Chemical Synthesis and NMR Solution Structure of Conotoxin GXIA from Conus geographus

Conotoxins are disulfide-rich peptides found in the venom of cone snails. Due to their exquisite potency and high selectivity for a wide range of voltage and ligand gated ion channels they are attractive drug leads in neuropharmacology. Recently, cone snails were found to have the capability to rapidly switch between venom types with different proteome profiles in response to predatory or defensive stimuli. A novel conotoxin, GXIA (original name G117), belonging to the I3-subfamily was identified as the major component of the predatory venom of piscivorous Conus geographus. Using 2D solution NMR spectroscopy techniques, we resolved the 3D structure for GXIA, the first structure reported for the I3-subfamily and framework XI family. The 32 amino acid peptide is comprised of eight cysteine residues with the resultant disulfide connectivity forming an ICK+1 motif. With a triple stranded β-sheet, the GXIA backbone shows striking similarity to several tarantula toxins targeting the voltage sensor of voltage gated potassium and sodium channels. Supported by an amphipathic surface, the structural evidence suggests that GXIA is able to embed in the membrane and bind to the voltage sensor domain of a putative ion channel target.

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Supramolecular propensity of suckerin proteins is driven by β-sheets and aromatic interactions as revealed by solution NMR

Biomaterials Science ◽

10.1039/c8bm00556g ◽

2018 ◽

Vol 6 (9) ◽

pp. 2440-2447 ◽

Cited By ~ 5

Author(s):

Akshita Kumar ◽

Harini Mohanram ◽

Kiat Whye Kong ◽

Rubayn Goh ◽

Shawn Hoon ◽

...

Keyword(s):

Solution Structure ◽

Solution Nmr ◽

Aromatic Interactions ◽

Β Sheets ◽

Β Sheet

The solution structure of a suckerin protein obtained by NMR illustrates β-sheet conformation with stabilising aromatic interactions in dynamic domains.

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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.

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Crystal structure of human mARC1 reveals its exceptional position among eukaryotic molybdenum enzymes

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1808576115 ◽

2018 ◽

Vol 115 (47) ◽

pp. 11958-11963 ◽

Cited By ~ 12

Author(s):

Christian Kubitza ◽

Florian Bittner ◽

Carsten Ginsel ◽

Antje Havemeyer ◽

Bernd Clement ◽

...

Keyword(s):

Crystal Structure ◽

Catalytic Mechanism ◽

Full Range ◽

3D Structure ◽

Cytochrome P450 Enzymes ◽

Oxygenated Compounds ◽

Online Databases ◽

Starting Point ◽

Wide Range ◽

Nitrogen Containing Compounds

Biotransformation enzymes ensure a viable homeostasis by regulating reversible cycles of oxidative and reductive reactions. The metabolism of nitrogen-containing compounds is of high pharmaceutical and toxicological relevance because N-oxygenated metabolites derived from reactions mediated by cytochrome P450 enzymes or flavin-dependent monooxygenases are in some cases highly toxic or mutagenic. The molybdenum-dependent mitochondrial amidoxime-reducing component (mARC) was found to be an extremely efficient counterpart, which is able to reduce the full range of N-oxygenated compounds and thereby mediates detoxification reactions. However, the 3D structure of this enzyme was unknown. Here we present the high-resolution crystal structure of human mARC. We give detailed insight into the coordination of its molybdenum cofactor (Moco), the catalytic mechanism, and its ability to reduce a wide range of N-oxygenated compounds. The identification of two key residues will allow future discrimination between mARC paralogs and ensure correct annotation. Since our structural findings contradict in silico predictions that are currently made by online databases, we propose domain definitions for members of the superfamily of Moco sulfurase C-terminal (MOSC) domain-containing proteins. Furthermore, we present evidence for an evolutionary role of mARC for the emergence of the xanthine oxidase protein superfamily. We anticipate the hereby presented crystal structure to be a starting point for future descriptions of MOSC proteins, which are currently poorly structurally characterized.

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Dilute Solution Structure of Bottlebrush Polymers

10.26434/chemrxiv.7556690 ◽

2019 ◽

Author(s):

Sarit Dutta ◽

Matthew A. Wade ◽

Dylan J. Walsh ◽

Damien Guironnet ◽

Simon A. Rogers ◽

...

