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Proteine und Enzyme sind äußerst vielseitige Biomaterialien, die aufgrund ihrer hohen Spezifität für Rezeptoren und Substrate, ihrer Abbaubarkeit, geringen Toxizität und insgesamt guten Biokompatibilität hervorragend für ein breites Spektrum medizinischer Anwendungen geeignet sind. Durch die Anordnung mehrerer nativer oder modifizierter Proteine zu nanometergroßen Protein‐Nanopartikeln können zusätzliche vorteilhafte Eigenschaften wie eine erhöhte Stabilität im Blutstrom erreicht werden. In diesem Aufsatz konzentrieren wir uns auf künstliche Nanopartikelsysteme, bei denen Proteine das Hauptstrukturelement sind und nicht nur als eingeschlossene Wirkstoffe transportiert werden. Während unter natürlichen Bedingungen lediglich bestimmte Proteine definierte Aggregate und Nanopartikel bilden, können durch chemische Modifikationen oder Veränderungen in der physikalischen Umgebung Nanopartikel aus vielen verschiedenen globulären Proteinen und Enzymen hergestellt werden. Fortschritte bei den Herstellungsmethoden von proteinbasierten Nanopartikeln haben zu einer neuen Generation von Nanosystemen geführt, die über einfache Wirkstofftransporter hinausgehen und vielfältige Anwendungen ermöglichen, wie z.B. gezielte Arzneimittelabgabe, Theranostik, Nanokatalyse und Proteintherapie. [ABSTRACT FROM AUTHOR]

Die aktuelle strukturbiologische Forschung fokussiert sich zunehmend auf humane Proteine und deren Komplexe. Diese Proteine müssen häufig in höheren eukaryotischen Expressionssystemen produziert werden, in welchen die Deuterierung des Proteins nur schwer umzusetzen ist. Dies limitiert die Anwendungsmöglichkeiten der NMR‐Spektroskopie stark für diese Systeme. In diesem Artikel präsentieren wir das XL‐ALSOFAST‐13C,1H]‐HMQC‐Experiment, welches sich durch eine stark verbesserte Sensitivität auf vollständig protonierten, hochmolekularen Komplexen auszeichnet. Im Durchschnitt konnte bei den getesteten Systemen mit Massen zwischen 100 und 240 kDa eine Verbesserung der Sensitivität um den Faktor drei erzielt werden, verglichen mit den aktuell besten publizierten Experimenten. Das Prinzip des XL‐ALSOFAST beruht auf der optimalen Nutzung von passiver Magnetisierung und der Minimierung von transversaler Relaxation durch das in diesem Artikel eingeführte Konzept der verzögerten Entkopplung. Die Kombination aus hoher Sensitivität und überlegener Artefaktunterdrückung macht XL‐ALSOFAST ideal für Untersuchungen an instabilen Membranproteinen oder zur Analyse von therapeutischen Antikörpern bei natürlicher 13C‐Häufigkeit. XL‐ALSOFAST und das Konzept der verzögerten Entkopplung wird daher mehr biologisch relevante Systeme für die NMR‐Spektroskopie zugänglich machen. [ABSTRACT FROM AUTHOR]

Environmental polarity is an important factor that drives biomolecular interactions to regulate cell function. Herein, a general method of using the fluorogenic probe NTPAN‐MI is reported to quantify the subcellular polarity change in response to protein unfolding. NTPAN‐MI fluorescence is selectively activated upon labeling unfolded proteins with exposed thiols, thereby reporting on the extent of proteostasis. NTPAN‐MI also reveals the collapse of the host proteome caused by influenza A virus infection. The emission profile of NTPAN‐MI contains information of the local polarity of the unfolded proteome, which can be resolved through spectral phasor analysis. Under stress conditions that disrupt different checkpoints of protein quality control, distinct patterns of dielectric constant distribution in the cytoplasm can be observed. However, in the nucleus, the unfolded proteome was found to experience a more hydrophilic environment across all the stress conditions, indicating the central role of nucleus in the stress response process. [ABSTRACT FROM AUTHOR]

Amyloids are characterized by their capacity to bind Congo red (CR), one of the most used amyloid‐specific dyes. The structural features of CR binding were unknown for years, mainly because of the lack of amyloid structures solved at high resolution. In the last few years, solid‐state NMR spectroscopy enabled the determination of the structural features of amyloids, such as the HET‐s prion forming domain (HET‐s PFD), which also has recently been used to determine the amyloid–CR interface at atomic resolution. Herein, we combine spectroscopic data with molecular docking, molecular dynamics, and excitonic quantum/molecular mechanics calculations to examine and rationalize CR binding to amyloids. In contrast to a previous assumption on the binding mode, our results suggest that CR binding to the HET‐s PFD involves a cooperative process entailing the formation of a complex with 1:1 stoichiometry. This provides a molecular basis to explain the bathochromic shift in the maximal absorbance wavelength when CR is bound to amyloids. [ABSTRACT FROM AUTHOR]

An azanorbornadiene bromovinyl sulfone reagent for cysteine‐selective bioconjugation has been developed. Subsequent reaction with dipyridyl tetrazine leads to bond cleavage and formation of a pyrrole‐linked conjugate. The latter involves ligation of the tetrazine to the azanorbornadiene‐tagged protein through inverse electron demand Diels–Alder cycloaddition with subsequent double retro‐Diels–Alder reactions to form a stable pyrrole linkage. The sequence of site‐selective bioconjugation followed by bioorthogonal bond cleavage was efficiently employed for the labelling of three different proteins. This method benefits from easy preparation of these reagents, selectivity for cysteine, and stability after reaction with a commercial tetrazine, which has potential for the routine preparation of protein conjugates for chemical biology studies. [ABSTRACT FROM AUTHOR]

