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Journal articles on the topic 'Conformational exploration'

Author: Grafiati

Published: 9 November 2024

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1

Herrington, Noah B., Yan Chak Li, David Stein, Gaurav Pandey, and Avner Schlessinger. "A comprehensive exploration of the druggable conformational space of protein kinases using AI-predicted structures." PLOS Computational Biology 20, no. 7 (July 24, 2024): e1012302. http://dx.doi.org/10.1371/journal.pcbi.1012302.

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Protein kinase function and interactions with drugs are controlled in part by the movement of the DFG and ɑC-Helix motifs that are related to the catalytic activity of the kinase. Small molecule ligands elicit therapeutic effects with distinct selectivity profiles and residence times that often depend on the active or inactive kinase conformation(s) they bind. Modern AI-based structural modeling methods have the potential to expand upon the limited availability of experimentally determined kinase structures in inactive states. Here, we first explored the conformational space of kinases in the PDB and models generated by AlphaFold2 (AF2) and ESMFold, two prominent AI-based protein structure prediction methods. Our investigation of AF2’s ability to explore the conformational diversity of the kinome at various multiple sequence alignment (MSA) depths showed a bias within the predicted structures of kinases in DFG-in conformations, particularly those controlled by the DFG motif, based on their overabundance in the PDB. We demonstrate that predicting kinase structures using AF2 at lower MSA depths explored these alternative conformations more extensively, including identifying previously unobserved conformations for 398 kinases. Ligand enrichment analyses for 23 kinases showed that, on average, docked models distinguished between active molecules and decoys better than random (average AUC (avgAUC) of 64.58), but select models perform well (e.g., avgAUCs for PTK2 and JAK2 were 79.28 and 80.16, respectively). Further analysis explained the ligand enrichment discrepancy between low- and high-performing kinase models as binding site occlusions that would preclude docking. The overall results of our analyses suggested that, although AF2 explored previously uncharted regions of the kinase conformational space and select models exhibited enrichment scores suitable for rational drug discovery, rigorous refinement of AF2 models is likely still necessary for drug discovery campaigns.

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Grininger, Christoph, Mario Leypold, Philipp Aschauer, Tea Pavkov-Keller, Lina Riegler-Berket, Rolf Breinbauer, and Monika Oberer. "Structural Changes in the Cap of Rv0183/mtbMGL Modulate the Shape of the Binding Pocket." Biomolecules 11, no. 9 (September 1, 2021): 1299. http://dx.doi.org/10.3390/biom11091299.

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Tuberculosis continues to be a major threat to the human population. Global efforts to eradicate the disease are ongoing but are hampered by the increasing occurrence of multidrug-resistant strains of Mycobacterium tuberculosis. Therefore, the development of new treatment, and the exploration of new druggable targets and treatment strategies, are of high importance. Rv0183/mtbMGL, is a monoacylglycerol lipase of M. tuberculosis and it is involved in providing fatty acids and glycerol as building blocks and as an energy source. Since the lipase is expressed during the dormant and active phase of an infection, Rv0183/mtbMGL is an interesting target for inhibition. In this work, we determined the crystal structures of a surface-entropy reduced variant K74A Rv0183/mtbMGL in its free form and in complex with a substrate mimicking inhibitor. The two structures reveal conformational changes in the cap region that forms a major part of the substrate/inhibitor binding region. We present a completely closed conformation in the free form and semi-closed conformation in the ligand-bound form. These conformations differ from the previously published, completely open conformation of Rv0183/mtbMGL. Thus, this work demonstrates the high conformational plasticity of the cap from open to closed conformations and provides useful insights into changes in the substrate-binding pocket, the target of potential small-molecule inhibitors.

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Everaert, D. H., O. M. Peeters, C. J. De Ranter, N. M. Blaton, A. van Aerschot, and P. Herdewijn. "Conformational Analysis of Substituent Effects on the Sugar Puckering Mode and the anti-HIV Activity of 2′,3′-Dideoxypyrimidine Nucleosides." Antiviral Chemistry and Chemotherapy 4, no. 5 (October 1993): 289–99. http://dx.doi.org/10.1177/095632029300400505.

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A comparison between the conformational parameters of eleven active and inactive anti-HIV 2′,3′-dideoxypyrimidine nucleosides and a series of 73 uridine and thymidine structures, revealed that our compounds, all having N-glycosidic bond torsion angles χ in the anti range, have pseudorotation phase angles P well distributed over both N (C3′- endo) and S [C2′- endo and C3′- exo) type sugar conformations and have both + sc and ap C4′-C5′ conformations. This means that solid state conformations characterized by P, χ and γ do not provide decisive information for predicting possible anti-HIV activity. We also found that any rationalization of the activity or inactivity of nucleosides in terms of the gauche effect of electronegative substituents on the furanose ring conformation, could not be demonstrated by using the semiempirical quantum chemical AM 1 method. Calculations of C3′-X3′ bond polarities indicate that anti-HIV activity in C3′-substituted nucleoside analogues is consistent with the presence of a positive C3′-X3′ bond polarity. Exploration of the conformational space of χ vs. γ for C3′- endo, C2′- endo and C3′- exo sugar puckering modes using the same AM1 method, reveals that although the C3′- endo [ P = 10°) region is about 2 kcal mol−1 lower than the C2′- endo region ( P = 170°), the C2′ - endo sugar puckering mode is the most accessible one due to the conformational flexibility about the minima. Our results also suggest that as P increases from 10°, through 170°, to 210°, the preferred range for -y dramatically shifts from almost exclusively around 50° (+ sc) at P = 10° to almost exclusively non + sc at P = 210°.