Keyword(s):

Brownian Dynamics ◽

Solution Structure ◽

Coarse Grained ◽

Poly Lactic Acid ◽

Linear Polymers ◽

Molecular Architecture ◽

Wide Range ◽

Conformational Properties ◽

Atomistic Structure ◽

Insight Into

<div>Bottlebrush polymers are a class of macromolecules that has recently found use</div><div>in a wide variety of materials, ranging from lubricating brushes and</div><div>nanostructured coatings to elastomeric gels that exhibit structural color. These</div><div>polymers are characterized by dense branches extending from a central backbone,</div><div>and thus have properties distinct from linear polymers. It remains a challenge</div><div>to specifically understand conformational properties of these molecules, due to</div><div>the wide range of architectural parameters that can be present in a system, and</div><div>thus there is a need to accurately characterize and model these molecules. In</div><div>this paper, we use a combination of viscometry, light scattering, and computer</div><div>simulations to gain insight into the conformational properties of dilute</div><div>bottlebrush polymers. We focus on a series of model bottlebrushes consisting of</div><div>a poly(norbornene) (PNB) backbone with poly(lactic acid) (PLA) side chains. We</div><div>demonstrate that intrinsic viscosity and hydrodynamic radius are experimental</div><div>observations \emph{sensitive} to molecular architecture, exhibiting distinct</div><div>differences with different choices of branch and backbone lengths. Informed by</div><div>the atomistic structure of this PNB-PLA system, we rationalize a coarse-grained</div><div>simulation model that we evaluate using a combination of Brownian Dynamics and</div><div>Monte Carlo simulations. We show that this exhibits quantitative matching to</div><div>experimental results, enabling us to characterize the overall shape of the</div><div>bottlebrush via a number of metrics that can be extended to more general</div><div>bottlebrush architectures.</div>

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The solution structure of pGolemi, a high affinity Mena EVH1 binding miniature protein, suggests explanations for paralog-specific binding to Ena/VASP homology (EVH) 1 domains

Biological Chemistry ◽

10.1515/bc.2009.045 ◽

2009 ◽

Vol 390 (5/6) ◽

Author(s):

Nina M. Link ◽

Cornelia Hunke ◽

Jonathan W. Mueller ◽

Jutta Eichler ◽

Peter Bayer

Keyword(s):

Solution Structure ◽

Specific Binding ◽

Transmembrane Protein ◽

Structural Data ◽

Adaptor Proteins ◽

Axonal Guidance ◽

High Affinity ◽

Binding Domains ◽

Wide Range ◽

Pancreatic Peptide

Abstract Ena/VASP homology 1 (EVH1) domains are polyproline binding domains that are present in a wide range of adaptor proteins, among them Ena/VASP proteins involved in actin remodeling and axonal guidance. The interaction of ActA, a transmembrane protein from the food-borne pathogen Listeria monocytogenes, with EVH1 domains has been shown to be crucial for recruitment of the host's actin skeleton and, as a consequence, for the infectivity of this bacterium. We present the structure of a synthetic high-affinity Mena EVH1 ligand, pGolemi, capable of paralog-specific binding, solved by NMR spectroscopy. This peptide shares the common pancreatic peptide fold with its scaffold, avian pancreatic peptide, but shows pivotal differences in the amino-terminus. The interplay of spatial fixation and flexibility appears to be the reason for its high affinity towards Mena EVH1. Combined with earlier investigations, our structural data shed light on the specificity determinants of pGolemi and the importance of additional binding epitopes around the residues Thr74 and Phe32 on EVH1 domains regulating paralog specificity. Our results are expected to facilitate the design of other high-affinity, paralog-specific EVH1 domain ligands, and serve as a fundament for the investigation of the molecular mode of action of EVH1 domains.

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Porous peptide frameworks generated by stacking non-self-complementary β-sheets

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314094376 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C562-C562

Author(s):

Dmitriy Soldatov ◽

Abdolreza Yazdani ◽

Julia Crewson ◽

Travis Fillion ◽

Aaron Smith ◽

...

Keyword(s):