Amphiphilic surface groups play an important role in many biological processes. The synthesis of amphiphilic polyphenylene dendrimer branches (dendrons), providing alternating hydrophilic and lipophilic surface groups and one reactive ethynyl group at the core is reported. The amphiphilic surface groups serve as biorecognition units that bind to the surface of adenovirus 5 (Ad5), which is a common vector in gene therapy. The Ad5/dendron complexes showed high gene transduction efficiencies in coxsackie‐adenovirus receptor (CAR)‐negative cells. Moreover, the dendrons offer incorporation of new functions at the dendron core by in situ post‐modifications, even when bound to the Ad5 surface. Surfaces coated with these dendrons were analyzed for their blood‐protein binding capacity, which is essential to predict their performance in the blood stream. A new platform for introducing bioactive groups to the Ad5 surface without chemically modifying the virus particles is provided. [ABSTRACT FROM AUTHOR]

The rhytidenone family comprises spirobisnaphthalene natural products isolated from the mangrove endophytic fungus Rhytidhysteron rufulum AS21B. The biomimetic synthesis of rhytidenone A was achieved by a Michael reaction/aldol/lactonization cascade in a single step from the proposed biosynthetic precursor rhytidenone F. Moreover, the mode of action of the highly cytotoxic rhytidenone F was investigated. The pulldown assay coupled with mass spectrometry analysis revealed the target protein PA28γ is covalently attached to rhytidenone F at the Cys92 residue. The interactions of rhytidenone F with PA28γ lead to the accumulation of p53, which is an essential tumor suppressor in humans. Consequently, the Fas‐dependent signaling pathway is activated to initiate cellular apoptosis. These studies have identified the first small‐molecule inhibitor targeting PA28γ, suggesting rhytidenone F may serve as a promising natural product lead for future anticancer drug development. [ABSTRACT FROM AUTHOR]

The design and scalable synthesis of robust 2D biological ultrathin films with a tunable structure and function and the ability to be easily transferred to a range of substrates remain key challenges in chemistry and materials science. Herein, we report the use of the thiol–disulfide exchange reaction in the synthesis of a macroscopic 2D ultrathin proteinaceous film with the potential for large‐scale fabrication and on‐demand encapsulation/release of functional molecules. The reaction between the Cys6–Cys127 disulfide bond of lysozyme and cysteine is chemo‐ and site‐selective. The partially unfolded lysozyme–cysteine monomers aggregate at the air/water or solid/liquid interface to form an ultra‐large 2D nanofilm (900 cm2) with about 100 % optical transparency. This material adheres to a wide range of substrates and encapsulates and releases a range of molecules without significantly affecting activity. [ABSTRACT FROM AUTHOR]

Benzoxepane derivatives were designed and synthesized, and one hit compound emerged as being effective in vitro with low toxicity. In vivo, this hit compound ameliorated both sickness behavior through anti‐inflammation in LPS‐induced neuroinflammatory mice model and cerebral ischemic injury through anti‐neuroinflammation in rats subjected to transient middle cerebral artery occlusion. Target fishing for the hit compound using photoaffinity probes led to identification of PKM2 as the target protein responsible for anti‐inflammatory effect of the hit compound. Furthermore, the hit exhibited an anti‐neuroinflammatory effect in vitro and in vivo by inhibiting PKM2‐mediated glycolysis and NLRP3 activation, indicating PKM2 as a novel target for neuroinflammation and its related brain disorders. This hit compound has a better safety profile compared to shikonin, a reported PKM2 inhibitor, identifying it as a lead compound in targeting PKM2 for the treatment of inflammation‐related diseases. [ABSTRACT FROM AUTHOR]

Prion‐like transcellular spreading of tau in Alzheimer's Disease (AD) is mediated by tau binding to cell surface heparan sulfate (HS). However, the structural determinants for tau–HS interaction are not well understood. Microarray and SPR assays of structurally defined HS oligosaccharides show that a rare 3‐O‐sulfation (3‐O‐S) of HS significantly enhances tau binding. In Hs3st1−/− (HS 3‐O‐sulfotransferase‐1 knockout) cells, reduced 3‐O‐S levels of HS diminished both cell surface binding and internalization of tau. In a cell culture, the addition of a 3‐O‐S HS 12‐mer reduced both tau cell surface binding and cellular uptake. NMR titrations mapped 3‐O‐S binding sites to the microtubule binding repeat 2 (R2) and proline‐rich region 2 (PRR2) of tau. Tau is only the seventh protein currently known to recognize HS 3‐O‐sulfation. Our work demonstrates that this rare 3‐O‐sulfation enhances tau–HS binding and likely the transcellular spread of tau, providing a novel target for disease‐modifying treatment of AD and other tauopathies. [ABSTRACT FROM AUTHOR]

Squaramate‐linked 2′‐deoxycytidine 5′‐O‐triphosphate was synthesized and found to be good substrate for KOD XL DNA polymerase in primer extension or PCR synthesis of modified DNA. The resulting squaramate‐linked DNA reacts with primary amines to form a stable diamide linkage. This reaction was used for bioconjugations of DNA with Cy5 and Lys‐containing peptides. Squaramate‐linked DNA formed covalent cross‐links with histone proteins. This reactive nucleotide has potential for other bioconjugations of nucleic acids with amines, peptides or proteins without need of any external reagent. [ABSTRACT FROM AUTHOR]

Chemical protein synthesis and biorthogonal modification chemistries allow production of unique proteins for a range of biological studies. Bond‐forming reactions for site‐selective protein labeling are commonly used in these endeavors. Selective bond‐cleavage reactions, however, are much less explored and still pose a great challenge. In addition, most of studies with modified proteins prepared by either total synthesis or semisynthesis have been applied mainly for in vitro experiments with very limited extension to live cells. Reported here is an approach for studying uniquely modified proteins containing a traceless cell delivery unit and palladium‐based cleavable element for chemical activation, and monitoring the effect of these proteins in live cells. This approach is demonstrated for the synthesis of a caged ubiquitin‐aldehyde, which was decaged for the inhibition of deubiquitinases in live cells. [ABSTRACT FROM AUTHOR]