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Liu, Jun, Xiao-Gen Zhou, Yang Zhang, and Gui-Jun Zhang. "CGLFold: a contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm." Bioinformatics 36, no. 8 (December 20, 2019): 2443–50. http://dx.doi.org/10.1093/bioinformatics/btz943.

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Abstract Motivation Regions that connect secondary structure elements in a protein are known as loops, whose slight change will produce dramatic effect on the entire topology. This study investigates whether the accuracy of protein structure prediction can be improved using a loop-specific sampling strategy. Results A novel de novo protein structure prediction method that combines global exploration and loop perturbation is proposed in this study. In the global exploration phase, the fragment recombination and assembly are used to explore the massive conformational space and generate native-like topology. In the loop perturbation phase, a loop-specific local perturbation model is designed to improve the accuracy of the conformation and is solved by differential evolution algorithm. These two phases enable a cooperation between global exploration and local exploitation. The filtered contact information is used to construct the conformation selection model for guiding the sampling. The proposed CGLFold is tested on 145 benchmark proteins, 14 free modeling (FM) targets of CASP13 and 29 FM targets of CASP12. The experimental results show that the loop-specific local perturbation can increase the structure diversity and success rate of conformational update and gradually improve conformation accuracy. CGLFold obtains template modeling score ≥ 0.5 models on 95 standard test proteins, 7 FM targets of CASP13 and 9 FM targets of CASP12. Availability and implementation The source code and executable versions are freely available at https://github.com/iobio-zjut/CGLFold. Supplementary information Supplementary data are available at Bioinformatics online.

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Gerbst, Alexey G., Vadim B. Krylov, Dmitry A. Argunov, Maksim I. Petruk, Arsenii S. Solovev, Andrey S. Dmitrenok, and Nikolay E. Nifantiev. "Influence of per-O-sulfation upon the conformational behaviour of common furanosides." Beilstein Journal of Organic Chemistry 15 (March 15, 2019): 685–94. http://dx.doi.org/10.3762/bjoc.15.63.

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The studies on the recently discovered pyranoside-into-furanoside rearrangement have led us to conformational investigations of furanosides upon their total sulfation. Experimental NMR data showed that in some cases drastic changes of the ring conformation occurred while sometimes only the conformation of the exocyclic C4–C5 linkage changed. Herein we describe a combined quantum chemical and NMR conformational investigation of three common monosaccharide furanosides as their propyl glycosides: α-mannose, β-glucose and β-galactose. Full exploration of the furanoside ring by means of ab initio calculations was performed and coupling constants were calculated for each of the low-energy conformers. The results demonstrated preferred trans-orientation of H4–H5 protons in the non-sulfated molecules which changed to gauche-orientation upon sulfation. The effect is less pronounced in the galactosides. For all the studied structures changes in the conformational distribution were revealed by quantum mechanical calculations, that explained the observed changes in intraring coupling constants occurring upon introduction of sulfates.

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6

Pantaleone, Stefano, Cecilia Irene Gho, Riccardo Ferrero, Valentina Brunella, and Marta Corno. "Exploration of the Conformational Scenario for α-, β-, and γ-Cyclodextrins in Dry and Wet Conditions, from Monomers to Crystal Structures: A Quantum-Mechanical Study." International Journal of Molecular Sciences 24, no. 23 (November 27, 2023): 16826. http://dx.doi.org/10.3390/ijms242316826.

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Cyclodextrins (CDs) constitute a class of cyclic oligosaccharides that are well recognized and largely applied in the drug delivery field, thanks to their biocompatibility, low cost, and the possibility to be derivatized in order to tune and optimize the complexation/release of the specific drug. The conformational flexibility of these systems is one of their key properties and requires a cost-effective methodology to be studied by combining the accuracy of results with the possibility of exploring a large set of conformations. In the present paper, we have explored the conformational potential energy surface of the monomers and dimers of α-, β-, and γ-cyclodextrins (i.e., 6, 7, and 8 monomeric units, respectively) by means of fast but accurate semiempirical methods, which are then refined by state-of-the-art DFT functionals. Moreover, the crystal structure is considered for a more suitable comparison with the IR spectrum experimentally recorded. Calculations are carried out in the gas phase and in water environments, applying both implicit and explicit treatments. We show that the conformation of the studied molecules changes from the gas phase to the water, even if treated implicitly, thus modifying their complexation capability.

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Stepanenko, Darya, Yuzhang Wang, and Carlos Simmerling. "Assessing pH-Dependent Conformational Changes in the Fusion Peptide Proximal Region of the SARS-CoV-2 Spike Glycoprotein." Viruses 16, no. 7 (July 2, 2024): 1066. http://dx.doi.org/10.3390/v16071066.

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One of the entry mechanisms of the SARS-CoV-2 coronavirus into host cells involves endosomal acidification. It has been proposed that under acidic conditions, the fusion peptide proximal region (FPPR) of the SARS-CoV-2 spike glycoprotein acts as a pH-dependent switch, modulating immune response accessibility by influencing the positioning of the receptor binding domain (RBD). This would provide indirect coupling of RBD opening to the environmental pH. Here, we explored this possible pH-dependent conformational equilibrium of the FPPR within the SARS-CoV-2 spike glycoprotein. We analyzed hundreds of experimentally determined spike structures from the Protein Data Bank and carried out pH-replica exchange molecular dynamics to explore the extent to which the FPPR conformation depends on pH and the positioning of the RBD. A meta-analysis of experimental structures identified alternate conformations of the FPPR among structures in which this flexible regions was resolved. However, the results did not support a correlation between the FPPR conformation and either RBD position or the reported pH of the cryo-EM experiment. We calculated pKa values for titratable side chains in the FPPR region using PDB structures, but these pKa values showed large differences between alternate PDB structures that otherwise adopt the same FPPR conformation type. This hampers the comparison of pKa values in different FPPR conformations to rationalize a pH-dependent conformational change. We supplemented these PDB-based analyses with all-atom simulations and used constant-pH replica exchange molecular dynamics to estimate pKa values in the context of flexibility and explicit water. The resulting titration curves show good reproducibility between simulations, but they also suggest that the titration curves of the different FPPR conformations are the same within the error bars. In summary, we were unable to find evidence supporting the previously published hypothesis of an FPPR pH-dependent equilibrium: neither from existing experimental data nor from constant-pH MD simulations. The study underscores the complexity of the spike system and opens avenues for further exploration into the interplay between pH and SARS-CoV-2 viral entry mechanisms.