Interlayer Space ◽

Specific Property ◽

Close Packing ◽

Bioactive Molecules ◽

Structural Motif ◽

Supramolecular Polymers ◽

Amino Acid Residues ◽

Crystalline Materials ◽

Wide Range ◽

Β Sheet

"One of major approaches in the design of cavity space in the solids utilizes non-self-complementary molecules[1]. The irregular shape of the molecules and/or specific directionality of potential H-bonds prevent close packing of the molecules and yields various architectures hosting a second component, from inclusion compounds and co-crystals to complex non-crystalline patterns in biology. The strategy of non-self-complementary molecules has been extended in our studies to 2D supramolecular polymers based on short peptides[2]. The formation of the peptide layer with a desired overall geometry is controlled by strong, charge-assisted H-bonds (arrows in the Figure) in a β-sheet-like network as well as the segregation of hydrophobic amino acid residues into the interlayer space. The H-bonds add stability to the whole architecture while the hydrophobic groups keep the stacking layers at a distance that generates a cavity space available to a second component (encircled ""G"" in the Figure). A wide range of inclusions and co-crystals have been prepared in our group based on a series of dipeptides and higher peptide oligomers. For example, the incorporation of various organic solvents and bioactive molecules have been demonstrated for leucyl-alanine and similar dipeptides: alcohols, amides, phenols, pyridines, polyols, vitamins, scents and flavors. The crystal structure studies reveal a surprisingly persistent structural motif that can be used for engineering of crystalline materials with a specific property. We believe this type of peptide matrix may be utilized in the solid state organic synthesis [3] as reactive molecules of the second component can be oriented in a predictable way with respect to each other. "

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NMR structure of bucandin, a neurotoxin from the venom of the Malayan krait (Bungarus candidus)

Biochemical Journal ◽

10.1042/bj3600539 ◽

2001 ◽

Vol 360 (3) ◽

pp. 539-548 ◽

Cited By ~ 13

Author(s):

Allan M. TORRES ◽

R. Manjunatha KINI ◽

Nirthanan SELVANAYAGAM ◽

Philip W. KUCHEL

Keyword(s):

Solution Structure ◽

Pharmacological Action ◽

Nmr Structure ◽

Side Chains ◽

X Ray ◽

Nmr Study ◽

C Terminus ◽

Mean Structure ◽

Β Sheets ◽

Β Sheet

A high-resolution solution structure of bucandin, a neurotoxin from Malayan krait (Bungarus candidus), was determined by 1H-NMR spectroscopy and molecular dynamics. The average backbone root-mean-square deviation for the 20 calculated structures and the mean structure is 0.47 Å (1 Å = 0.1nm) for all residues and 0.24 Å for the well-defined region that spans residues 23–58. Secondary-structural elements include two antiparallel β-sheets characterized by two and four strands. According to recent X-ray analysis, bucandin adopts a typical three-finger loop motif and yet it has some peculiar characteristics that set it apart from other common α-neurotoxins. The presence of a fourth strand in the second antiparallel β-sheet had not been observed before in three-finger toxins, and this feature was well represented in the NMR structure. Although the overall fold of the NMR structure is similar to that of the X-ray crystal structure, there are significant differences between the two structures that have implications for the pharmacological action of the toxin. These include the extent of the β-sheets, the conformation of the region spanning residues 42–49 and the orientation of some side chains. In comparison with the X-ray structure, the NMR structure shows that the hydrophobic side chains of Trp27 and Trp36 are stacked together and are orientated towards the tip of the middle loop. The NMR study also showed that the two-stranded β-sheet incorporated in the first loop, as defined by residues 1–22, and the C-terminus from Asn59, is probably flexible relative to the rest of the molecule. On the basis of the dispositions of the hydrophobic and hydrophilic side chains, the structure of bucandin is clearly different from those of cytotoxins.

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Molecular Targets Involved in the Neuroprotection Mediated by Terpenoids

Planta Medica ◽

10.1055/a-0953-6738 ◽

2019 ◽

Vol 85 (17) ◽

pp. 1304-1315 ◽

Cited By ~ 4

Author(s):

Laura González-Cofrade ◽

Beatriz de las Heras ◽

Luis Apaza Ticona ◽

Olga M. Palomino

Keyword(s):

Therapeutic Potential ◽

Cell Damage ◽

Biological Activities ◽

Neuronal Cell ◽

Molecular Targets ◽

Research Activity ◽

Neuroprotective Effects ◽

Therapeutic Value ◽

Wide Range ◽

Drug Leads

AbstractNatural products and their derivatives represent the most consistently successful source of drug leads. Terpenoids, a structurally diverse group, are secondary metabolites widely distributed in nature, endowed with a wide range of biological activities such as antibacterial, anti-inflammatory, antitumoral, or neuroprotective effects, which consolidate their therapeutic value. During the last decades, and taking into consideration the prevalence of aging-related diseases, research activity into the neuroprotective effects of these types of compounds has increased enormously. Several signaling pathways involved in neuroprotection are targets of their mechanism of action and mediate their pleiotropic protective activity in neuronal cell damage. In the present review, molecular basis of the neuroprotection exerted by terpenoids is presented, focusing on preclinical evidence of the therapeutic potential of diterpenoids and triterpenoids on neurodegenerative disorders. By acting on diverse mechanisms simultaneously, terpenoids have been emphasized as promising multitarget agents.

