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Pandey SK, Cifra M. Tubulin Vibration Modes Are in the Subterahertz Range, and Their Electromagnetic Absorption Is Affected by Water. J Phys Chem Lett 2024; 15:8334-8342. [PMID: 39110643 DOI: 10.1021/acs.jpclett.4c01553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Many proteins are thought to coordinate distant sites in their structures through a concerted action of global structural vibrations. However, the direct experimental spectroscopic detection of these vibration modes is rather elusive. We used normal-mode analysis to explore the dominant vibration modes of an all-atom model of the tubulin protein and described their characteristics using a large ensemble of tubulin structures. We quantified the frequency range of the normal vibrational modes to be in the subterahertz band, specifically between ∼40 and ∼160 GHz. Adding water layers to the model increases the frequencies of the low-frequency modes and narrows the frequency variations of the modes among the protein ensemble. We also showed how the electromagnetic absorption of tubulin vibration modes is affected by vibrational damping. These results contribute to our understanding of tubulin's vibrational and electromagnetic properties and provide a foundation for future attempts to control protein behavior via external electromagnetic fields.
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Affiliation(s)
- Saurabh Kumar Pandey
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Prague 18200, Czechia
| | - Michal Cifra
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Prague 18200, Czechia
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2
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Di Gregorio E, Staelens M, Hosseinkhah N, Karimpoor M, Liburd J, Lim L, Shankar K, Tuszyński JA. Raman Spectroscopy Reveals Photobiomodulation-Induced α-Helix to β-Sheet Transition in Tubulins: Potential Implications for Alzheimer's and Other Neurodegenerative Diseases. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:1093. [PMID: 38998698 PMCID: PMC11243591 DOI: 10.3390/nano14131093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/03/2024] [Accepted: 06/12/2024] [Indexed: 07/14/2024]
Abstract
In small clinical studies, the application of transcranial photobiomodulation (PBM), which typically delivers low-intensity near-infrared (NIR) to treat the brain, has led to some remarkable results in the treatment of dementia and several neurodegenerative diseases. However, despite the extensive literature detailing the mechanisms of action underlying PBM outcomes, the specific mechanisms affecting neurodegenerative diseases are not entirely clear. While large clinical trials are warranted to validate these findings, evidence of the mechanisms can explain and thus provide credible support for PBM as a potential treatment for these diseases. Tubulin and its polymerized state of microtubules have been known to play important roles in the pathology of Alzheimer's and other neurodegenerative diseases. Thus, we investigated the effects of PBM on these cellular structures in the quest for insights into the underlying therapeutic mechanisms. In this study, we employed a Raman spectroscopic analysis of the amide I band of polymerized samples of tubulin exposed to pulsed low-intensity NIR radiation (810 nm, 10 Hz, 22.5 J/cm2 dose). Peaks in the Raman fingerprint region (300-1900 cm-1)-in particular, in the amide I band (1600-1700 cm-1)-were used to quantify the percentage of protein secondary structures. Under this band, hidden signals of C=O stretching, belonging to different structures, are superimposed, producing a complex signal as a result. An accurate decomposition of the amide I band is therefore required for the reliable analysis of the conformation of proteins, which we achieved through a straightforward method employing a Voigt profile. This approach was validated through secondary structure analyses of unexposed control samples, for which comparisons with other values available in the literature could be conducted. Subsequently, using this validated method, we present novel findings of statistically significant alterations in the secondary structures of polymerized NIR-exposed tubulin, characterized by a notable decrease in α-helix content and a concurrent increase in β-sheets compared to the control samples. This PBM-induced α-helix to β-sheet transition connects to reduced microtubule stability and the introduction of dynamism to allow for the remodeling and, consequently, refreshing of microtubule structures. This newly discovered mechanism could have implications for reducing the risks associated with brain aging, including neurodegenerative diseases like Alzheimer's disease, through the introduction of an intervention following this transition.