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Popov, Michael E., Ilya V. Kashparov, and Sergey N. Ruzheinikov. "Exploration of conformational space of small biological compounds." Biochemical Society Transactions 28, no. 5 (October 1, 2000): A412. http://dx.doi.org/10.1042/bst028a412b.

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9

Ozcelik, Ani, Raquel Pereira-Cameselle, and José Lorenzo Alonso-Gómez. "From Allenes to Spirobifluorenes: On the Way to Device-compatible Chiroptical Systems." Current Organic Chemistry 24, no. 23 (December 28, 2020): 2737–54. http://dx.doi.org/10.2174/1385272824999201013164534.

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The last decade has seen a huge growth in the construction of chiral systems to expand the scope of chiroptical applications. Dependence of chiroptical response on molecular conformation typically leads to low chiroptical intensities of chiral systems that feature several conformations in solution. In this respect, allenes were employed for the preparation of open and cyclic oligomers as well as molecular cages, presenting remarkable chiroptical responses in solution. Their molecular chirality was also transferred to metal surfaces, yet photoisomerization of allenes limited their further exploration. In search of a more robust chiral axis, theoretical and experimental studies confirmed that spirobifluorenes could give rise to stable systems with tailored optical and chiroptical properties. Additionally, incorporating a conformational lock into spirobifluorene cyclic architectures served as an efficient strategy towards the generation of distinct helical molecular orbitals. This review article outlines our results on developing device-compatible chiroptical systems through axially chiral allenes and spirobifluorenes. The contribution from other research groups is presented briefly.

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Afrasiabi, Fatemeh, Ramin Dehghanpoor, and Nurit Haspel. "Integrating Rigidity Analysis into the Exploration of Protein Conformational Pathways Using RRT* and MC." Molecules 26, no. 8 (April 16, 2021): 2329. http://dx.doi.org/10.3390/molecules26082329.

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To understand how proteins function on a cellular level, it is of paramount importance to understand their structures and dynamics, including the conformational changes they undergo to carry out their function. For the aforementioned reasons, the study of large conformational changes in proteins has been an interest to researchers for years. However, since some proteins experience rapid and transient conformational changes, it is hard to experimentally capture the intermediate structures. Additionally, computational brute force methods are computationally intractable, which makes it impossible to find these pathways which require a search in a high-dimensional, complex space. In our previous work, we implemented a hybrid algorithm that combines Monte-Carlo (MC) sampling and RRT*, a version of the Rapidly Exploring Random Trees (RRT) robotics-based method, to make the conformational exploration more accurate and efficient, and produce smooth conformational pathways. In this work, we integrated the rigidity analysis of proteins into our algorithm to guide the search to explore flexible regions. We demonstrate that rigidity analysis dramatically reduces the run time and accelerates convergence.

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Nicholls, Robert A., Marcus Fischer, Stuart McNicholas, and Garib N. Murshudov. "Conformation-independent structural comparison of macromolecules withProSMART." Acta Crystallographica Section D Biological Crystallography 70, no. 9 (August 29, 2014): 2487–99. http://dx.doi.org/10.1107/s1399004714016241.

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The identification and exploration of (dis)similarities between macromolecular structures can help to gain biological insight, for instance when visualizing or quantifying the response of a protein to ligand binding. Obtaining a residue alignment between compared structures is often a prerequisite for such comparative analysis. If the conformational change of the protein is dramatic, conventional alignment methods may struggle to provide an intuitive solution for straightforward analysis. To make such analyses more accessible, theProcrustes Structural Matching Alignment and Restraints Tool(ProSMART) has been developed, which achieves a conformation-independent structural alignment, as well as providing such additional functionalities as the generation of restraints for use in the refinement of macromolecular models. Sensible comparison of protein (or DNA/RNA) structures in the presence of conformational changes is achieved by enforcing neither chain nor domain rigidity. The visualization of results is facilitated by popular molecular-graphics software such asCCP4mgandPyMOL, providing intuitive feedback regarding structural conservation and subtle dissimilarities between close homologues that can otherwise be hard to identify. Automatically generated colour schemes corresponding to various residue-based scores are provided, which allow the assessment of the conservation of backbone and side-chain conformations relative to the local coordinate frame. Structural comparison tools such asProSMARTcan help to break the complexity that accompanies the constantly growing pool of structural data into a more readily accessible form, potentially offering biological insight or influencing subsequent experiments.

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Verkhivker, Gennady, Mohammed Alshahrani, and Grace Gupta. "Exploring Conformational Landscapes and Cryptic Binding Pockets in Distinct Functional States of the SARS-CoV-2 Omicron BA.1 and BA.2 Trimers: Mutation-Induced Modulation of Protein Dynamics and Network-Guided Prediction of Variant-Specific Allosteric Binding Sites." Viruses 15, no. 10 (September 27, 2023): 2009. http://dx.doi.org/10.3390/v15102009.