Die Ligation von α‐Ketosäure‐Hydroxylamin (KAHA) erlaubt die chemoselektive Verknüpfung von ungeschützten Peptidsegmenten unter Bildung einer Amidbindung. Die zurzeit meistgenutzte Variante basiert auf einem fünfgliedrigen cyclischen Hydroxylamin, welches einen Homoserinester als Hauptligationsprodukt bildet. Ein neues viergliedriges cyclisches Hydroxylamin wurde synthetisiert, um die natürliche Aminosäure Threonin an der Ligationsstelle bildet. Dieses Monomer wurde für die Synthese der Proteine UbcH5a (146 Aminosäuren) und TI I27 (89 Aminosäuren) eingesetzt. Sowohl das so synthetisierte UbcH5a als auch die Variante, die unter Verwendung des fünfgliedrigen zyklischen Hydroxylamins synthetisiert wurde, zeigten identische Aktivitäten gegenüber der rekombinanten Variante in einem Ubiquitinierungs‐Assay. [ABSTRACT FROM AUTHOR]

It is a textbook knowledge that protein photoluminescence stems from the three aromatic amino acid residues of tryptophan(Trp), tyrosine (Tyr), and phenylalanine (Phe), with predominant contributions from Trp. Recently, inspired by the intrinsic emission of nonaromatic amino acids and poly(amino acids) in concentrated solutions and solids, we revisited protein light emission using bovine serum albumin (BSA) as a model. BSA is virtually nonemissive in dilute solutions (≤0.1 mg mL−1), but highly luminescent upon concentration or aggregation, showing unique concentration‐enhanced emission and aggregation‐induced emission (AIE) characteristics. Notably, apart from well‐documented UV luminescence, bright blue emission is clearly observed. Furthermore, persistent room‐temperature phosphorescence (p‐RTP) is achieved even in the amorphous solids under ambient conditions. This visible emission can be rationalized by the clustering‐triggered emission (CTE) mechanism. These findings not only provide an in‐depth understanding of the emissive properties of proteins, but also hold strong implications for further elucidating the basis of tissue autofluorescence. [ABSTRACT FROM AUTHOR]

During the total chemical synthesis of the water‐soluble globular Haemophilus Influenzae DNA ligase (Hin‐Lig), we observed the surprising phenomenon of a soluble peptide segment that failed to undergo native chemical ligation. Based on dynamic light scattering and transmission electron microscopy experiments, we determined that the peptide formed soluble colloidal particles in a homogeneous solution containing 6 m guanidine hydrochloride. Conventional peptide performance‐improving strategies, such as installation of a terminal/side‐chain Arg tag or O‐acyl isopeptide, failed to enable the reaction, presumably because of their inability to disrupt the formation of soluble colloidal particles. However, a removable backbone modification strategy recently developed for the synthesis of membrane proteins did disrupt the formation of the colloids, and the desired ligation of this soluble but unreactive system was eventually accomplished. This work demonstrates that an appropriate solution dispersion state, in addition to good peptide solubility, is a prerequisite for successful peptide ligation. [ABSTRACT FROM AUTHOR]

Peptidbindungen verbinden Aminosäuren in Proteinen und Polypeptiden. Sie zählen zu den Amidbindungen, die Proteinen und synthetischen Polyamiden ihre enorme Stärke verleihen. Obwohl Proteine und Polyamide in Natur und Technik mechanischen Kräften ausgesetzt sind, ist der Einfluss der Kraft auf die Stabilität der Amid‐ und Peptidbindung noch weitgehend unbekannt. Mittels Einzelmolekülkraftspektroskopie entdeckten wir, dass Kräfte von nur einigen hundert pN die Amidhydrolyse 109‐fach beschleunigen, was bisher nur von proteolytischen Enzymen bekannt war. Die drastische Beschleunigung bei geringer Kraft geht einer moderaten weiteren Beschleunigung bei Kräften im nN‐Bereich voraus. Quantenmechanochemische Ab‐initio‐Rechnungen erklären diese experimentellen Befunde sowohl mechanistisch als auch kinetisch. Unsere Ergebnisse zeigen, dass die Stabilität der Amidbindung entgegen bisherigen Annahmen stark kraftabhängig ist. Sie vermitteln ein grundlegendes Verständnis der Rolle mechanischer Aktivierung bei der Amidhydrolyse und weisen den Weg für mögliche Anwendungen, vom Recycling makromolekularer Reststoffe bis hin zum Design biotechnologisch hergestellter proteolytischer Enzyme. [ABSTRACT FROM AUTHOR]

In this study, via a simple one‐step method, chiral copper sulfide quantum dots (d/l‐QDs) were prepared using d‐/l‐penicillamine (d‐/l‐Pen). The anisotropy factor of d/l‐QDs was as high as 0.01. The d/l‐QDs can be used as photocatalysts to cleave proteins. Notably, the l‐QDs displayed the highest catalytic performance under left‐circularly polarized light irradiation. Mechanistic investigations indicate the generation of hydroxyl radicals as the reactive species that cause the cutting of proteins. [ABSTRACT FROM AUTHOR]