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Affiliation(s)
- Elisabetta Di Gregorio
- Department of Physics, Faculty of Science, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Mechanical and Aerospace Engineering (DIMEAS), Faculty of Biomedical Engineering, Polytechnic University of Turin, 10129 Turin, Italy
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Michael Staelens
- Department of Physics, Faculty of Science, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Instituto de Física Corpuscular, CSIC–Universitat de València, Carrer Catedràtic José Beltrán 2, 46980 Paterna, Spain
| | | | | | | | - Lew Lim
- Vielight Inc., Toronto, ON M4Y 2G8, Canada
| | - Karthik Shankar
- Department of Electrical and Computer Engineering, Faculty of Engineering, University of Alberta, Edmonton, AB T6G 1H9, Canada
| | - Jack A. Tuszyński
- Department of Physics, Faculty of Science, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Mechanical and Aerospace Engineering (DIMEAS), Faculty of Biomedical Engineering, Polytechnic University of Turin, 10129 Turin, Italy
- Department of Data Science and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland
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3
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Saura MLP, Cajachagua CL, Balan A, General IJ. Phosphate uptake in PhoX: Molecular mechanisms. Int J Biol Macromol 2024; 269:131993. [PMID: 38705335 DOI: 10.1016/j.ijbiomac.2024.131993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/07/2024]
Abstract
PhoX is a high-affinity phosphate binding protein, present in Xanthomonas citri, a phytopathogen responsible for the citrus canker disease. Performing molecular dynamics simulations and different types of computational analyses, we study the molecular mechanisms at play in relation to phosphate binding, revealing the global functioning of the protein: PhoX naturally oscillates along its global normal modes, which allow it to explore both bound and unbound conformations, eventually attracting a nearby negative phosphate ion to the highly positive electrostatic potential on its surface, particularly close to the binding pocket. There, several hydrogen bonds are formed with the two main domains of the structure. Phosphate creates, in this way, a strong bridge that connects the domains, keeping itself between them, in a tight closed conformation, explaining its high binding affinity.
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Affiliation(s)
- María Luz Perez Saura
- School of Science and Technology, Universidad Nacional de San Martin, 25 de Mayo y Francia, San Martín 1650, Buenos Aires, Argentina
| | - Cindy Lee Cajachagua
- Universidade de São Paulo (USP), Instituto de Ciências Biomédicas II (ICBII), São Paulo,São Paulo, Brazil
| | - Andrea Balan
- Universidade de São Paulo (USP), Instituto de Ciências Biomédicas II (ICBII), São Paulo,São Paulo, Brazil
| | - Ignacio J General
- School of Science and Technology, Universidad Nacional de San Martin, ICIFI and CONICET, 25 de Mayo y Francia, San Martín 1650, Buenos Aires, Argentina.
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4
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Basu D, Dastidar SG. Molecular Dynamics and Machine Learning reveal distinguishing mechanisms of Competitive Ligands to perturb α,β-Tubulin. Comput Biol Chem 2024; 108:108004. [PMID: 38157659 DOI: 10.1016/j.compbiolchem.2023.108004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 11/25/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
The mechanisms of action of ligands competing for the Colchicine Binding Site (CBS) of the α,β-Tubulin are non-standard compared to the commonly witnessed ligand-induced inhibition of proteins. This is because their potencies are not solely judged by the binding affinity itself, but also by their capacity to bias the conformational states of the dimer. Regarding the latter requirement, it is observed that ligands competing for the same pocket that binds colchicine exhibit divergence in potential clinical outcomes. Molecular dynamics-based ∼5.2 µs sampling of α,β-Tubulin complexed with four different ligands has revealed that each ligand has its customized way of influencing the complex. Primarily, it is the proportion of twisting and/or bending characteristic of modes of the intrinsic dynamics which is revealed to be 'fundamental' to tune this variation in the mechanism. The milder influence of 'bending' makes a ligand (TUB092), better classifiable under the group of vascular disrupting agents (VDAs), which are phenotypically effective on cytoskeletons; whereas a stronger impact of 'bending' makes the classical ligand Colchicine (COL) a better Anti-Mitotic agent (AMA). Two other ligands BAL27862 (2RR) and Nocodazole (NZO) fall in the intermediate zone as they fail to explicitly induce bending modes. Random Forest Classification method and K-means Clustering is applied to reveal the efficiency of Machine Learning methods in classifying the Tubulin conformations according to their ligand-specific perturbations and to highlight the significance of specific amino acid residues, mostly positioned in the α-β and β-β interfaces involved in the mechanism. These key residues responsible to yield discriminative actions of the ligands are likely to be highly useful in future endeavours to design more precise inhibitors.
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Affiliation(s)
- Debadrita Basu
- Biological Sciences, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata 700091, India
| | - Shubhra Ghosh Dastidar
- Biological Sciences, Bose Institute, EN 80, Sector V, Bidhan Nagar, Kolkata 700091, India.
