Switchable Zinc(II)-Responsive Globular β-Sheet Peptide

: The scorpion toxins are the largest potassium channel-blocking peptide family. The understanding of toxin binding interfaces is usually restricted by two classical binding interfaces: one is the toxin α-helix motif, the other is the antiparallel β-sheet motif. In this review, such traditional knowledge was updated by another two different binding interfaces: one is BmKTX toxin using the turn motif between the α-helix and antiparallel β-sheet domains as the binding interface, the other is Ts toxin using turn motif between the β-sheet in the N-terminal and α-helix domains as the binding interface. Their interaction analysis indicated that the scarce negatively charged residues in the scorpion toxins played a critical role in orientating the toxin binding interface. In view of the toxin negatively charged amino acids as “binding interface regulator”, the law of scorpion toxin-potassium channel interaction was proposed, that is, the polymorphism of negatively charged residue distribution determines the diversity of toxin binding interfaces. Such law was used to develop scorpion toxin-potassium channel recognition control technique. According to this technique, three Kv1.3 channel-targeted peptides, using BmKTX as the template, were designed with the distinct binding interfaces from that of BmKTX through modulating the distribution of toxin negatively charged residues. In view of the potassium channel as the common targets of different animal toxins, the proposed law was also shown to helpfully orientate the binding interfaces of other animal toxins. Clearly, the toxin-potassium channel interaction law would strongly accelerate the research and development of different potassium channelblocking animal toxins in the future.

Download Full-text

Insight into the HIV-1 Vif SOCS-box–ElonginBC interaction

Open Biology ◽

10.1098/rsob.130100 ◽

2013 ◽

Vol 3 (11) ◽

pp. 130100 ◽

Cited By ~ 7

Author(s):

Zhisheng Lu ◽

Julien R. C. Bergeron ◽

R. Andrew Atkinson ◽

Torsten Schaller ◽

Dennis A. Veselkov ◽

...

Keyword(s):

Solution Structure ◽

Hydrophobic Interactions ◽

Dynamic Information ◽

Ubiquitin Ligase Complex ◽

Biophysical Studies ◽

Viral Infectivity Factor ◽

Β Sheet ◽

Socs Box ◽

Insight Into ◽

Hiv 1

The HIV-1 viral infectivity factor (Vif) neutralizes cell-encoded antiviral APOBEC3 proteins by recruiting a cellular ElonginB (EloB)/ElonginC (EloC)/Cullin5-containing ubiquitin ligase complex, resulting in APOBEC3 ubiquitination and proteolysis. The suppressors-of-cytokine-signalling-like domain (SOCS-box) of HIV-1 Vif is essential for E3 ligase engagement, and contains a BC box as well as an unusual proline-rich motif. Here, we report the NMR solution structure of the Vif SOCS–ElonginBC (EloBC) complex. In contrast to SOCS-boxes described in other proteins, the HIV-1 Vif SOCS-box contains only one α-helical domain followed by a β-sheet fold. The SOCS-box of Vif binds primarily to EloC by hydrophobic interactions. The functionally essential proline-rich motif mediates a direct but weak interaction with residues 101–104 of EloB, inducing a conformational change from an unstructured state to a structured state. The structure of the complex and biophysical studies provide detailed insight into the function of Vif's proline-rich motif and reveal novel dynamic information on the Vif–EloBC interaction.

Download Full-text

Crystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists

Scientific Reports ◽

10.1038/s41598-021-82660-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Matthias Zeug ◽

Nebojsa Markovic ◽

Cristina V. Iancu ◽

Joanna Tripp ◽

Mislav Oreb ◽

...

Keyword(s):