Proteins in living cells interact specifically or nonspecifically with an enormous number of biomolecules. To understand the behavior of proteins under intracellular crowding conditions, it is indispensable to observe their three‐dimensional (3D) structures at the atomic level in a physiologically natural environment. We demonstrate the first de novo protein structure determinations in eukaryotes with the sf9 cell/baculovirus system using NMR data from living cells exclusively. The method was applied to five proteins, rat calmodulin, human HRas, human ubiquitin, T. thermophilus HB8 TTHA1718, and Streptococcus protein G B1 domain. In all cases, we could obtain structural information from well‐resolved in‐cell 3D nuclear Overhauser effect spectroscopy (NOESY) data, suggesting that our method can be a standard tool for protein structure determinations in living eukaryotic cells. For three proteins, we achieved well‐converged 3D structures. Among these, the in‐cell structure of protein G B1 domain was most accurately determined, demonstrating that a helix‐loop region is tilted away from a β‐sheet compared to the conformation in diluted solution. [ABSTRACT FROM AUTHOR]

Current practical methods for finding the equilibrium dissociation constant, Kd, of protein–small molecule complexes have inherent sources of inaccuracy. Introduced here is "accurate constant via transient incomplete separation" (ACTIS), which appears to be free of inherent sources of inaccuracy. Conceptually, a short plug of the pre‐equilibrated protein–small molecule mixture is pressure‐propagated in a capillary, causing fast transient incomplete separation of the complex from the unbound small molecule. A superposition of signals from these two components is measured near the capillary exit and used to calculate a fraction of unbound small molecule, which, in turn, is used to calculate Kd. Herein the validity of ACTIS is proven theoretically, its accuracy is verified by computer simulation, and its practical use is demonstrated. ACTIS has the potential to become a reference‐standard method for determining Kd values of protein–small molecule complexes. [ABSTRACT FROM AUTHOR]

Polyunsaturated fatty acids (PUFAs) such as docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) are essential fatty acids. PUFA synthases are composed of three to four subunits and each create a specific PUFA without undesirable byproducts. However, detailed biosynthetic mechanisms for controlling final product profiles have been obscure. Here, the bacterial DHA and EPA synthases were carefully dissected by in vivo and in vitro experiments. In vitro analysis with two KS domains (KSA and KSC) and acyl‐acyl carrier protein (ACP) substrates showed that KSA accepted short‐ to medium‐chain substrates while KSC accepted medium‐ to long‐chain substrates. Unexpectedly, condensation from C18 to C20, the last elongation step in EPA biosynthesis, was catalyzed by KSA domains in both EPA and DHA synthases. Conversely, condensation from C20 to C22, the last elongation step for DHA biosynthesis, was catalyzed by the KSC domain in DHA synthase. KSC domains therefore determine the chain lengths. [ABSTRACT FROM AUTHOR]

Protein misfolding and aberrant aggregations are associated with multiple prevalent and intractable diseases. Inhibition of amyloid assembly is a promising strategy for the treatment of amyloidosis. Reported here is the design and synthesis of a reactive conjugated polymer, a poly(p‐phenylene vinylene) derivative, functionalized with p‐nitrophenyl esters (PPV‐NP) and it inhibits the assembly of amyloid proteins, degrades preformed fibrils, and reduces the cytotoxicity of amyloid aggregations in living cells. PPV‐NP is attached to the proteins through hydrophobic interactions and irreversible covalent linkage. PPV‐NP also exhibited the capacity to eliminate Aβ plaques in brain slices in ex vivo assays. This work represents an innovative attempt to inhibit protein pathogenic aggregates, and may offer insights into the development of therapeutic strategies for amyloidosis. [ABSTRACT FROM AUTHOR]

Cycloheximide (CHX) is an inhibitor of eukaryotic translation elongation that has played an essential role in the study of protein synthesis. Despite its ubiquity, few studies have been directed towards accessing synthetic CHX derivatives, even though such efforts may lead to protein synthesis inhibitors with improved or alternate properties. Described here is the total synthesis of CHX and analogues, and the establishment of structure–activity relationships (SAR) responsible for translation inhibition. The SAR studies aided the design of more potent compounds, one of which irreversibly blocks ribosomal elongation, preserves polysome profiles, and may be a broadly useful tool for investigating protein synthesis. [ABSTRACT FROM AUTHOR]

Magic‐angle spinning (MAS) is an essential ingredient in a wide variety of solid‐state NMR experiments. The standard procedures to adjust the rotor angle are not highly accurate, resulting in a slight misadjustment of the rotor from the magic angle (θRL=tan-12) on the order of a few millidegrees. This small missetting has no significant impact on the overall spectral resolution, but is sufficient to reintroduce anisotropic interactions. Shown here is that site‐specific 1H‐15N dipolar couplings can be accurately measured in a heavily deuterated protein. This method can be applied at arbitrarily high MAS frequencies, since neither rotor synchronization nor particularly high radiofrequency field strengths are required. The off‐MAS method allows the quantification of order parameters for very dynamic residues, which often escape an analysis using existing methods. [ABSTRACT FROM AUTHOR]