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5
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Ersoy A, Altintel B, Livnat Levanon N, Ben-Tal N, Haliloglu T, Lewinson O. Computational analysis of long-range allosteric communications in CFTR. eLife 2023; 12:RP88659. [PMID: 38109179 PMCID: PMC10727502 DOI: 10.7554/elife.88659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023] Open
Abstract
Malfunction of the CFTR protein results in cystic fibrosis, one of the most common hereditary diseases. CFTR functions as an anion channel, the gating of which is controlled by long-range allosteric communications. Allostery also has direct bearings on CF treatment: the most effective CFTR drugs modulate its activity allosterically. Herein, we integrated Gaussian network model, transfer entropy, and anisotropic normal mode-Langevin dynamics and investigated the allosteric communications network of CFTR. The results are in remarkable agreement with experimental observations and mutational analysis and provide extensive novel insight. We identified residues that serve as pivotal allosteric sources and transducers, many of which correspond to disease-causing mutations. We find that in the ATP-free form, dynamic fluctuations of the residues that comprise the ATP-binding sites facilitate the initial binding of the nucleotide. Subsequent binding of ATP then brings to the fore and focuses on dynamic fluctuations that were present in a latent and diffuse form in the absence of ATP. We demonstrate that drugs that potentiate CFTR's conductance do so not by directly acting on the gating residues, but rather by mimicking the allosteric signal sent by the ATP-binding sites. We have also uncovered a previously undiscovered allosteric 'hotspot' located proximal to the docking site of the phosphorylated regulatory (R) domain, thereby establishing a molecular foundation for its phosphorylation-dependent excitatory role. This study unveils the molecular underpinnings of allosteric connectivity within CFTR and highlights a novel allosteric 'hotspot' that could serve as a promising target for the development of novel therapeutic interventions.
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Affiliation(s)
- Ayca Ersoy
- Department of Chemical Engineering, Bogazici UniversityIstanbulTurkey
- Polymer Research Center, Bogazici UniversityIstanbulTurkey
| | - Bengi Altintel
- Department of Chemical Engineering, Bogazici UniversityIstanbulTurkey
- Polymer Research Center, Bogazici UniversityIstanbulTurkey
| | - Nurit Livnat Levanon
- Department of Molecular Microbiology, Bruce and Ruth Rappaport Faculty of Medicine, Technion-Israel Institute of TechnologyTel AvivIsrael
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv UniversityTel-AvivIsrael
| | - Turkan Haliloglu
- Department of Chemical Engineering, Bogazici UniversityIstanbulTurkey
- Polymer Research Center, Bogazici UniversityIstanbulTurkey
| | - Oded Lewinson
- Department of Molecular Microbiology, Bruce and Ruth Rappaport Faculty of Medicine, Technion-Israel Institute of TechnologyTel AvivIsrael
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6
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Eren E, Watts NR, Randazzo D, Palmer I, Sackett DL, Wingfield PT. Structural basis of microtubule depolymerization by the kinesin-like activity of HIV-1 Rev. Structure 2023; 31:1233-1246.e5. [PMID: 37572662 PMCID: PMC10592302 DOI: 10.1016/j.str.2023.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 04/07/2023] [Accepted: 07/18/2023] [Indexed: 08/14/2023]
Abstract
HIV-1 Rev is an essential regulatory protein that transports unspliced and partially spliced viral mRNAs from the nucleus to the cytoplasm for the expression of viral structural proteins. During its nucleocytoplasmic shuttling, Rev interacts with several host proteins to use the cellular machinery for the advantage of the virus. Here, we report the 3.5 Å cryo-EM structure of a 4.8 MDa Rev-tubulin ring complex. Our structure shows that Rev's arginine-rich motif (ARM) binds to both the acidic surfaces and the C-terminal tails of α/β-tubulin. The Rev-tubulin interaction is functionally homologous to that of kinesin-13, potently destabilizing microtubules at sub-stoichiometric levels. Expression of Rev in astrocytes and HeLa cells shows that it can modulate the microtubule cytoskeleton within the cellular environment. These results show a previously undefined regulatory role of Rev.
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Affiliation(s)
- Elif Eren
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Norman R Watts
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Davide Randazzo
- Light Imaging Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ira Palmer
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dan L Sackett
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul T Wingfield
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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7
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Mansoor Hussain UH, Basheer Ahamed SI. Structural impact of pathogenic SNPs on β-tubulin using molecular dynamics study. J Biomol Struct Dyn 2023; 41:8230-8240. [PMID: 36218086 DOI: 10.1080/07391102.2022.2130986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/26/2022] [Indexed: 10/17/2022]
Abstract
Single nucleotide polymorphisms (SNPs) in the TUBB1 (β-tubulin) gene have been implicated as the primary cause of macro thrombocytopenia. Therefore it is essential to identify the potential SNPs which are harmful to cause diseases such as macro thrombocytopenia. The impact caused by these variants on β-tubulin is twofold, both structural and functional. Multiple in-silico tools were used to scrutinise the most deleterious nsSNPs (non-synonymous SNPs) via sequence and structure-based approaches. Further, the β-tubulin protein model incorporating identified mutants was subjected to MD (molecular dynamic) simulations to analyse the impact on protein structure. A total of 2974 SNPs of TUBB1 were retrieved from various sources, and 32 nsSNPs were identified. By screening through sequence-based technique, 13 variants were detected as deleterious and further structure-based filtration was carried out to find thermally destabilising variants. Finally, three variants have been detected as highly destabilising by the mCSM server and chosen for the MD study. All three variants are present in the N-terminal, Intermediate, and C-terminal regions, breaking the spatial arrangement required for microtubule assembly. The spatial arrangement of these variants is in deviation with respect to WT (wild type) β-tubulin. The protein model was subjected to a simulation period of 100 ns. The FEL analysis revealed multiple clusters with minor populations indicating the unstable conformation adapted by the β-tubulin. The normal mode vector analysis exhibited high-intensity flexible motions at the C-terminal end, responsible for binding with MAPs (microtubule-associated proteins), an essential region in microtubule assembly. All these results reveal that the SNP's predicted eventually influence the spatial arrangement of β-tubulin, which would disturb the stacking arrangement of αβ tubulin dimer in microtubule assembly. The present study may set a path to cure the diseases like macro thrombocytopenia.Communicated by Ramaswamy H. Sarma.