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Omics for Bioprospecting and Drug Discovery from Bacteria and Microalgae

Antibiotics ◽

10.3390/antibiotics9050229 ◽

2020 ◽

Vol 9 (5) ◽

pp. 229 ◽

Cited By ~ 1

Author(s):

Reuben Maghembe ◽

Donath Damian ◽

Abdalah Makaranga ◽

Stephen Samwel Nyandoro ◽

Sylvester Leonard Lyantagaye ◽

...

Keyword(s):

Genomic Analysis ◽

Metabolome Analysis ◽

High Throughput Analysis ◽

Culture Optimization ◽

Wide Range ◽

Epigenetic Modulation ◽

Biological Entities ◽

Next Generation Sequencing Ngs ◽

Physiological Variations ◽

Drug Leads

“Omics” represent a combinatorial approach to high-throughput analysis of biological entities for various purposes. It broadly encompasses genomics, transcriptomics, proteomics, lipidomics, and metabolomics. Bacteria and microalgae exhibit a wide range of genetic, biochemical and concomitantly, physiological variations owing to their exposure to biotic and abiotic dynamics in their ecosystem conditions. Consequently, optimal conditions for adequate growth and production of useful bacterial or microalgal metabolites are critically unpredictable. Traditional methods employ microbe isolation and ‘blind’-culture optimization with numerous chemical analyses making the bioprospecting process laborious, strenuous, and costly. Advances in the next generation sequencing (NGS) technologies have offered a platform for the pan-genomic analysis of microbes from community and strain downstream to the gene level. Changing conditions in nature or laboratory accompany epigenetic modulation, variation in gene expression, and subsequent biochemical profiles defining an organism’s inherent metabolic repertoire. Proteome and metabolome analysis could further our understanding of the molecular and biochemical attributes of the microbes under research. This review provides an overview of recent studies that have employed omics as a robust, broad-spectrum approach for screening bacteria and microalgae to exploit their potential as sources of drug leads by focusing on their genomes, secondary metabolite biosynthetic pathway genes, transcriptomes, and metabolomes. We also highlight how recent studies have combined molecular biology with analytical chemistry methods, which further underscore the need for advances in bioinformatics and chemoinformatics as vital instruments in the discovery of novel bacterial and microalgal strains as well as new drug leads.

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The Single Disulfide-Directed β-Hairpin Fold: Role of Disulfide Bond in Folding and Effect of an Additional Disulfide Bond on Stability

Australian Journal of Chemistry ◽

10.1071/ch19386 ◽

2020 ◽

Vol 73 (4) ◽

pp. 312

Author(s):

Balasubramanyam Chittoor ◽

Bankala Krishnarjuna ◽

Rodrigo A. V. Morales ◽

Raymond S. Norton

Keyword(s):

Disulfide Bond ◽

Disulfide Bonds ◽

Solution Structure ◽

Conformational Stability ◽

Disulfide Bridge ◽

Solution Nmr ◽

Peptide Epitope ◽

The Core ◽

Native Fold

Disulfide bonds play a key role in the oxidative folding, conformational stability, and functional activity of many peptides. A few disulfide-rich peptides with privileged architecture such as the inhibitor cystine knot motif have garnered attention as templates in drug design. The single disulfide-directed β-hairpin (SDH), a novel fold identified more recently in contryphan-Vc1, has been shown to possess remarkable thermal, conformational, and chemical stability and can accept a short bioactive epitope without compromising the core structure of the peptide. In this study, we demonstrated that the single disulfide bond is critical in maintaining the native fold by replacing both cysteine residues with serine. We also designed an analogue with an additional, non-native disulfide bridge by replacing Gln1 and Tyr9 with Cys. Contryphan-Vc11–22[Q1C, Y9C] was synthesised utilising orthogonal cysteine protection and its solution structure determined using solution NMR spectroscopy. This analogue maintained the overall fold of native contryphan-Vc1. Previous studies had shown that the β-hairpin core of contryphan-Vc1 was resistant to proteolysis by trypsin and α-chymotrypsin but susceptible to cleavage by pepsin. Contryphan-Vc11–22[Q1C, Y9C] proved to be completely resistant to pepsin, thus confirming our design strategy. These results highlight the role of the disulfide bond in maintaining the SDH fold and provide a basis for the design of more stable analogues for peptide epitope grafting.

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