Techniken der Hochdurchsatz‐DNA‐Sequenzierung haben eine Revolution in der Genomik ausgelöst, die in viele Bereiche der Lebens‐ und Naturwissenschaften eingedrungen ist. Die bemerkenswerten Eigenschaften der parallelen DNA‐Sequenzierung, wie hohe Sensitivität und Spezifität, hoher Durchsatz und Multiplexkapazität, führten zu Anwendungen als "molekulare Zählwerke" (molecular counter) für die Entdeckung niedermolekularer und peptidbasierter Inhibitoren, für die Hochdurchsatzbiochemie, die Protein‐ und Zelldetektion, die Diagnostik und sogar die Materialienwissenschaften. Ein wichtiger Aspekt bei der Extrapolation der DNA‐Sequenzierung auf "nichtklassische" Anwendungen besteht in der Anforderung, Nukleinsäure‐Barcodes an die interessierenden Entitäten anzuhängen. In diesem Aufsatz werden die chemischen und biochemischen Ansätze beschrieben, die ein einfaches Nukleinsäure‐Barcoding von proteinhaltigen und nichtproteinhaltigen Materialien ermöglicht haben. Wir zeigen Beispiele für die Verwendung von nachgelagerten Technologien, die durch DNA‐codierte Moleküle ermöglicht wurden. In Anbetracht der Tatsache, dass kommerziell erhältliche Hochdurchsatzsequenzer vor weniger als 15 Jahren eingeführt wurden, glauben wir, dass sich diesbezügliche Anwendungen auch in den kommenden Jahren zur Marktreife entwickeln werden. Strichcodes aus DNA: Die massive parallele DNA‐Sequenzierung bietet eine bemerkenswerte Nachempfindlichkeit, Spezifität und Durchsatzkapazität, die zu ihrer Anwendung als „molekulares Zählwerk" in vielen Forschungsbereichen geführt haben. Dieser Aufsatz beschreibt die Ansätze zur Anbringung von DNA‐Barcodes an biologische und nichtbiologische Materialien und stellt Techniken vor, die durch DNA‐codierte Moleküle ermöglicht wurden. [ABSTRACT FROM AUTHOR]

Despite the importance of protein–surface interactions in both biology and biotechnology, our understanding of their origins is limited due to a paucity of experimental studies of the thermodynamics behind such interactions. In response, we have characterized the extent to which interaction with a chemically well‐defined macroscopic surface alters the stability of protein L. To do so, we site‐specifically attached a redox‐reporter‐modified protein variant to a hydroxy‐terminated monolayer on a gold surface and then used electrochemistry to monitor its guanidine denaturation and determine its folding free energy. Comparison with the free energy seen in solution indicates that interaction with this surface stabilizes the protein by 6 kJ mol−1, a value that is in good agreement with theoretical estimates of the entropic consequences of surface‐induced excluded volume effects, thus suggesting that chemically specific interactions with this surface (e.g., electrostatic interactions) are limited in magnitude. [ABSTRACT FROM AUTHOR]

Carbon bonds (C‐bonds) are the highly directional noncovalent interactions between carbonyl‐oxygen acceptors and sp3‐hybridized‐carbon σ‐hole donors through n→σ* electron delocalization. We have shown the ubiquitous existence of C‐bonds in proteins with the help of careful protein structure analysis and quantum calculations, and have precisely determined C‐bond energies. The importance of conventional noncovalent interactions such as hydrogen bond (H‐bonds) and halogen bond (X‐bonds) in the structure and function of biological molecules are well established, while carbon bonds C‐bonds have still to be recognized. We have shown that C‐bonds are present in proteins, contribute enthalpically to the overall hydrophobic interaction and play a significant role in the photodissociation mechanism of myoglobin and the binding of nucleobases to proteins. [ABSTRACT FROM AUTHOR]

Atom transfer radical polymerization (ATRP) can be carried out in a flask completely open to air using a biocatalytic system composed of glucose oxidase (GOx) and horseradish peroxidase (HRP) with an active copper catalyst complex. Nanomolar concentrations of the enzymes and ppm amounts of Cu provided excellent control over the polymerization of oligo(ethylene oxide) methyl ether methacrylate (OEOMA500), generating polymers with high molecular weight (Mn>70 000) and low dispersities (1.13≤Đ≤1.27) in less than an hour. The continuous oxygen supply was necessary for the generation of radicals and polymer chain growth as demonstrated by temporal control and by inducing hypoxic conditions. In addition, the enzymatic cascade polymerization triggered by oxygen was used for a protein and DNA functionalized with initiators to form protein‐b‐POEOMA and DNA‐b‐POEOMA bioconjugates, respectively. [ABSTRACT FROM AUTHOR]

Abstract: The natural product family of fusicoccanes are stabilizers of 14‐3‐3 mediated protein–protein interactions (PPIs), some of which possess antitumor activity. In this study, the first use of molecular dynamics (MD) to rationally design PPI stabilizers with increased potency is presented. Synthesis of a focused library, with subsequent characterization by fluorescence polarization, mutational studies, and X‐ray crystallography confirmed the power of the MD‐based design approach, revealing the potential for an additional hydrogen bond with the 14‐3‐3 protein to lead to significantly increased potency. Additionally, these compounds exert their action in a cellular environment with increased potency. The newly found polar interaction could provide an anchoring point for new small‐molecule PPI stabilizers. These results facilitate the development of fusicoccanes towards drugs or tool compounds, as well as allowing the study of the fundamental principles behind PPI stabilization. [ABSTRACT FROM AUTHOR]

Abstract: There has been growing interest in performing organocatalysis within a supramolecular system as a means of controlling reaction reactivity and stereoselectivity. Here, a protein is used as a host for iminium catalysis. A pyrrolidine moiety is covalently linked to biotin and introduced to the protein host streptavidin for organocatalytic activity. Whereas in traditional systems stereoselectivity is largely controlled by the substituents added to the organocatalyst, enantiomeric enrichment by the reported supramolecular system is completely controlled by the host. Also, the yield of the model reaction increases over 10‐fold when streptavidin is included. A 1.1 Å crystal structure of the protein–catalyst complex and molecular simulations of a key intermediate reveal the chiral scaffold surrounding the organocatalytic reaction site. This work illustrates that proteins can be an excellent supramolecular host for driving stereoselective secondary amine organocatalysis. [ABSTRACT FROM AUTHOR]