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A significant body of experimental structures of SARS-CoV-2 spike trimers for the BA.1 and BA.2 variants revealed a considerable plasticity of the spike protein and the emergence of druggable binding pockets. Understanding the interplay of conformational dynamics changes induced by the Omicron variants and the identification of cryptic dynamic binding pockets in the S protein is of paramount importance as exploring broad-spectrum antiviral agents to combat the emerging variants is imperative. In the current study, we explore conformational landscapes and characterize the universe of binding pockets in multiple open and closed functional spike states of the BA.1 and BA.2 Omicron variants. By using a combination of atomistic simulations, a dynamics network analysis, and an allostery-guided network screening of binding pockets in the conformational ensembles of the BA.1 and BA.2 spike conformations, we identified all experimentally known allosteric sites and discovered significant variant-specific differences in the distribution of binding sites in the BA.1 and BA.2 trimers. This study provided a structural characterization of the predicted cryptic pockets and captured the experimentally known allosteric sites, revealing the critical role of conformational plasticity in modulating the distribution and cross-talk between functional binding sites. We found that mutational and dynamic changes in the BA.1 variant can induce the remodeling and stabilization of a known druggable pocket in the N-terminal domain, while this pocket is drastically altered and may no longer be available for ligand binding in the BA.2 variant. Our results predicted the experimentally known allosteric site in the receptor-binding domain that remains stable and ranks as the most favorable site in the conformational ensembles of the BA.2 variant but could become fragmented and less probable in BA.1 conformations. We also uncovered several cryptic pockets formed at the inter-domain and inter-protomer interface, including functional regions of the S2 subunit and stem helix region, which are consistent with the known role of pocket residues in modulating conformational transitions and antibody recognition. The results of this study are particularly significant for understanding the dynamic and network features of the universe of available binding pockets in spike proteins, as well as the effects of the Omicron-variant-specific modulation of preferential druggable pockets. The exploration of predicted druggable sites can present a new and previously underappreciated opportunity for therapeutic interventions for Omicron variants through the conformation-selective and variant-specific targeting of functional sites involved in allosteric changes.

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CAI, Liangliang, and Andrew Wee. "Topology Selectivity of a Conformationally Flexible Precursor by Selenium Doping." ECS Meeting Abstracts MA2024-01, no. 16 (August 9, 2024): 1210. http://dx.doi.org/10.1149/ma2024-01161210mtgabs.

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Conformational arrangements within nanostructures play a crucial role in shaping the overall configuration and determining the properties, for example in covalent/metal organic framework (COF/MOF) synthesis. In on-surface synthesis, conformational diversity often leads to uncontrollable or disordered structures. Therefore, exploration on controlling and directing the conformational arrangements is significant in achieving desired nanoarchitectures. In this study, a conformationally flexible precursor 2,4,6-tris(3-bromophenyl)-1,3,5-triazine (mTBPT) was employed, and a random phase consisting of C3h and Cs conformers was first obtained after deposition of mTBPT on Cu(111) from room temperature (RT) to ~365 K as expected. By low coverage (0.01 ML) selenium (Se) doping, we achieved the selectivity of the C3h conformer greatly and improved the nanopore structural homogeneity. The ordered 2D metal organic nanostructure from mTBPT could be fulfilled by Se doping from RT to ~365 K, and the deposition sequence of mTBPT and Se did not make any difference. Through the combination of high-resolution scanning tunneling microscopy and non-contact atomic force microscopy, we explored the regulation of the conformationally flexible mTBPT on Cu(111) and achieved the high topology selectivity by low coverage Se doping. Density functional theory calculations revealed the energy regulation of organometallics before and after Se doping at atomic level. These results could enrich the on-surface synthesis toolbox of conformationally flexible precursors, for the design of complex nanoarchitectures, and for future development of engineered nanomaterials and nanodevices. Figure 1

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14

Uppuladinne, Mallikarjunachari V. N., Archana Achalere, Uddhavesh Sonavane, and Rajendra Joshi. "Probing the structure of human tRNA₃^Lys in the presence of ligands using docking, MD simulations and MSM analysis." RSC Advances 13, no. 37 (2023): 25778–96. http://dx.doi.org/10.1039/d3ra03694d.

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15

Margerit, William, Antoine Charpentier, Cathy Maugis-Rabusseau, Johann Christian Schön, Nathalie Tarrat, and Juan Cortés. "IGLOO: An Iterative Global Exploration and Local Optimization Algorithm to Find Diverse Low-Energy Conformations of Flexible Molecules." Algorithms 16, no. 10 (October 12, 2023): 476. http://dx.doi.org/10.3390/a16100476.

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The exploration of the energy landscape of a chemical system is essential for understanding and predicting its observable properties. In most cases, this is a challenging task due to the high complexity of such landscapes, which often consist of multiple, possibly hierarchical basins that are difficult to locate and thoroughly explore. In this study, we introduce a novel method, called IGLOO (Iterative Global Exploration and Local Optimization), which aims to achieve a more efficient global exploration of the conformational space compared to existing techniques. The method utilizes a tree-based exploration inspired by the Rapidly exploring Random Tree (RRT) algorithm originating from robotics. IGLOO dynamically adjusts its exploration strategy to both homogeneously scan the landscape and focus on promising regions, avoiding redundant exploration. We evaluated IGLOO using models of two polypeptides and compared its performance to the traditional basin-hopping method and a hybrid method that also incorporates the RRT algorithm. We find that IGLOO outperforms both alternative methods in terms of efficiently and comprehensively exploring the molecular conformational space. This approach can be easily generalized to other chemical systems such as molecules on surfaces or crystalline systems.

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Hazrah, Arsh S., Mohamad Al-Jabiri, Raiden Speelman, and Wolfgang Jäger. "A rotational spectroscopic and ab initio study of cis- and trans-(−)-carveol: further insights into conformational dynamics in monoterpenes and monoterpenoids." Physical Chemistry Chemical Physics 23, no. 28 (2021): 15159–68. http://dx.doi.org/10.1039/d1cp02101j.