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8
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Flores-León CD, Dominguez L, Aguayo-Ortiz R. Molecular basis of Toxoplasma gondii oryzalin resistance from a novel α-tubulin binding site model. Arch Biochem Biophys 2022; 730:109398. [PMID: 36116504 DOI: 10.1016/j.abb.2022.109398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022]
Abstract
Oryzalin (ORY) is a dinitroaniline derivative that inhibits the microtubule polymerization in plants and parasitic protozoa by selectively binding to the α-tubulin subunit. This herbicidal agent exhibits good antiprotozoal activity against major human parasites, such as Toxoplasma gondii (toxoplasmosis), Leishmania mexicana (leishmaniasis), and Plasmodium falciparum (malaria). Previous chemical mutagenesis assays on T. gondii α-tubulin (TgAT) have identified key mutations that lead to ORY resistance. Herein, we employed alchemical free energy methods and molecular dynamics simulations to determine if the ORY resistance mutations either decrease the TgAT's affinity of the compound or increase the protein stability. Our results here suggest that L136F and V202F mutations significantly decrease the affinity of ORY to TgAT, while T239I and V252L mutations diminish TgAT's flexibility. On the other hand, protein stability predictors determined that R243S mutation reduces TgAT stability due to the loss of its salt bridge interaction with E27. Interestingly, molecular dynamics simulations confirm that the loss of this key interaction leads to ORY binding site closure. Our study provides a better insight into the TgAT-ORY interaction, further supporting our recently proposed ORY-binding site.
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Affiliation(s)
- Carlos D Flores-León
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Laura Dominguez
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Rodrigo Aguayo-Ortiz
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico.
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9
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Khabudaev KV, Petrova DP, Bedoshvili YD, Likhoshway YV, Grachev MA. Molecular Evolution of Tubulins in Diatoms. Int J Mol Sci 2022; 23:618. [PMID: 35054799 PMCID: PMC8776100 DOI: 10.3390/ijms23020618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 01/29/2023] Open
Abstract
Microtubules are formed by α- and β-tubulin heterodimers nucleated with γ-tubulin. Tubulins are conserved eukaryotic proteins. Previously, it was shown that microtubules are involved in diatom silica frustule morphogenesis. Diatom frustules are varied, and their morphology is species-specific. Despite the attractiveness of the problem of elucidating the molecular mechanisms of genetically programmed morphogenesis, the structure and evolution of diatom tubulins have not been studied previously. Based on available genomic and transcriptome data, we analyzed the phylogeny of the predicted amino acid sequences of diatom α-, β- and γ-tubulins and identified five groups for α-tubulins, six for β-tubulins and four for γ-tubulins. We identified characteristic amino acids of each of these groups and also analyzed possible posttranslational modification sites of diatom tubulins. According to our results, we assumed what changes occurred in the diatom tubulin structures during their evolution. We also identified which tubulin groups are inherent in large diatom taxa. The similarity between the evolution of diatom tubulins and the evolution of diatoms suggests that molecular changes in α-, β- and γ-tubulins could be one of the factors in the formation of a high morphological diversity of diatoms.
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Affiliation(s)
| | | | - Yekaterina D. Bedoshvili
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, 664033 Irkutsk, Russia; (K.V.K.); (D.P.P.); (Y.V.L.); (M.A.G.)