Abstract: Reaction of the Au–C N chelate [Au(bnpy)Cl2] with the full‐length zinc finger (ZnF; ZnCys3His) of HIV nucleocapsid protein NCp7 results in C–S aryl transfer from the AuIII organometallic species to a cysteine of the ZnF. The reaction is general and occurs even for finger 3 of the transcription factor Sp1, containing a ZnCys2His2 coordination sphere. This reaction is the first demonstration of group transfer from a coordination compound to biologically important zinc fingers, and is especially noteworthy for the ZnCys2His2 transcription factors. The work expands the corpus of organometallic species which can efficiently modify biomolecules through C‐atom transfer. The electronic features of the gold compound leading to this unexpected reaction were explored by X‐ray absorption spectroscopy. [ABSTRACT FROM AUTHOR]

Abstract: Cysteamine dioxygenase (ADO) is a thiol dioxygenase whose study has been stagnated by the ambiguity as to whether or not it possesses an anticipated protein‐derived cofactor. Reported herein is the discovery and elucidation of a Cys‐Tyr cofactor in human ADO, crosslinked between Cys220 and Tyr222 through a thioether (C−S) bond. By genetically incorporating an unnatural amino acid, 3,5‐difluoro‐tyrosine (F2‐Tyr), specifically into Tyr222 of human ADO, an autocatalytic oxidative carbon–fluorine bond activation and fluoride release were identified by mass spectrometry and 19F NMR spectroscopy. These results suggest that the cofactor biogenesis is executed by a powerful oxidant during an autocatalytic process. Unlike that of cysteine dioxygenase, the crosslinking results in a minimal structural change of the protein and it is not detectable by routine low‐resolution techniques. Finally, a new sequence motif, C‐X‐Y‐Y(F), is proposed for identifying the Cys‐Tyr crosslink. [ABSTRACT FROM AUTHOR]

Abstract: Längere Verweilzeiten vom Wirkstoff am Zielmolekül (Target) können zu länger anhaltender Arzneimittelwirksamkeit, verbesserten pharmakodynamischen Eigenschaften und kinetischer Selektivität gegenüber Antitargets mit schnellen Dissoziationsraten führen. Bisher wurden nur wenige Strategien gefunden, um die Verweilzeit des Wirkstoffs rational zu modulieren und dadurch diese Schlüsseleigenschaft in den Medikamentenentwicklungsprozess zu integrieren. Die Wechselwirkung zwischen einem Halogenrest am Inhibitor und einer aromatischen Seitenkette im Zielprotein kann die Inhibitorverweilzeit signifikant erhöhen. Als Modell für den archetypischen Bindungsmodus eines ATP‐kompetitiven Typ‐I‐Inhibitors mit einer konstitutiv aktiven Kinase wurde die Wechselwirkung der Serin/Threonin‐Kinase Haspin mit 5‐Iodotubercidin(5‐iTU)‐Derivaten verwendet und gezeigt, dass die Inhibitorverweilzeit deutlich mit der Größe und Polarisierbarkeit des Halogenatoms zunimmt. Mithilfe kinetischer, thermodynamischer und struktureller Messungen sowie Bindungsenergieberechnungen liefern wir eine detaillierte mechanistische Charakterisierung der halogenaromatischen π‐Interaktionen in Haspin‐Inhibitor‐Komplexen. [ABSTRACT FROM AUTHOR]

Abstract: The spatiotemporal dynamics of proteins and organelles play an important role in controlling diverse cellular processes. Optogenetic tools using photosensitive proteins and chemically induced dimerization (CID), which allow control of protein dimerization, have been used to elucidate the dynamics of biological systems and to dissect the complicated biological regulatory networks. However, the inherent limitations of current optogenetic and CID systems remain a significant challenge for the fine‐tuning of cellular activity at precise times and locations. Herein, we present a novel chemo‐optogenetic approach, photoswitchable chemically induced dimerization (psCID), for controlling cellular function by using blue light in a rapid and reversible manner. Moreover, psCID is tunable; that is, the dimerization and dedimerization degrees can be fine‐tuned by applying different doses of illumination. Using this approach, we control the localization of proteins and positioning of organelles in live cells with high spatial (μm) and temporal (ms) precision. [ABSTRACT FROM AUTHOR]

Catenanes are intriguing molecular architectures with unique properties. Herein, we report the cellular synthesis of protein catenanes containing folded structural domains, aided by synergy between p53 dimerization and SpyTag/SpyCatcher chemistry. Concatenation of green fluorescent protein (GFP) was shown to increase chemical stability without disrupting the fluorescence properties, and concatenated dihydrofolate reductase (DHFR) exhibited a melting temperature around 4 °C higher and catalytic activity around 27 % higher than the wild-type DHFR and the cyclic/linear controls. Catenation also confers considerable proteolytic resistance on DHFR. The results suggest that catenation could enhance both the stability and activity of folded proteins, thus making topology engineering an attractive approach for tailoring protein properties without varying their native sequences. [ABSTRACT FROM AUTHOR]

In nature, proteins self-assemble into various structures with different dimensions. To construct these nanostructures in laboratories, normally proteins with different symmetries are selected. However, most of these approaches are engineering-intensive and highly dependent on the accuracy of the protein design. Herein, we report that a simple native protein LecA assembles into one-dimensional nanoribbons and nanowires, two-dimensional nanosheets, and three-dimensional layered structures controlled mainly by small-molecule assembly-inducing ligands RnG ( n=1, 2, 3, 4, 5) with varying numbers of ethylene oxide repeating units. To understand the formation mechanism of the different morphologies controlled by the small-molecule structure, molecular simulations were performed from microscopic and mesoscopic view, which presented a clear relationship between the molecular structure of the ligands and the assembled patterns. These results introduce an easy strategy to control the assembly structure and dimension, which could shed light on controlled protein assembly. [ABSTRACT FROM AUTHOR]