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17

Budzianowski, A., and A. Katrusiak. "Thermodynamic exploration of conformational space of 1,2-ethylene glycol." Acta Crystallographica Section A Foundations of Crystallography 64, a1 (August 23, 2008): C612—C613. http://dx.doi.org/10.1107/s010876730808029x.

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18

Zimmerman, Maxwell I., and Gregory R. Bowman. "FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs." Journal of Chemical Theory and Computation 11, no. 12 (November 20, 2015): 5747–57. http://dx.doi.org/10.1021/acs.jctc.5b00737.

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19

Sfriso, Pedro, Adam Hospital, Agustí Emperador, and Modesto Orozco. "Exploration of conformational transition pathways from coarse-grained simulations." Bioinformatics 29, no. 16 (June 5, 2013): 1980–86. http://dx.doi.org/10.1093/bioinformatics/btt324.

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20

Mannella, Carmen. "In Silico Exploration of Alternative Conformational States of VDAC." Molecules 28, no. 8 (April 8, 2023): 3309. http://dx.doi.org/10.3390/molecules28083309.

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VDAC (Voltage-Dependent Anion-selective Channel) is the primary metabolite pore in the mitochondrial outer membrane (OM). Atomic structures of VDAC, consistent with its physiological “open” state, are β-barrels formed by 19 transmembrane (TM) β-strands and an N-terminal segment (NTERM) that folds inside the pore lumen. However, structures are lacking for VDAC’s partially “closed” states. To provide clues about possible VDAC conformers, we used the RoseTTAFold neural network to predict structures for human and fungal VDAC sequences modified to mimic removal from the pore wall or lumen of “cryptic” domains, i.e., segments buried in atomic models yet accessible to antibodies in OM-bound VDAC. Predicted in vacuo structures for full-length VDAC sequences are 19-strand β-barrels similar to atomic models, but with weaker H-bonding between TM strands and reduced interactions between NTERM and the pore wall. Excision of combinations of “cryptic” subregions yields β-barrels with smaller diameters, wide gaps between N- and C-terminal β-strands, and in some cases disruption of the β-sheet (associated with strained backbone H-bond registration). Tandem repeats of modified VDAC sequences also were explored, as was domain swapping in monomer constructs. Implications of the results for possible alternative conformational states of VDAC are discussed.

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Coulibaly, Penayori Marie-Aimée, Souleymane Coulibaly, Evrard Ablo, Seiny Roger N’Dri, Kassi Amian Brise Benjamin, Drissa Sissouma, and Adjou Ané. "Unveiling the synthesis and spectral characterizations of novel (E)-furan-2-yl acrylohydrazides: an exploration in molecular design." PeerJ Organic Chemistry 6 (August 16, 2024): e11. http://dx.doi.org/10.7717/peerj-ochem.11.

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In this study, we present the synthesis of novel derivatives of 3-furan-2-yl acrylohydrazide using a meticulous three-step reaction sequence. The synthesis ends up in the condensation of (E)-3-(furan-2-yl) acrylohydrazide (3) with diverse benzaldehyde and acetophenone derivatives. Comprehensive characterization of the synthesized compounds was achieved through 1D nuclear magnetic resonance spectroscopic analyses (1H and 13C NMR), 2D nuclear magnetic resonance spectroscopy (HSQC, NOESY), and high-resolution mass spectrometry (HRMS). The investigation of 1H NMR data at room temperature in deuterated dimethyl sulfoxide (DMSO-d6 ) unveiled the existence of (E)-3-(furan-2-yl) acrylohydrazide derivatives (4a–h) in a conformational equilibrium, manifesting as a mixture of synperiplanar E (sp E) and antiperiplanar E (ap E), Notably, compounds 4a and 4b predominantly adopted the sp E conformer (Ec=c sp EC=N), while the remaining compounds (4c–h), favored the antiperiplanar conformation (Ec=c ap EC=N) even if for the 4g compound it was challenging to determine the EC=N conformer. These findings contribute valuable insights into the conformational dynamics of this class of compounds, holding significance for applications in diverse scientific domains.

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Barnett-Norris, Judy, Frank Guarnieri, Dow P. Hurst, and Patricia H. Reggio. "Exploration of Biologically Relevant Conformations of Anandamide, 2-Arachidonylglycerol, and Their Analogues Using Conformational Memories." Journal of Medicinal Chemistry 41, no. 24 (November 1998): 4861–72. http://dx.doi.org/10.1021/jm9803471.

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Pasala, Chiranjeevi, Sahil Sharma, Tanaya Roychowdhury, Elisabetta Moroni, Giorgio Colombo, and Gabriela Chiosis. "N-Glycosylation as a Modulator of Protein Conformation and Assembly in Disease." Biomolecules 14, no. 3 (February 27, 2024): 282. http://dx.doi.org/10.3390/biom14030282.

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Glycosylation, a prevalent post-translational modification, plays a pivotal role in regulating intricate cellular processes by covalently attaching glycans to macromolecules. Dysregulated glycosylation is linked to a spectrum of diseases, encompassing cancer, neurodegenerative disorders, congenital disorders, infections, and inflammation. This review delves into the intricate interplay between glycosylation and protein conformation, with a specific focus on the profound impact of N-glycans on the selection of distinct protein conformations characterized by distinct interactomes—namely, protein assemblies—under normal and pathological conditions across various diseases. We begin by examining the spike protein of the SARS virus, illustrating how N-glycans regulate the infectivity of pathogenic agents. Subsequently, we utilize the prion protein and the chaperone glucose-regulated protein 94 as examples, exploring instances where N-glycosylation transforms physiological protein structures into disease-associated forms. Unraveling these connections provides valuable insights into potential therapeutic avenues and a deeper comprehension of the molecular intricacies that underlie disease conditions. This exploration of glycosylation’s influence on protein conformation effectively bridges the gap between the glycome and disease, offering a comprehensive perspective on the therapeutic implications of targeting conformational mutants and their pathologic assemblies in various diseases. The goal is to unravel the nuances of these post-translational modifications, shedding light on how they contribute to the intricate interplay between protein conformation, assembly, and disease.