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10
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Molecular dynamics simulations and Gaussian network model for designing antibody mimicking protein towards dengue envelope protein. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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11
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Mechanisms of influence of the microtubule over-stabilizing ligands on the structure and intrinsic dynamics of α,β-Tubulin. Comput Biol Chem 2021; 96:107617. [PMID: 34942453 DOI: 10.1016/j.compbiolchem.2021.107617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/24/2021] [Accepted: 12/06/2021] [Indexed: 11/23/2022]
Abstract
The intervention into the cell cycle progression by administering microtubule over-stabilizing ligands that arrest the mitotic cell division by preventing spindle dissociation, is a promising strategy to fight against cancers. The building blocks of the microtubules and the spindles, i.e. the α,β-tubulin dimer, upon binding of such ligands, stay more comfortably in the microtubular multimeric form; the phenomenon of which is the key to the said over-stabilization. Using two such over-stabilizing ligands, Taxol and Taxotere, the present work reports the collective changes that these ligands induce on the structure and dynamics of the α,β-tubulin dimer which could be reconciled as the molecular basis of the over-stabilization of the microtubules; the trends have been found to be statistically significant across all independent calculations on them. The ligand binding increases the coherence between the residue communities of the two opposite faces of the β-subunit, which in a periodic arrangement in microtubule are knwon to form intermolecular contact with each other. This is likely to create an indirect cooperativity between those structural regions and this is a consequence of the reshuffling of the internal network of interactions upon ligand binding. Such reorganizations are also complemented by the increased contributions of the softer modes of the intrinsic dynamics more, which is likely to increase the plasticity of the system favourable for making structural adjustments in a multimer. Further, the ligands are able to compensate the drawback of lacking one phosphate group in protein-GDP interactions compared to the same for protein-GTP and this is in agreement with the hints form the earlier reports. The findings form a mechanistic basis of the enhanced capacity of the α,β-tubulin dimer to get more favourably accommodated into the microtubule superstructure upon binding either of Taxol and Taxotere.
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12
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Nasedkin A, Ermilova I, Swenson J. Atomistic molecular dynamics simulations of tubulin heterodimers explain the motion of a microtubule. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:927-940. [PMID: 34215900 PMCID: PMC8448678 DOI: 10.1007/s00249-021-01553-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/24/2021] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
Microtubules are essential parts of the cytoskeleton that are built by polymerization of tubulin heterodimers into a hollow tube. Regardless that their structures and functions have been comprehensively investigated in a modern soft matter, it is unclear how properties of tubulin heterodimer influence and promote the self-assembly. A detailed knowledge of such structural mechanisms would be helpful in drug design against neurodegenerative diseases, cancer, diabetes etc. In this work atomistic molecular dynamics simulations were used to investigate the fundamental dynamics of tubulin heterodimers in a sheet and a short microtubule utilizing well-equilibrated structures. The breathing motions of the tubulin heterodimers during assembly show that the movement at the lateral interface between heterodimers (wobbling) dominates in the lattice. The simulations of the protofilament curvature agrees well with recently published experimental data, showing curved protofilaments at polymerization of the microtubule plus end. The tubulin heterodimers exposed at the microtubule minus end were less curved and displayed altered interactions at the site of sheet closure around the outmost heterodimers, which may slow heterodimer binding and polymerization, providing a potential explanation for the limited dynamics observed at the minus end.
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Affiliation(s)
- Alexandr Nasedkin
- Department of Physics, Chalmers University of Technology, SE 41296 Göteborg, Sweden
| | - Inna Ermilova
- Department of Physics, Chalmers University of Technology, SE 41296 Göteborg, Sweden
| | - Jan Swenson
- Department of Physics, Chalmers University of Technology, SE 41296 Göteborg, Sweden
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13
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Lv D, Li J, Ye S. The Assembly Switch Mechanism of FtsZ Filament Revealed by All-Atom Molecular Dynamics Simulations and Coarse-Grained Models. Front Microbiol 2021; 12:639883. [PMID: 33859629 PMCID: PMC8042166 DOI: 10.3389/fmicb.2021.639883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/05/2021] [Indexed: 01/14/2023] Open
Abstract
Bacterial cytoskeletal protein FtsZ binds and hydrolyzes GTP, and assembles into dynamic filaments that are essential for cell division. Here, we used a multi-scale computational strategy that combined all-atom molecular dynamics (MD) simulations and coarse-grained models to reveal the conformational dynamics of assembled FtsZ. We found that the top end of a filament is highly dynamic and can undergo T-to-R transitions in both GTP- and GDP-bound states. We observed several subcategories of nucleation related dimer species, which leading to a feasible nucleation pathway. In addition, we observed that FtsZ filament exhibits noticeable amounts of twisting, indicating a substantial helicity of the FtsZ filament. These results agree with the previously models and experimental data. Anisotropy network model (ANM) analysis revealed a polymerization enhanced assembly cooperativity, and indicated that the cooperative motions in FtsZ are encoded in the structure. Taken together, our study provides a molecular-level understanding of the diversity of the structural states of FtsZ and the relationships among polymerization, hydrolysis, and cooperative assembly, which should shed new light on the molecular basis of FtsZ’s cooperativity.