Crystal Structures ◽

Active Site ◽

Enzyme Engineering ◽

Base Catalysis ◽

Oxidative Decarboxylation ◽

Transition State Stabilization ◽

Major Bottleneck ◽

Hydroxybenzoic Acids ◽

Potassium Binding ◽

Β Sheet

AbstractHydroxybenzoic acids, like gallic acid and protocatechuic acid, are highly abundant natural compounds. In biotechnology, they serve as critical precursors for various molecules in heterologous production pathways, but a major bottleneck is these acids’ non-oxidative decarboxylation to hydroxybenzenes. Optimizing this step by pathway and enzyme engineering is tedious, partly because of the complicating cofactor dependencies of the commonly used prFMN-dependent decarboxylases. Here, we report the crystal structures (1.5–1.9 Å) of two homologous fungal decarboxylases, AGDC1 from Arxula adenivorans, and PPP2 from Madurella mycetomatis. Remarkably, both decarboxylases are cofactor independent and are superior to prFMN-dependent decarboxylases when heterologously expressed in Saccharomyces cerevisiae. The organization of their active site, together with mutational studies, suggests a novel decarboxylation mechanism that combines acid–base catalysis and transition state stabilization. Both enzymes are trimers, with a central potassium binding site. In each monomer, potassium introduces a local twist in a β-sheet close to the active site, which primes the critical H86-D40 dyad for catalysis. A conserved pair of tryptophans, W35 and W61, acts like a clamp that destabilizes the substrate by twisting its carboxyl group relative to the phenol moiety. These findings reveal AGDC1 and PPP2 as founding members of a so far overlooked group of cofactor independent decarboxylases and suggest strategies to engineer their unique chemistry for a wide variety of biotechnological applications.

Download Full-text

Anti-Parallel β-Hairpin Structure in Soluble Aβ Oligomers of Aβ40-Dutch and Aβ40-Iowa

International Journal of Molecular Sciences ◽

10.3390/ijms22031225 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1225

Author(s):

Ziao Fu ◽

William E. Van Nostrand ◽

Steven O. Smith

Keyword(s):

Amyloid Β ◽

Amyloid Angiopathy ◽

Aβ Oligomers ◽

Dominant Component ◽

Fibril Structure ◽

Predominant Component ◽

Aβ Aggregation ◽

Aβ Fibrils ◽

Soluble Aβ Oligomers ◽

Β Sheet

The amyloid-β (Aβ) peptides are associated with two prominent diseases in the brain, Alzheimer’s disease (AD) and cerebral amyloid angiopathy (CAA). Aβ42 is the dominant component of cored parenchymal plaques associated with AD, while Aβ40 is the predominant component of vascular amyloid associated with CAA. There are familial CAA mutations at positions Glu22 and Asp23 that lead to aggressive Aβ aggregation, drive vascular amyloid deposition and result in degradation of vascular membranes. In this study, we compared the transition of the monomeric Aβ40-WT peptide into soluble oligomers and fibrils with the corresponding transitions of the Aβ40-Dutch (E22Q), Aβ40-Iowa (D23N) and Aβ40-Dutch, Iowa (E22Q, D23N) mutants. FTIR measurements show that in a fashion similar to Aβ40-WT, the familial CAA mutants form transient intermediates with anti-parallel β-structure. This structure appears before the formation of cross-β-sheet fibrils as determined by thioflavin T fluorescence and circular dichroism spectroscopy and occurs when AFM images reveal the presence of soluble oligomers and protofibrils. Although the anti-parallel β-hairpin is a common intermediate on the pathway to Aβ fibrils for the four peptides studied, the rate of conversion to cross-β-sheet fibril structure differs for each.

Download Full-text

Interfacial Crystallization and Supramolecular Self-Assembly of Spider Silk Inspired Protein at the Water-Air Interface

Materials ◽

10.3390/ma14154239 ◽

2021 ◽

Vol 14 (15) ◽

pp. 4239

Author(s):

Pezhman Mohammadi ◽

Fabian Zemke ◽

Wolfgang Wagermaier ◽

Markus B. Linder

Keyword(s):

Self Assembly ◽

Spider Silk ◽

Assembly Process ◽

Protein Solution ◽

Time Resolved ◽

Macromolecular Assembly ◽

X Ray Scattering ◽

Air Interface ◽

Fundamental Research ◽

Β Sheet

Macromolecular assembly into complex morphologies and architectural shapes is an area of fundamental research and technological innovation. In this work, we investigate the self-assembly process of recombinantly produced protein inspired by spider silk (spidroin). To elucidate the first steps of the assembly process, we examined highly concentrated and viscous pendant droplets of this protein in air. We show how the protein self-assembles and crystallizes at the water–air interface into a relatively thick and highly elastic skin. Using time-resolved in situ synchrotron X-ray scattering measurements during the drying process, we showed that the skin evolved to contain a high β-sheet amount over time. We also found that β-sheet formation strongly depended on protein concentration and relative humidity. These had a strong influence not only on the amount, but also on the ordering of these structures during the β-sheet formation process. We also showed how the skin around pendant droplets can serve as a reservoir for attaining liquid–liquid phase separation and coacervation from the dilute protein solution. Essentially, this study shows a new assembly route which could be optimized for the synthesis of new materials from a dilute protein solution and determine the properties of the final products.