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Zhou, Shuangyan, Jie Cheng, Ting Yang, Mingyue Ma, Wenying Zhang, Shuai Yuan, Glenn V. Lo, and Yusheng Dou. "Exploration of the Misfolding Mechanism of Transthyretin Monomer: Insights from Hybrid-Resolution Simulations and Markov State Model Analysis." Biomolecules 9, no. 12 (December 17, 2019): 889. http://dx.doi.org/10.3390/biom9120889.

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Misfolding and aggregation of transthyretin (TTR) is widely known to be responsible for a progressive systemic disorder called amyloid transthyretin (ATTR) amyloidosis. Studies suggest that TTR aggregation is initiated by a rate-limiting dissociation of the homo-tetramer into its monomers, which can rapidly misfold and self-assemble into amyloid fibril. Thus, exploring conformational change involved in TTR monomer misfolding is of vital importance for understanding the pathogenesis of ATTR amyloidosis. In this work, microsecond timescale hybrid-resolution molecular dynamics (MD) simulations combined with Markov state model (MSM) analysis were performed to investigate the misfolding mechanism of the TTR monomer. The results indicate that a macrostate with partially unfolded conformations may serve as the misfolded state of the TTR monomer. This misfolded state was extremely stable with a very large equilibrium probability of about 85.28%. With secondary structure analysis, we found the DAGH sheet in this state to be significantly destroyed. The CBEF sheet was relatively stable and sheet structure was maintained. However, the F-strand in this sheet was likely to move away from E-strand and reform a new β-sheet with the H-strand. This observation is consistent with experimental finding that F and H strands in the outer edge drive the misfolding of TTR. Finally, transition pathways from a near native state to this misfolded macrostate showed that the conformational transition can occur either through a native-like β-sheet intermediates or through partially unfolded intermediates, while the later appears to be the main pathway. As a whole, we identified a potential misfolded state of the TTR monomer and elucidated the misfolding pathway for its conformational transition. This work can provide a valuable theoretical basis for understanding of TTR aggregation and the pathogenesis of ATTR amyloidosis at the atomic level.

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Lu, Jianzhang, Chu Wang, Yingying Ma, Kaifeng Liu, Xueqi Fu, and Shu Xing. "Exploration of the Product Specificity of chitosanase CsnMY002 and Mutants Using Molecular Dynamics Simulations." Molecules 28, no. 3 (January 20, 2023): 1048. http://dx.doi.org/10.3390/molecules28031048.

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Chitosanase CsnMY002 is a new type of enzyme isolated from Bacillus subtilis that is used to prepare chitosan oligosaccharide. Although mutants G21R and G21K could increase Chitosan yield and thus increase the commercial value of the final product, the mechanism by which this happens is not known. Herein, we used molecular dynamics simulations to explore the conformational changes in CsnMY002 wild type and mutants when they bind substrates. The binding of substrate changed the conformation of protein, stretching and deforming the active and catalytic region. Additionally, the mutants caused different binding modes and catalysis, resulting in different degrees of polymerization of the final Chitooligosaccharide degradation product. Finally, Arg37, Ile145 ~ Gly148 and Trp204 are important catalytic residues of CsnMY002. Our study provides a basis for the engineering of chitosanases.

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26

Harmat, Zita, Dániel Dudola, and Zoltán Gáspári. "DIPEND: An Open-Source Pipeline to Generate Ensembles of Disordered Segments Using Neighbor-Dependent Backbone Preferences." Biomolecules 11, no. 10 (October 12, 2021): 1505. http://dx.doi.org/10.3390/biom11101505.

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Ensemble-based structural modeling of flexible protein segments such as intrinsically disordered regions is a complex task often solved by selection of conformers from an initial pool based on their conformity to experimental data. However, the properties of the conformational pool are crucial, as the sampling of the conformational space should be sufficient and, in the optimal case, relatively uniform. In other words, the ideal sampling is both efficient and exhaustive. To achieve this, specialized tools are usually necessary, which might not be maintained in the long term, available on all platforms or flexible enough to be tweaked to individual needs. Here, we present an open-source and extendable pipeline to generate initial protein structure pools for use with selection-based tools to obtain ensemble models of flexible protein segments. Our method is implemented in Python and uses ChimeraX, Scwrl4, Gromacs and neighbor-dependent backbone distributions compiled and published previously by the Dunbrack lab. All these tools and data are publicly available and maintained. Our basic premise is that by using residue-specific, neighbor-dependent Ramachandran distributions, we can enhance the efficient exploration of the relevant region of the conformational space. We have also provided a straightforward way to bias the sampling towards specific conformations for selected residues by combining different conformational distributions. This allows the consideration of a priori known conformational preferences such as in the case of preformed structural elements. The open-source and modular nature of the pipeline allows easy adaptation for specific problems. We tested the pipeline on an intrinsically disordered segment of the protein Cd3ϵ and also a single-alpha helical (SAH) region by generating conformational pools and selecting ensembles matching experimental data using the CoNSEnsX+ server.

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Cossins, Benjamin P., Ali Hosseini, and Victor Guallar. "Exploration of Protein Conformational Change with PELE and Meta-Dynamics." Journal of Chemical Theory and Computation 8, no. 3 (February 9, 2012): 959–65. http://dx.doi.org/10.1021/ct200675g.