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Affiliation(s)
- Dashuai Lv
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jingyuan Li
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Institute of Quantitative Biology, Hangzhou, China
| | - Sheng Ye
- Life Sciences Institute, Zhejiang University, Hangzhou, China.,Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
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14
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Jernigan RL, Sankar K, Jia K, Faraggi E, Kloczkowski A. Computational Ways to Enhance Protein Inhibitor Design. Front Mol Biosci 2021; 7:607323. [PMID: 33614705 PMCID: PMC7886686 DOI: 10.3389/fmolb.2020.607323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/08/2020] [Indexed: 11/22/2022] Open
Abstract
Two new computational approaches are described to aid in the design of new peptide-based drugs by evaluating ensembles of protein structures from their dynamics and through the assessing of structures using empirical contact potential. These approaches build on the concept that conformational variability can aid in the binding process and, for disordered proteins, can even facilitate the binding of more diverse ligands. This latter consideration indicates that such a design process should be less restrictive so that multiple inhibitors might be effective. The example chosen here focuses on proteins/peptides that bind to hemagglutinin (HA) to block the large-scale conformational change for activation. Variability in the conformations is considered from sets of experimental structures, or as an alternative, from their simple computed dynamics; the set of designe peptides/small proteins from the David Baker lab designed to bind to hemagglutinin, is the large set considered and is assessed with the new empirical contact potentials.
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Affiliation(s)
- Robert L. Jernigan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Kannan Sankar
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Kejue Jia
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Eshel Faraggi
- Research and Information Systems, LLC, Indianapolis, IN, United States
- Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, IN, United States
| | - Andrzej Kloczkowski
- Battelle Center for Mathematical Medicine, Nationwide Children's Hospital, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University, Columbus, OH, United States
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15
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González-Durruthy M, Rial R, Cordeiro MND, Liu Z, Ruso JM. Exploring the conformational binding mechanism of fibrinogen induced by interactions with penicillin β-lactam antibiotic drugs. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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16
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Neto RDAM, Santos CBR, Henriques SVC, Machado LDO, Cruz JN, da Silva CHTDP, Federico LB, Oliveira EHCD, de Souza MPC, da Silva PNB, Taft CA, Ferreira IM, Gomes MRF. Novel chalcones derivatives with potential antineoplastic activity investigated by docking and molecular dynamics simulations. J Biomol Struct Dyn 2020; 40:2204-2216. [DOI: 10.1080/07391102.2020.1839562] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Raimundo de A. M. Neto
- Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Macapá, Brasil
| | - Cleydson B. R. Santos
- Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Macapá, Brasil
| | | | - Letícia de O. Machado
- Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Macapá, Brasil
| | - Jorddy N. Cruz
- Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Macapá, Brasil
| | | | - Leonardo B. Federico
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brasil
| | | | | | | | - Carlton A. Taft
- Centro Brasileiro de Pesquisas Físicas, Urca, Rio de Janeiro, Brasil
| | | | - Madson R. F. Gomes
- Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Macapá, Brasil
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17
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Sharma A, Talimarada D, Yadav UP, Singh N, Reddy AS, Bag D, Biswas K, Baidya A, Borale AN, Shinde D, Singh S, Holla H. Design and Synthesis of New Tubulin Polymerization Inhibitors Inspired from Combretastatin A‐4: An Anticancer Agent. ChemistrySelect 2020. [DOI: 10.1002/slct.202003170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Akanksha Sharma
- Department of Chemistry Central University of Karnataka Kalaburagi 585367 India
| | | | - Umesh Prasad Yadav
- Department of Human Genetics and Molecular Medicine Central University of Punjab Bathinda 151001 India
| | - Nidhi Singh
- Centre for Chemical and Pharmaceutical Sciences Central University of Punjab Bathinda 151001 India
| | - A. Sudharshan Reddy
- Department of Chemistry Central University of Karnataka Kalaburagi 585367 India
| | - Debojyoti Bag
- Department of Chemistry Central University of Karnataka Kalaburagi 585367 India
| | - Krishna Biswas
- Department of Chemistry Central University of Karnataka Kalaburagi 585367 India
| | - Amit Baidya
- Department of Chemistry Central University of Karnataka Kalaburagi 585367 India
| | - Asha N Borale
- Department of Chemistry Central University of Karnataka Kalaburagi 585367 India
| | | | - Sandeep Singh
- Department of Human Genetics and Molecular Medicine Central University of Punjab Bathinda 151001 India
| | - Harish Holla
- Department of Chemistry Central University of Karnataka Kalaburagi 585367 India
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18
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de Oliveira PV, Goulart L, Dos Santos CL, Rossato J, Fagan SB, Zanella I, Cordeiro MNDS, Ruso JM, González-Durruthy M. Computational Modeling of Environmental Co-exposure on Oil-Derived Hydrocarbon Overload by Using Substrate-Specific Transport Protein (TodX) with Graphene Nanostructures. Curr Top Med Chem 2020; 20:2308-2325. [PMID: 32819247 DOI: 10.2174/1568026620666200820145412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 12/07/2022]
Abstract
BACKGROUND Bioremediation is a biotechnology field that uses living organisms to remove contaminants from soil and water; therefore, they could be used to treat oil spills from the environment. METHODS Herein, we present a new mechanistic approach combining Molecular Docking Simulation and Density Functional Theory to modeling the bioremediation-based nanointeractions of a heterogeneous mixture of oil-derived hydrocarbons by using pristine and oxidized graphene nanostructures and the substrate-specific transport protein (TodX) from Pseudomonas putida. RESULTS The theoretical evidences pointing that the binding interactions are mainly based on noncovalent bonds characteristic of physical adsorption mechanism mimicking the "Trojan-horse effect". CONCLUSION These results open new horizons to improve bioremediation strategies in over-saturation conditions against oil-spills and expanding the use of nanotechnologies in the context of environmental modeling health and safety.