Download Full-text

Online biophysical predictions for SARS-CoV-2 proteins

BMC Molecular and Cell Biology ◽

10.1186/s12860-021-00362-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Luciano Kagami ◽

Joel Roca-Martínez ◽

Jose Gavaldá-García ◽

Pathmanaban Ramasamy ◽

K. Anton Feenstra ◽

...

Keyword(s):

Protein Sequence ◽

Three Dimensional ◽

Dimensional Structure ◽

Static Structure ◽

Homologous Proteins ◽

Structure Based Drug Design ◽

Protein Protein Interaction ◽

Link Type ◽

Dynamics Simulations ◽

Β Sheet

Abstract Background The SARS-CoV-2 virus, the causative agent of COVID-19, consists of an assembly of proteins that determine its infectious and immunological behavior, as well as its response to therapeutics. Major structural biology efforts on these proteins have already provided essential insights into the mode of action of the virus, as well as avenues for structure-based drug design. However, not all of the SARS-CoV-2 proteins, or regions thereof, have a well-defined three-dimensional structure, and as such might exhibit ambiguous, dynamic behaviour that is not evident from static structure representations, nor from molecular dynamics simulations using these structures. Main We present a website (https://bio2byte.be/sars2/) that provides protein sequence-based predictions of the backbone and side-chain dynamics and conformational propensities of these proteins, as well as derived early folding, disorder, β-sheet aggregation, protein-protein interaction and epitope propensities. These predictions attempt to capture the inherent biophysical propensities encoded in the sequence, rather than context-dependent behaviour such as the final folded state. In addition, we provide the biophysical variation that is observed in homologous proteins, which gives an indication of the limits of their functionally relevant biophysical behaviour. Conclusion The https://bio2byte.be/sars2/ website provides a range of protein sequence-based predictions for 27 SARS-CoV-2 proteins, enabling researchers to form hypotheses about their possible functional modes of action.

Download Full-text

Nanostructure of bioactive glass affects bone cell attachment via protein restructuring upon adsorption

Scientific Reports ◽

10.1038/s41598-021-85050-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ukrit Thamma ◽

Tia J. Kowal ◽

Matthias M. Falk ◽

Himanshu Jain

Keyword(s):

Bioactive Glass ◽

Cell Response ◽

Interfacial Layer ◽

Cell Attachment ◽

Bone Cell ◽

Nano Structure ◽

Rgd Sequence ◽

Engineered Tissue ◽

Α Helix ◽

Β Sheet

AbstractThe nanostructure of engineered bioscaffolds has a profound impact on cell response, yet its understanding remains incomplete as cells interact with a highly complex interfacial layer rather than the material itself. For bioactive glass scaffolds, this layer comprises of silica gel, hydroxyapatite (HA)/carbonated hydroxyapatite (CHA), and absorbed proteins—all in varying micro/nano structure, composition, and concentration. Here, we examined the response of MC3T3-E1 pre-osteoblast cells to 30 mol% CaO–70 mol% SiO2 porous bioactive glass monoliths that differed only in nanopore size (6–44 nm) yet resulted in the formation of HA/CHA layers with significantly different microstructures. We report that cell response, as quantified by cell attachment and morphology, does not correlate with nanopore size, nor HA/CHO layer micro/nano morphology, or absorbed protein amount (bovine serum albumin, BSA), but with BSA’s secondary conformation as indicated by its β-sheet/α-helix ratio. Our results suggest that the β-sheet structure in BSA interacts electrostatically with the HA/CHA interfacial layer and activates the RGD sequence of absorbed adhesion proteins, such as fibronectin and vitronectin, thus significantly enhancing the attachment of cells. These findings provide new insight into the interaction of cells with the scaffolds’ interfacial layer, which is vital for the continued development of engineered tissue scaffolds.

Download Full-text