Proteins are naturally formed by domains edging their functional and structural properties. A domain out of the context of an entire protein can retain its structure and to some extent also function on its own. These properties rationalize construction of artificial fusion multidomain proteins with unique combination of various functions. Information on the specific functional and structural characteristics of individual domains in the context of new artificial fusion proteins is inevitably encoded in sequential order of composing domains defining their mutual spatial positions. So the challenges in designing new proteins with new domain combinations lie dominantly in structure/function prediction and its context dependency. Despite the enormous body of publications on artificial fusion proteins, the task of their structure/function prediction is complex and nontrivial. The degree of spatial freedom facilitated by a linker between domains and their mutual orientation driven by noncovalent interactions is beyond a simple and straightforward methodology to predict their structure with reasonable accuracy. In the presented manuscript, we tested methodology using available modeling tools and computational methods. We show that the process and methodology of such prediction are not straightforward and must be done with care even when recently introduced AlphaFold II is used. We also addressed a question of benchmarking standards for prediction of multidomain protein structures-x-ray or Nuclear Magnetic Resonance experiments. On the study of six two-domain protein chimeras as well as their composing domains and their x-ray structures selected from PDB, we conclude that the major obstacle for justified prediction is inappropriate sampling of the conformational space by the explored methods. On the other hands, we can still address particular steps of the methodology and improve the process of chimera proteins prediction.
Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural products research. Currently, reliance on a disparate set of non-standardized, insular, and specialized databases presents a series of challenges for data access, both within the discipline and for integration and interoperability between related fields. The fundamental elements of exchange are referenced structure-organism pairs that establish relationships between distinct molecular structures and the living organisms from which they were identified. Consolidating and sharing such information via an open platform has strong transformative potential for natural products research and beyond. This is the ultimate goal of the newly established LOTUS initiative, which has now completed the first steps toward the harmonization, curation, validation and open dissemination of 750,000+ referenced structure-organism pairs. LOTUS data is hosted on Wikidata and regularly mirrored on https://lotus.naturalproducts.net. Data sharing within the Wikidata framework broadens data access and interoperability, opening new possibilities for community curation and evolving publication models. Furthermore, embedding LOTUS data into the vast Wikidata knowledge graph will facilitate new biological and chemical insights. The LOTUS initiative represents an important advancement in the design and deployment of a comprehensive and collaborative natural products knowledge base.
Počítačová předpověď proteinových mutací vedoucí ke zvýšení jejich afinity k cílovému proteinu není běžně používaný, ale užitečný nástroj proteinového inženýrství. Zde ukazujeme, že dostupnými výpočetními prostředky je možné předpovědět zvýšení afinity receptoru 1 k interferonu-γ. U dvou, ze čtrnácti předpovězených mutant, došlo k pětinásobnému zvýšení disociační rovnovážné konstanty Kd jak bylo ukázáno měřením povrchovou plasmonovou resonancí, SPR.
Computer design of mutations increasing affinity to the target protein is not a standard but useful tool of protein engineering. Here we show that it is possible to apply relatively simple and accessible computer techniques based on empirical potential to predict mutants of receptor 1 to interferon-γ. Two out of fourteen designed mutants showed about five-fold increase of dissociation equilibrium constant K d as measured by surface plasmon resonance, SPR.
AIM: To analyze the genesis of hypertrophic cardiomyopathy on a large cohort of patients from molecular genetics point of view and perform the functional analysis of the 3D molecular model of defective myosin-7 protein in silico. METHODS: The study enrolled 153 patients with diagnosed hypertrophic cardiomyopathy from different parts of the Czech Republic. DNA samples were analyzed for mutations in exons 21 and 22 of the MYH7 gene, which have been associated with high mutation clustering. The 3D model of human myosin-7 was built using the x-ray structure of nucleotide-free scallop myosin S1 as the structural template. We performed de novo structure prediction of mutant and wild type peptides spanning the 769-788 amino acids region of the myosin-7 protein. RESULTS: The Arg870His and Asp778Val amino acid alterations were found in 2 unrelated patients with a severe form of hypertrophic cardiomyopathy. The Asp778Val variation was chosen for subsequent 3D molecular modeling in silico. The mutation of the Asp by Val not only changes the character of the interaction pattern with other amino acids or ions but Val, being a small hydrophobic amino acid, can also completely change the stability of the region. CONCLUSION: Mutation location in the MYH7 gene and changes in amino acid composition may have a crucial negative impact on the outcome of the disease in patients with hypertrophic cardiomyopathy. In addition, a mutation that changes the charge of the amino acid is more likely to affect protein function than a conservative mutation.