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Affiliation(s)
| | - Luiza Goulart
- Nanoscience Department, Universidade Franciscana, 97010-032 Rio Grande do Sul-RS, Brazil
| | | | - Jussane Rossato
- Nanoscience Department, Universidade Franciscana, 97010-032 Rio Grande do Sul-RS, Brazil
| | - Solange Binotto Fagan
- Nanoscience Department, Universidade Franciscana, 97010-032 Rio Grande do Sul-RS, Brazil
| | - Ivana Zanella
- Nanoscience Department, Universidade Franciscana, 97010-032 Rio Grande do Sul-RS, Brazil
| | - M Natália D S Cordeiro
- LAQV-REQUINTE of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169- 007 Porto, Portugal
| | - Juan M Ruso
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Michael González-Durruthy
- LAQV-REQUINTE of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169- 007 Porto, Portugal,Soft Matter and Molecular Biophysics Group, Department of Applied Physics, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
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19
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Mapping the underlying mechanisms of fibrinogen benzothiazole drug interactions using computational and experimental approaches. Int J Biol Macromol 2020; 163:730-744. [PMID: 32653381 DOI: 10.1016/j.ijbiomac.2020.07.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/16/2020] [Accepted: 07/06/2020] [Indexed: 11/22/2022]
Abstract
Three-dimensional conformational crystallographic binding-modes are of paramount importance to understand the docking mechanism of protein-ligand interactions and to identify potential "leading drugs" conformers towards rational drugs-design. Herein, we present an integrated computational-experimental study tackling the problem of multiple binding modes among the ligand 3-(2-Benzothiazolylthio)-propane sulfonic acid (BTS) and the fibrinogen receptor (E-region). Based on molecular docking simulations, we found that the free energy of binding values for nine of different BTS-docking complexes (i.e., BTS-pose_1-9) were very close. We have also identified a docking-mechanism of BTS-interaction mainly based on non-covalent hydrophobic interactions with H-bond contacts stabilizing the fibrinogen-BTS docking complexes. Interestingly, the different BTS-poses_1-9 were found to be able to block the fibrinogen binding site (E-region) by inducing local perturbations in effector and allosteric residues, reducing the degree of collectivity in its flexibility normal modes. As such, we theoretically suggest that the BTS-binding modes can significantly affect the physiological condition of the unoccupied fibrinogen protein structure by bringing global and local perturbations in the frequency domain spectra. The proposed theoretical mechanisms, the interactions involved and the conformational changes suggested, were further corroborated by different experimental techniques such as isothermal titration calorimetry (ITC), zeta potential, UV-vis, fluorescence and small angle X-ray scattering (SAXS). The combined results shall open new avenues towards the application of complex supra-molecular information in rational drugs-design.
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20
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Gaetani R, Zizzi EA, Deriu MA, Morbiducci U, Pesce M, Messina E. When Stiffness Matters: Mechanosensing in Heart Development and Disease. Front Cell Dev Biol 2020; 8:334. [PMID: 32671058 PMCID: PMC7326078 DOI: 10.3389/fcell.2020.00334] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/16/2020] [Indexed: 12/20/2022] Open
Abstract
During embryonic morphogenesis, the heart undergoes a complex series of cellular phenotypic maturations (e.g., transition of myocytes from proliferative to quiescent or maturation of the contractile apparatus), and this involves stiffening of the extracellular matrix (ECM) acting in concert with morphogenetic signals. The maladaptive remodeling of the myocardium, one of the processes involved in determination of heart failure, also involves mechanical cues, with a progressive stiffening of the tissue that produces cellular mechanical damage, inflammation, and ultimately myocardial fibrosis. The assessment of the biomechanical dependence of the molecular machinery (in myocardial and non-myocardial cells) is therefore essential to contextualize the maturation of the cardiac tissue at early stages and understand its pathologic evolution in aging. Because systems to perform multiscale modeling of cellular and tissue mechanics have been developed, it appears particularly novel to design integrated mechano-molecular models of heart development and disease to be tested in ex vivo reconstituted cells/tissue-mimicking conditions. In the present contribution, we will discuss the latest implication of mechanosensing in heart development and pathology, describe the most recent models of cell/tissue mechanics, and delineate novel strategies to target the consequences of heart failure with personalized approaches based on tissue engineering and induced pluripotent stem cell (iPSC) technologies.