The dark- and light-adapted states of YtvA LOV domains exhibit distinct excited-state behavior. We have employed high-level QM(MS-CASPT2)/MM calculations to study the photochemical reactions of the dark- and light-adapted states. The photoreaction from the dark-adapted state starts with an S1→T1 intersystem crossing followed by a triplet-state hydrogen transfer from the thiol to the flavin moiety that produces a diradical intermediate, and a subsequent internal conversion that triggers a barrierless C−S bond formation in the S0 state. The energy profiles for these transformations are different for the four conformers of the dark-adapted state considered. The photochemistry of the light-adapted state does not involve the triplet state: photoexcitation to the S1 state triggers C−S bond cleavage followed by recombination in the S0 state; both these processes are essentially barrierless and thus ultrafast. The present work offers new mechanistic insights into the photoresponse of flavin-containing blue-light photoreceptors. [ABSTRACT FROM AUTHOR]

The basicity of highly protonated cytochrome c (cyt c) and myoglobin (myo) ions were investigated using tandem mass spectrometry, ion-molecule reactions (IMRs), and theoretical calculations as a function of charge state. Surprisingly, highly charged protein ions (HCPI) can readily protonate non-polar molecules and inert gases, including Ar, O2, and N2 in thermal IMRs. The most HCPIs that can be observed are over 130 kJ mol−1 less basic than the least basic neutral organic molecules known (tetrafluoromethane and methane). Based on theoretical calculations, it is predicted that protonated cyt c and myo ions should spontaneously lose a proton to vacuum for charge states in which every third residue is protonated. In this study, HCPIs are formed where every fourth residue on average is protonated. These results indicate that protein ions in higher charge states can be formed using a low-pressure ion source to reduce proton-transfer reactions between protein ions and gases from the atmosphere. [ABSTRACT FROM AUTHOR]

Nonvolatile salts are essential for the structures and functions of many proteins and protein complexes but can severely degrade performance of native mass spectrometry by adducting to protein and protein complex ions, thereby reducing sensitivity and mass measuring accuracy. Small nanoelectrospray emitters are used to form protein and protein complex ions directly from high-ionic-strength (>150 m m) nonvolatile buffers with salts that mimic the extracellular environment. Charge-state distributions are not obtained for proteins and protein complexes from six commonly used nonvolatile buffers and ≥150 m m Na+ with conventionally sized nanoelectrospray emitter tips but are resolved with 0.5 μm tips. This method enables mass measurements of proteins and protein complexes directly from a variety of commonly used buffers with high concentrations of nonvolatile salts and eliminates the need to buffer exchange into volatile ammonium buffers traditionally used in native mass spectrometry. [ABSTRACT FROM AUTHOR]

Protein structure and function is dependent on myriad noncovalent interactions. Direct detection and characterization of these weak interactions in large biomolecules, such as proteins, is experimentally challenging. Herein, we report the first observation and measurement of long-range 'through-space' scalar couplings between methyl and backbone carbonyl groups in proteins. These J couplings are indicative of the presence of noncovalent C−H⋅⋅⋅π hydrogen-bond-like interactions involving the amide π network. Experimentally detected scalar couplings were corroborated by a natural bond orbital analysis, which revealed the orbital nature of the interaction and the origins of the through-space J couplings. The experimental observation of this type of CH⋅⋅⋅π interaction adds a new dimension to the study of protein structure, function, and dynamics by NMR spectroscopy. [ABSTRACT FROM AUTHOR]

Single-molecule fluorescence resonance energy transfer (sm-FRET) has become a widely used tool to reveal dynamic processes and molecule mechanisms hidden under ensemble measurements. However, the upper limit of fluorescent species used in sm-FRET is still orders of magnitude lower than the association affinity of many biological processes under physiological conditions. Herein, we introduce single-molecule photoactivation FRET (sm-PAFRET), a general approach to break the concentration barrier by using photoactivatable fluorophores as donors. We demonstrate sm-PAFRET by capturing transient FRET states and revealing new reaction pathways during translation using μ m fluorophore labeled species, which is 2-3 orders of magnitude higher than commonly used in sm-FRET measurements. sm-PAFRET serves as an easy-to-implement tool to lift the concentration barrier and discover new molecular dynamic processes and mechanisms under physiological concentrations. [ABSTRACT FROM AUTHOR]

An amide 1H-Chemical Exchange Saturation Transfer (CEST) experiment is presented for studies of conformational exchange in proteins. The approach, exploiting spin-state-selective magnetization transfer, completely suppresses undesired NOE-based dips in CEST profiles so that chemical exchange processes can be studied. The methodology is demonstrated with applications involving proteins that interconvert on the millisecond timescale between major and invisible minor states, and accurate amide 1H chemical shifts of the minor conformer are obtained in each case. The spin-state-selective magnetization transfer approach offers unique possibilities for quantitative studies of protein exchange through 1H-CEST. [ABSTRACT FROM AUTHOR]

Ultrasmall nanoparticles (USNPs), usually defined as NPs with core in the size range 1-3 nm, are a class of nanomaterials which show unique physicochemical properties, often different from larger NPs of the same material. Moreover, there are also indications that USNPs might have distinct properties in their biological interactions. For example, recent in vivo experiments suggest that some USNPs escape the liver, spleen, and kidney, in contrast to larger NPs that are strongly accumulated in the liver. Here, we present a simple approach to study the biomolecular interactions at the USNPs bio-nanointerface, opening up the possibility to systematically link these observations to microscopic molecular principles. [ABSTRACT FROM AUTHOR]

A fluid material with high protein content (120-310 mg mL−1) was formed through the ordered self-assembly of native proteins segregated from water. This material is instantly prepared by the simple mixing of a protein solution with anionic and cationic surfactants. By changing the ratio of the surfactants based on the electrostatic characteristics of the target protein, we observed that the surfactants could function as a versatile molecular glue for protein assembly. Moreover, these protein assemblies could be disassembled back into an aqueous solution depending on the salt conditions. Owing to the water-retaining properties of the hydrophilic part of surfactants, the proteins in this material are in a water-rich environment, which maintains their native structure and function. The inclusion of water also provides functional extensibility to this material, as demonstrated by the preparation of an enzymatically active gel. We anticipate that the unique features of this material will permit the use of proteins not only in solution but also as elements of integrated functionalized materials. [ABSTRACT FROM AUTHOR]