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Kondo, Hiroko, Noriaki Okimoto, Gentaro Morimoto, and Makoto Taiji. "Exploration of Free-Energy Profiles With Conformational Changes of Proteins." Biophysical Journal 98, no. 3 (January 2010): 26a. http://dx.doi.org/10.1016/j.bpj.2009.12.153.

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Pastor, Nina, César Millán-Pacheco, and D. Alejandro Fernández-Velasco. "Exploration of the Conformational Landscape of an Amyloidogenic Ig Domain." Biophysical Journal 100, no. 3 (February 2011): 211a. http://dx.doi.org/10.1016/j.bpj.2010.12.1366.

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30

Ullah, Ahammed, Nasif Ahmed, Subrata Dey Pappu, Swakkhar Shatabda, A. Z. M. Dayem Ullah, and M. Sohel Rahman. "Efficient conformational space exploration in ab initio protein folding simulation." Royal Society Open Science 2, no. 8 (August 2015): 150238. http://dx.doi.org/10.1098/rsos.150238.

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Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic–polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency.

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31

Li, Yan, Xiang Li, and Zigang Dong. "Exploration of gated ligand binding recognizes an allosteric site for blocking FABP4–protein interaction." Physical Chemistry Chemical Physics 17, no. 48 (2015): 32257–67. http://dx.doi.org/10.1039/c5cp04784f.

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32

Guarnieri, Frank, and Harel Weinstein. "Conformational Memories and the Exploration of Biologically Relevant Peptide Conformations: An Illustration for the Gonadotropin-Releasing Hormone." Journal of the American Chemical Society 118, no. 24 (January 1996): 5580–89. http://dx.doi.org/10.1021/ja952745o.

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33

Wang, Yan, and Krzysztof Kuczera. "Multidimensional Conformational Free Energy Surface Exploration: Helical States of Alanand AibnPeptides." Journal of Physical Chemistry B 101, no. 26 (June 1997): 5205–13. http://dx.doi.org/10.1021/jp964027+.

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34

Malliavin, Thérèse E., Antonio Mucherino, Carlile Lavor, and Leo Liberti. "Systematic Exploration of Protein Conformational Space Using a Distance Geometry Approach." Journal of Chemical Information and Modeling 59, no. 10 (August 23, 2019): 4486–503. http://dx.doi.org/10.1021/acs.jcim.9b00215.

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35

Andrade, Laize A. F., Josué M. Silla, Susanna L. Stephens, Kirk Marat, Elaine F. F. da Cunha, Teodorico C. Ramalho, Jennifer van Wijngaarden, and Matheus P. Freitas. "Conformational Exploration of Enflurane in Solution and in a Biological Environment." Journal of Physical Chemistry A 119, no. 43 (October 19, 2015): 10735–42. http://dx.doi.org/10.1021/acs.jpca.5b08087.

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36

Mustoe, Anthony M., Hashim M. Al-Hashimi, and Charles L. Brooks. "A Coarse Grain RNA Model for Exploration of RNA Conformational Space." Biophysical Journal 100, no. 3 (February 2011): 238a. http://dx.doi.org/10.1016/j.bpj.2010.12.1518.

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37

Venkateswararao, Eeda, Manoj Manickam, Pullareddy Boggu, Youngsoo Kim, and Sang-Hun Jung. "Exploration of benzamidochromenone derivatives with conformational restrictor as interleukin-5 inhibitors." Bioorganic & Medicinal Chemistry 23, no. 10 (May 2015): 2498–504. http://dx.doi.org/10.1016/j.bmc.2015.03.045.

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38

Benayad, Zakarya, and Guillaume Stirnemann. "Enhanced conformational space exploration for biomolecules using denoising diffusion probabilistic models." Biophysical Journal 123, no. 3 (February 2024): 296a—297a. http://dx.doi.org/10.1016/j.bpj.2023.11.1848.

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39

Fonseca, Rasmus, Dimitar V. Pachov, Julie Bernauer, and Henry van den Bedem. "Characterizing RNA ensembles from NMR data with kinematic models." Nucleic Acids Research 42, no. 15 (August 11, 2014): 9562–72. http://dx.doi.org/10.1093/nar/gku707.

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Abstract Functional mechanisms of biomolecules often manifest themselves precisely in transient conformational substates. Researchers have long sought to structurally characterize dynamic processes in non-coding RNA, combining experimental data with computer algorithms. However, adequate exploration of conformational space for these highly dynamic molecules, starting from static crystal structures, remains challenging. Here, we report a new conformational sampling procedure, KGSrna, which can efficiently probe the native ensemble of RNA molecules in solution. We found that KGSrna ensembles accurately represent the conformational landscapes of 3D RNA encoded by NMR proton chemical shifts. KGSrna resolves motionally averaged NMR data into structural contributions; when coupled with residual dipolar coupling data, a KGSrna ensemble revealed a previously uncharacterized transient excited state of the HIV-1 trans-activation response element stem–loop. Ensemble-based interpretations of averaged data can aid in formulating and testing dynamic, motion-based hypotheses of functional mechanisms in RNAs with broad implications for RNA engineering and therapeutic intervention.

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40

Sobornova, Valentina V., Konstantin V. Belov, Michael A. Krestyaninov, and Ilya A. Khodov. "Influence of Solvent Polarity on the Conformer Ratio of Bicalutamide in Saturated Solutions: Insights from NOESY NMR Analysis and Quantum-Chemical Calculations." International Journal of Molecular Sciences 25, no. 15 (July 28, 2024): 8254. http://dx.doi.org/10.3390/ijms25158254.

