. Ardejani
    • , Louis Noodleman
    •  & Jeffery W. Kelly

  • Article |

    Artificial intrinsically disordered proteins (A-IDPs) have now been shown to form exclusionary, intracellular droplets that can be designed using simple principles that are based on the aromatic/aliphatic ratio and molecular weight. Droplets that sequester an enzyme and modulate enzyme efficiency on the basis of the molecular weight of the A-IDPs were also engineered using A-IDPs as a minimal condensate scaffold.

    • Michael Dzuricky
    • , Bradley A. Rogers
    •  & Ashutosh Chilkoti

  • News & Views |

    Is a nanoscale hydrophobic bowl wet or dry when dissolved in water? It turns out that the answer depends on the architecture of its rim. A molecular host decorated with four methyl groups around its rim pointing inward, rather than up, has now been shown to expel water from the bowl, making it dry and sticky.

    • Shekhar Garde

  • Article |

    The mechanism of nucleation for α-synuclein (α-Syn) aggregation and amyloid formation in Parkinson’s disease is unclear. Now, α-Syn has been shown to undergo liquid–liquid phase separation and a liquid-to-solid-like transition leading to amyloid fibril formation. This raises the possibility that liquid–liquid phase separation is a key pathogenic mechanism behind α-Syn aggregation in Parkinson’s disease.

    • Soumik Ray
    • , Nitu Singh
    •  & Samir K. Maji

  • Article |

    Aβ42 oligomers are key toxic species associated with protein aggregation; however, the molecular pathways determining the dynamics of oligomer populations have remained unknown. Now, direct measurements of oligomer populations, coupled to theory and computer simulations, define and quantify the dynamics of Aβ42 oligomers formed during amyloid aggregation.

    • Thomas C. T. Michaels
    • , Andela Šarić
    •  & Tuomas P. J. Knowles

  • Article |

    The Varkud satellite ribozyme, which catalyses site-specific RNA cleavage and ligation, is an important model to understand RNA catalysis. Now, a combination of theoretical and experimental work has revealed new details about its catalytic mechanism. Mg2+ is shown to play an important role in organizing the active site, and the proton transfers in the transition state have also been identified.

    • Abir Ganguly
    • , Benjamin P. Weissman
    •  & Darrin M. York

  • Article |

    Understanding how structural dynamics contribute to protein function is a longstanding challenge in structural biology. Now, time-resolved X-ray solution scattering following an infrared laser-induced temperature jump has been used to probe functional, intramolecular motions in the dynamic enzyme cyclophilin A.

    • Michael C. Thompson
    • , Benjamin A. Barad
    •  & James S. Fraser

  • Article |

    High concentrations of prebiotic molecules and dry–wet cycles are difficult to achieve in a submerged system. Now, it has been shown that temperature gradients across gas bubbles in submerged rock pores can provide these conditions. Molecules are continuously accumulated at the warm side of bubbles at the gas–water interface, which enables or enhances many prebiotically relevant processes.

    • Matthias Morasch
    • , Jonathan Liu
    •  & Dieter Braun

  • News & Views |

    The longstanding ‘polyelectrolyte theory of the gene’ proposes that a multiply charged backbone is the universal signature of all genetic polymer systems that support life. Now, the first tenable challenge to this theory has been mounted, through the successful engineering of enzymes which can synthesize and reverse-transcribe from an artificial, uncharged nucleic acid analogue.

    • Asha Brown
    •  & Tom Brown

  • News & Views |

    Maleimide–thiol adducts are popular in both bioconjugation and materials chemistry, however, they are unstable under physiological conditions. Now, a mechanochemical approach uses pulling forces to stabilize maleimide–thiol adducts and improve the stability of polymer–protein conjugates.

    • Cody J. Higginson
    •  & Phillip B. Messersmith

  • News & Views |

    Potassium channels rapidly move K+ ions across cell membranes while blocking Na+, but how these two effects are achieved simultaneously has remained unclear. Now, extensive molecular simulations show a single mechanism that features fully dehydrated ions can explain both rapid transport and impeccable selectivity.

    • Ben Corry

  • Article |

    The [4Fe4S]2+ cluster-containing DNA-repair enzyme MUTYH helps safeguard the integrity of Watson–Crick base pairing and the human genetic code. The MUTYH [4Fe4S]2+ cluster mediates DNA redox signalling and DNA lesion identification. Now, a MUTYH pathologic variant associated with catastrophic [4Fe4S]2+ cluster redox degradation, impairment of DNA signalling and human colonic tumorigenesis has been identified.

    • Kevin J. McDonnell
    • , Joseph A. Chemler
    •  & Stephen B. Gruber

  • Article |

    Cholesterol embedded in lipid membranes strongly promotes the aggregation of Aβ42 that is associated with Alzheimer's disease. Now, a kinetic analysis has shown that the mechanism of action responsible for this effect involves the introduction of a heterogeneous nucleation pathway that enhances the primary nucleation rate of Aβ42 aggregation by up to 20-fold.