- MeSH
- databáze genetické MeSH
- DNA analýza MeSH
- dospělí MeSH
- hodnocení rizik MeSH
- hypertrofická kardiomyopatie diagnóza genetika patologie MeSH
- kohortové studie MeSH
- lidé MeSH
- mladý dospělý MeSH
- molekulární modely MeSH
- mutace MeSH
- myosiny genetika MeSH
- počítačová simulace MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- mladý dospělý MeSH
- mužské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- kazuistiky MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
Blood flukes of the genus Schistosoma cause the disease schistosomiasis that infects over 200 million people worldwide. Treatment relies on just one drug, and new therapies are needed should drug resistance emerge. Schistosoma mansoni cathepsin B1 (SmCB1) is a gut-associated protease that digests host blood proteins as source of nutrients. It is under evaluation as a therapeutic target. Enzymatic activity of the SmCB1 zymogen is prevented by the pro-peptide that sterically blocks the active site until activation of the zymogen to the mature enzyme. We investigated the structure-inhibition relationships of how the SmCB1 pro-peptide interacts with the enzyme core using a SmCB1 zymogen model and pro-peptide-derived synthetic fragments. Two regions were identified within the pro-peptide that govern its inhibitory interaction with the enzyme core: an "active site region" and a unique "heparin-binding region" that requires heparin. The latter region is apparently only found in the pro-peptides of cathepsins B associated with the gut of trematode parasites. Finally, using the active site region as a template and a docking model of SmCB1, we designed a series of inhibitors mimicking the pro-peptide structure, the best of which yielded low micromolar inhibition constants. Overall, we identify a novel glycosaminoglycan-mediated mechanism of inhibition by the pro-peptide that potentially regulates zymogen activation and describe a promising design strategy to develop antischistosomal drugs.
- MeSH
- chromatografie afinitní MeSH
- heparin farmakologie MeSH
- inhibitory proteinkinas chemická syntéza chemie farmakologie MeSH
- katalytická doména účinky léků MeSH
- kathepsin B antagonisté a inhibitory metabolismus MeSH
- molekulární modely MeSH
- molekulární struktura MeSH
- peptidové mapování MeSH
- peptidy chemie farmakologie MeSH
- prasata MeSH
- racionální návrh léčiv MeSH
- Schistosoma mansoni enzymologie MeSH
- sekundární struktura proteinů MeSH
- střevní sliznice chemie MeSH
- vztahy mezi strukturou a aktivitou MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The structure of proteins as well as their folding/unfolding equilibrium are commonly attributed to H-bonding and hydrophobic interactions. We have used the molecular dynamic simulations in an explicit water environment based on the standard empirical potential as well as more accurately (and thus also more reliably) on the QM/MM potential. The simulations where the dispersion term was suppressed have led to a substantial change of the tryptophan-cage protein structure (unfolded structure). This structure cannot fold without the dispersion energy term, whereas, if it is covered fully, the system finds its native structure relatively quickly. This implies that after such physical factors as temperature and pH, the dispersion energy is an important factor in protein structure determination as well as in the protein folding/unfolding equilibrium. The loss of dispersion also affected the R-helical structure. On the other hand, weakening the electrostatic interactions (and thus H-bonding) affected the R-helical structure only to a minor extent.
The behavior of HIV-1 protease in aqueous NaCl and KCl solutions is investigated by kinetic measurements and molecular dynamics simulations. Experiments show cation-specific effects on the enzymatic activity. The initial velocity of peptide substrate hydrolysis increases with salt concentration more dramatically in potassium than in sodium chloride solutions. Furthermore, significantly higher catalytic efficiencies (k(cat)/K(M)) are observed in the presence of K+ compared to Na+ at comparable salt concentrations. Molecular dynamics simulations provide insight into this ion-specific behavior. Sodium is attracted more strongly than potassium to the protein surface primarily due to stronger interactions with carboxylate side chain groups of aspartates and glutamates. These effects are of particular importance for acidic amino acid residues at or near the active site of the enzyme, including a pair of aspartates at the entrance to the reaction cavity. We infer that the presence of more Na+ than K+ at the active site leads to a lower increase in enzymatic activity with increasing salt concentration in the presence of Na+, likely due to the ability of the alkali cations at the active site to lower the efficiency of substrate binding.
- MeSH
- draslík metabolismus MeSH
- HIV-proteasa metabolismus MeSH
- ionty metabolismus MeSH
- lidé MeSH
- simulace molekulární dynamiky MeSH
- sodík metabolismus MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
Ameloblastin (AMBN) was originally believed to be an enamel-specific extracellular matrix glycoprotein secreted by ameloblasts. Recently, AMBN expression was also detected in developing mesenchymal dental hard tissues, in trauma-induced reparative dentin, and during early craniofacial bone formation. The function and structure of AMBN still remain ambiguous, and there are no known proteins with similar primary sequences. We therefore performed a bio-informatic analysis of AMBN to model ab initio the three-dimensional structure of the molecule. The results suggest that AMBN is a two-domain, intrinsically unstructured protein (IUP). The analysis did not reveal any regions with structural similarity to known receptor-ligand systems, and did not identify any higher-order structures similar to functional regions in other known sequences. The AMBN model predicts 11 defined regions exposed on the surface, internalizing the rest of the molecule including a human-specific insert. Molecular dynamics analysis identified one specific and several non-specific calcium-binding regions, mostly at the C-terminal part of the molecule. The model is supported by previous observations that AMBN is a bipolar calcium-binding molecule and hints at a possible role in protein-protein interactions. The model provides information useful for further studies on the function of AMBN.
- MeSH
- aminokyselinové motivy MeSH
- chemické modely MeSH
- financování organizované MeSH
- lidé MeSH
- molekulární modely MeSH
- neuronové sítě (počítačové) MeSH
- proteiny vázající vápník chemie MeSH
- proteiny zubní skloviny chemie MeSH
- sekvence aminokyselin MeSH
- terciární struktura proteinů MeSH
- Check Tag
- lidé MeSH