Ribonucleic acids (RNA) frequently associate with proteins in many biological processes to form more or less stable complex structures. The characterization of RNA-protein complex structures and binding interfaces by nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography, or strategies based on chemical crosslinking, however, can be quite challenging. Herein, we have explored the use of an alternative method, native top-down mass spectrometry (MS), for probing of complex stoichiometry and protein binding sites at the single-residue level of RNA. Our data show that the electrostatic interactions between HIV-1 TAR RNA and a peptide comprising the arginine-rich binding region of tat protein are sufficiently strong in the gas phase to survive phosphodiester backbone cleavage of RNA by collisionally activated dissociation (CAD), thus allowing its use for probing tat binding sites in TAR RNA by top-down MS. Moreover, the MS data reveal time-dependent 1:2 and 1:1 stoichiometries of the TAR-tat complexes and suggest structural rearrangements of TAR RNA induced by binding of tat peptide. [ABSTRACT FROM AUTHOR]

Zurück zum Anfang: Margaret Dayhoffs 1966 formulierte Hypothese zum Ursprung der Proteine ist heute ein akzeptiertes Modell für die Entstehung großer, funktioneller Proteine aus kurzen, einfachen Peptiden. Die grundsätzliche Frage, wie das erste Protein entstanden ist, besteht jedoch fort. Die von Dayhoff entwickelten Werkzeuge und Hypothesen sowie die heute über 65 Millionen bekannten Proteinsequenzen geben uns alle Möglichkeiten an die Hand, dieser Frage nachzugehen. [ABSTRACT FROM AUTHOR]

The ability to make artificial lipid bilayers compatible with a wide range of environments, and with sufficient structural rigidity for manual handling, would open up a wealth of opportunities for their more routine use in real-world applications. Although droplet interface bilayers (DIBs) have been demonstrated in a host of laboratory applications, from chemical logic to biosynthesis reaction vessels, their wider use is hampered by a lack of mechanical stability and the largely manual methods employed in their production. Multiphase microfluidics has enabled us to construct hierarchical triple emulsions with a semipermeable shell, in order to form robust, bilayer-bound, droplet networks capable of communication with their external surroundings. These constructs are stable in air, water, and oil environments and overcome a critical obstacle of achieving structural rigidity without compromising environmental interaction. This paves the way for practical application of artificial membranes or droplet networks in diverse areas such as medical applications, drug testing, biophysical studies and their use as synthetic cells. [ABSTRACT FROM AUTHOR]

Encapsulating biological materials in lipid vesicles is of interest for mimicking cells; however, except in some particular cases, such processes do not occur spontaneously. Herein, we developed a simple and robust method for encapsulating proteins in fatty acid vesicles in high yields. Fatty acid based, membrane-free coacervates spontaneously sequester proteins and can reversibly form membranous vesicles upon varying the pH value, the precrowding feature in coacervates allowing for protein encapsulation within vesicles. We then produced enzyme-enriched vesicles and show that enzymatic reactions can occur in these micrometric capsules. This work could be of interest in the field of synthetic biology for building microreactors. [ABSTRACT FROM AUTHOR]

Inspired by biosystems, a process is proposed for preparing next-generation artificial polymer receptors with molecular recognition abilities capable of programmable site-directed modification following construction of nanocavities to provide multi-functionality. The proposed strategy involves strictly regulated multi-step chemical modifications: 1) fabrication of scaffolds by molecular imprinting for use as molecular recognition fields possessing reactive sites for further modifications at pre-determined positions, and 2) conjugation of appropriate functional groups with the reactive sites by post-imprinting modifications to develop programmed functionalizations designed prior to polymerization, allowing independent introduction of multiple functional groups. The proposed strategy holds promise as a reliable, affordable, and versatile approach, facilitating the emergence of polymer-based artificial antibodies bearing desirable functions that are beyond those of natural antibodies. [ABSTRACT FROM AUTHOR]

Single-cell analysis techniques are essential for understanding the microheterogeneity and functions of cells. Low-copy-number proteins play important roles in cell functioning, but their measurement in single cells remains challenging. Herein, we report an approach, called plasmonic immunosandwich assay (PISA), for probing low-copy-number proteins in single cells. This approach combined in vivo immunoaffinity extraction and plasmon-enhanced Raman scattering (PERS). Target proteins were specifically extracted from the cells by microprobes modified with monoclonal antibody or molecularly-imprinted polymer (MIP), followed by labeling with Raman-active nanotags. The PERS detection, with Raman intensity enhanced by 9 orders of magnitude, provided ultrasensitive detection at the single-molecule level. Using this approach, we found that alkaline phosphatase and survivin were expressed in distinct levels in cancer and normal cells, and that extended culture passage resulted in reduced expression of survivin. We further developed acupuncture needle-based PISA for probing low-copy-number proteins in living bodies. [ABSTRACT FROM AUTHOR]

A triple-quantum 1H Carr-Purcell-Meiboom-Gill NMR relaxation dispersion experiment is presented that uses methyl group probes as reporters of conformational exchange in highly deuterated, methyl-protonated proteins. Significantly larger dispersion profiles, by as much as a factor of nine, can be obtained relative to single-quantum approaches, thus offering very significant advantages in applications involving interconverting conformers with only small changes in structure or in studies of rare states that are at very low populations. Applications to a number of protein systems are presented where the utility of the method, including its improved sensitivity to chemical exchange processes, is established. [ABSTRACT FROM AUTHOR]