    • Johnny Habchi
    • , Sean Chia
    •  & Michele Vendruscolo

  • Article |

    Living systems rely on externally tuneable and stimuli-responsive conformational changes of proteins and protein assemblies for a wide range of essential functions. A combination of experimental and computational analyses has now enabled the fabrication of a rationally designed, synthetic, stimuli-responsive protein assembly through modulation of its free-energy landscape.

    • Robert Alberstein
    • , Yuta Suzuki
    •  & F. Akif Tezcan

  • Article |

    Mapping energy landscapes has proved to be a powerful approach for studying reaction mechanisms. Now, this strategy has been applied to determine the activation energies and entropies that characterize the molecular steps in the misfolding and aggregation of the amyloid-β peptide, revealing striking differences between the thermodynamic signatures of primary and secondary nucleation.

    • Samuel I. A. Cohen
    • , Risto Cukalevski
    •  & Sara Linse

  • Article |

    Spectroscopists and theorists are closing in on an understanding of the origin of oscillatory features in the spectral response of light-harvesting complexes to femtosecond pulsed excitation. Now, the photosynthetic Fenna–Matthews–Olson complex is probed by femtosecond pump–probe spectroscopy and compared with a series of genetically modified mutants with distinct excitonic interactions, allowing electronic and vibrational contributions to coherence to be distinguished.

    • Margherita Maiuri
    • , Evgeny E. Ostroumov
    •  & Gregory D. Scholes

  • News & Views |

    Water is increasingly recognized as being of paramount importance in biological processes, yet its exact role remains difficult to elucidate. Now, the motion of water molecules within and around a synthetic peptide-amphiphile nanofibre has been precisely determined, showing significant differences between its core and surface.

    • Yoshimitsu Itoh
    •  & Takuzo Aida

  • Article |

    Ultrafast-scanning fluorescence correlation spectroscopy has now been used to measure the molecular interactions underlying the phase behaviour of disordered proteins. Sequence-encoded conformational fluctuations of these proteins are shown to give rise to phase-separated droplets of surprisingly low concentrations. These results provide insight into how the structural features of the droplets affect the properties of liquid-phase intracellular organelles.

    • Ming-Tzo Wei
    • , Shana Elbaum-Garfinkle
    •  & Clifford P. Brangwynne

  • Article |

    The self-propagation of misfolded conformations of tau occurs in neurodegenerative diseases, including Alzheimer's disease. The microtubule-binding region, tau244-372, reproduces much of the aggregation behaviour of tau in cells and animal models. Now, it has been shown that a 31-residue peptide from tau's R3 domain forms a cross-β conformation that efficiently seeds aggregation of tau244-372 in cells.

    • Jan Stöhr
    • , Haifan Wu
    •  & William F. DeGrado

  • Article |

    A dynamic foldamer scaffold has now been ligated to a water-compatible, metal-centred binding site and a conformationally responsive fluorophore to form a receptor mimic that inserts into the membrane of artificial vesicles. Binding of specific carboxylate ligands induces a global conformational change that depends on the structure of the ligand, and can be detected via fluorescence.

    • Francis G. A. Lister
    • , Bryden A. F. Le Bailly
    •  & Jonathan Clayden

  • Article |

    Simple peptides are shown to assemble into well-defined amyloid phases with paracrystalline surfaces that can catalyse reactions in an enantioselective manner. Modifying individual amino acids in the building blocks enables the structure of the assembled aggregates, and the reactions that they can catalyse, to be controlled predictably.

    • Tolulope O. Omosun
    • , Ming-Chien Hsieh
    •  & David G. Lynn

  • Article |

    The analysis of complex (bio)molecules by NMR spectroscopy is often complicated by limitations in sensitivity. Now, it has been shown that 13C NMR signals are strongly enhanced in solution by resonant microwave irradiation of a nitroxide polarizer. This method exhibits up to one-thousand-fold improvements in sensitivity, which stands to greatly improve the detail with which small molecules and metabolites can be studied.

    • Guoquan Liu
    • , Marcel Levien
    •  & Marina Bennati

  • Article |

    Cation–π interactions are critical for the adhesion proteins of marine organisms, yet the energetics of cation–π interactions in underwater environments remains uncharted. Nanoscale force measurements and NMR spectroscopy reveal that interfacial confinement fundamentally alters the energetics of cation–π mediated assembly.

    • Matthew A. Gebbie
    • , Wei Wei
    •  & Jacob N. Israelachvili

  • Article |

    An unanswered question in the RNA world scenario is how sequence information could be transferred during replication of duplex RNA. Without the aid of sophisticated enzymes, strand reannealing occurs more quickly than template-directed synthesis. Now, a plausible prebiotic solution to this problem is presented, in which a viscous solvent enables information transfer from a gene-length double-stranded template.

    • Christine He
    • , Isaac Gállego
    •  & Nicholas V. Hud

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