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The study presents a thorough and detailed analysis of bicalutamide’s structural and conformational properties. Quantum chemical calculations were employed to explore the conformational properties of the molecule, identifying significant energy differences between conformers. Analysis revealed that hydrogen bonds stabilise the conformers, with notable variations in torsion angles. Conformers were classified into ‘closed’ and ‘open’ types based on the relative orientation of the cyclic fragments. NOE spectroscopy in different solvents (CDCl3 and DMSO-d6) was used to study the conformational preferences of the molecule. NOESY experiments provided the predominance of ‘closed’ conformers in non-polar solvents and a significant presence of ‘open’ conformers in polar solvents. The proportions of open conformers were 22.7 ± 3.7% in CDCl3 and 59.8 ± 6.2% in DMSO-d6, while closed conformers accounted for 77.3 ± 3.7% and 40.2 ± 6.2%, respectively. This comprehensive study underscores the solvent environment’s impact on its structural behaviour. The findings significantly contribute to a deeper understanding of conformational dynamics, stimulating further exploration in drug development.

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41

Woo, Hyung-June. "Exploration of the conformational space of myosin recovery stroke via molecular dynamics." Biophysical Chemistry 125, no. 1 (January 2007): 127–37. http://dx.doi.org/10.1016/j.bpc.2006.07.001.

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42

Rajendaran, Senthilnathan, Arunchalam Jothi, and Veerappan Anbazhagan. "Targeting the glycan of receptor binding domain with jacalin as a novel approach to develop a treatment against COVID-19." Royal Society Open Science 7, no. 9 (September 2020): 200844. http://dx.doi.org/10.1098/rsos.200844.

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In silico analysis revealed that a lectin, jacalin from jackfruit seeds, recognizes a glycosylated region of the receptor-binding domain (RBD) of SARS-CoV2. Jacalin binding induces conformational changes in RBD and significantly affects its interaction with human angiotensin-converting enzyme 2. The result may open up exploration of lectin-based strategies against COVID-19.

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43

Yu, Zhiping, Zhen Wang, Xiuzhen Cui, Zanxia Cao, Wanyunfei Zhang, Kunxiao Sun, and Guodong Hu. "Conformational States of the GDP- and GTP-Bound HRAS Affected by A59E and K117R: An Exploration from Gaussian Accelerated Molecular Dynamics." Molecules 29, no. 3 (January 30, 2024): 645. http://dx.doi.org/10.3390/molecules29030645.

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The HRAS protein is considered a critical target for drug development in cancers. It is vital for effective drug development to understand the effects of mutations on the binding of GTP and GDP to HRAS. We conducted Gaussian accelerated molecular dynamics (GaMD) simulations and free energy landscape (FEL) calculations to investigate the impacts of two mutations (A59E and K117R) on GTP and GDP binding and the conformational states of the switch domain. Our findings demonstrate that these mutations not only modify the flexibility of the switch domains, but also affect the correlated motions of these domains. Furthermore, the mutations significantly disrupt the dynamic behavior of the switch domains, leading to a conformational change in HRAS. Additionally, these mutations significantly impact the switch domain’s interactions, including their hydrogen bonding with ligands and electrostatic interactions with magnesium ions. Since the switch domains are crucial for the binding of HRAS to effectors, any alterations in their interactions or conformational states will undoubtedly disrupt the activity of HRAS. This research provides valuable information for the design of drugs targeting HRAS.

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44

Stortz, Carlos A., and Ariel M. Sarotti. "Exhaustive exploration of the conformational landscape of mono- and disubstituted five-membered rings by DFT and MP2 calculations." RSC Advances 9, no. 42 (2019): 24134–45. http://dx.doi.org/10.1039/c9ra03524a.

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The conformational landscape of 22 different non, mono-, and disubstituted compounds with a five-membered ring was thoroughly explored by ab initio (MP2) and DFT (B3LYP and M06-2X) methods with the 6-311+G** basis set.

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45

YAMAGUCHI, Takumi, Tokio WATANABE, Hirokazu YAGI, and Koichi KATO. "Exploration of Conformational Spaces of Oligosaccharides byCombining Molecular Dynamics Simulation and NMR Spectroscopy." Journal of Computer Chemistry, Japan 17, no. 1 (2018): 1–7. http://dx.doi.org/10.2477/jccj.2018-0011.

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46

Fukunishi, H., O. Watanabe, and S. Takada. "Speeding up protein conformational exploration by phantom chain model and replica exchange method." Seibutsu Butsuri 40, supplement (2000): S165. http://dx.doi.org/10.2142/biophys.40.s165_3.

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47

Cheatham, Thomas. "41 A full exploration of the conformational ensembles of nucleic acid structural motifs." Journal of Biomolecular Structure and Dynamics 33, sup1 (May 18, 2015): 28. http://dx.doi.org/10.1080/07391102.2015.1032590.

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48

Sjöqvist, Jonas, Rafael C. González-Cano, Juan T. López Navarrete, Juan Casado, M. Carmen Ruiz Delgado, Mathieu Linares, and Patrick Norman. "A combined MD/QM and experimental exploration of conformational richness in branched oligothiophenes." Phys. Chem. Chem. Phys. 16, no. 45 (2014): 24841–52. http://dx.doi.org/10.1039/c4cp03365e.

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Ramakrishnan, R., Bala Ramachandran, and J. F. Pekny. "A dynamic Monte Carlo algorithm for exploration of dense conformational spaces in heteropolymers." Journal of Chemical Physics 106, no. 6 (February 8, 1997): 2418–25. http://dx.doi.org/10.1063/1.473791.

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Duce, Celia, Susanna Monti, Roberto Solaro, and Maria Rosaria Tiné. "Ionic Peptide Aggregation: Exploration of Conformational Dynamics in Aqueous Solution by Computational Techniques." Journal of Physical Chemistry B 111, no. 5 (February 2007): 1165–75. http://dx.doi.org/10.1021/jp066307n.

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