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Affiliation(s)
- Roberto Gaetani
- Department of Molecular Medicine, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome, Italy.,Department of Bioengineering, Sanford Consortium for Regenerative Medicine, University of California, San Diego, San Diego, CA, United States
| | - Eric Adriano Zizzi
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Marco Agostino Deriu
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Umberto Morbiducci
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Maurizio Pesce
- Tissue Engineering Research Unit, "Centro Cardiologico Monzino," IRCCS, Milan, Italy
| | - Elisa Messina
- Department of Maternal, Infantile, and Urological Sciences, "Umberto I" Hospital, Sapienza University of Rome, Rome, Italy
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21
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Fedorov VA, Orekhov PS, Kholina EG, Zhmurov AA, Ataullakhanov FI, Kovalenko IB, Gudimchuk NB. Mechanical properties of tubulin intra- and inter-dimer interfaces and their implications for microtubule dynamic instability. PLoS Comput Biol 2019; 15:e1007327. [PMID: 31469822 PMCID: PMC6742422 DOI: 10.1371/journal.pcbi.1007327] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 09/12/2019] [Accepted: 08/08/2019] [Indexed: 11/18/2022] Open
Abstract
Thirteen tubulin protofilaments, made of αβ-tubulin heterodimers, interact laterally to produce cytoskeletal microtubules. Microtubules exhibit the striking property of dynamic instability, manifested in their intermittent growth and shrinkage at both ends. This behavior is key to many cellular processes, such as cell division, migration, maintenance of cell shape, etc. Although assembly and disassembly of microtubules is known to be linked to hydrolysis of a guanosine triphosphate molecule in the pocket of β-tubulin, detailed mechanistic understanding of corresponding conformational changes is still lacking. Here we take advantage of the recent generation of in-microtubule structures of tubulin to examine the properties of protofilaments, which serve as important microtubule assembly and disassembly intermediates. We find that initially straight tubulin protofilaments, relax to similar non-radially curved and slightly twisted conformations. Our analysis further suggests that guanosine triphosphate hydrolysis primarily affects the flexibility and conformation of the inter-dimer interface, without a strong impact on the shape or flexibility of αβ-heterodimer. Inter-dimer interfaces are significantly more flexible compared to intra-dimer interfaces. We argue that such a difference in flexibility could be key for distinct stability of the plus and minus microtubule ends. The higher flexibility of the inter-dimer interface may have implications for development of pulling force by curving tubulin protofilaments during microtubule disassembly, a process of major importance for chromosome motions in mitosis.
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Affiliation(s)
| | - Philipp S. Orekhov
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Sechenov University, Moscow, Russia
| | | | - Artem A. Zhmurov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Sechenov University, Moscow, Russia
| | - Fazoil I. Ataullakhanov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya B. Kovalenko
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
- Sechenov University, Moscow, Russia
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, Federal Medical and Biological Agency of Russia, Moscow, Russia
- Astrakhan State University, Astrakhan, Russia
- Peoples’ Friendship University of Russia (RUDN University), Moscow, Russia
| | - Nikita B. Gudimchuk
- Department of Physics, Lomonosov Moscow State University, Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, Russia
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22
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González-Durruthy M, Scanavachi G, Rial R, Liu Z, Cordeiro MNDS, Itri R, Ruso JM. Structural and energetic evolution of fibrinogen toward to the betablocker interactions. Int J Biol Macromol 2019; 137:405-419. [PMID: 31265849 DOI: 10.1016/j.ijbiomac.2019.06.229] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/10/2019] [Accepted: 06/28/2019] [Indexed: 11/29/2022]
Abstract
We present a computational analysis coupled with experimental studies, focusing on the binding-interaction between beta-adrenoreceptor blocking agents (acebutolol and propranolol) with fibrinogen protein (E-region). Herein, computational modeling on structural validation and flexibility properties of fibrinogen E-region showed that the E-region interacting residues, which form the funnel-shaped hydrophobic cavity for ligand-binding, can be efficiently modeled. The obtained free energy of binding (FEB) values for the docking complexes, namely acebutolol/fibrinogen E-region and propranolol/fibrinogen E-region, were very close and amounted to - 6.9 kcal/mol and - 6.8 kcal/mol, respectively. They were supported by a high binding-accuracy (R.M.S.D < 2 Å) for the best crystallographic binding-poses in both cases. In this regard, we identify a docking-mechanism of interaction for the propranolol and acebutolol mainly based on non-covalent hydrophobic contacts with the fibrinogen E-region binding-site. Besides, the beta-adrenoreceptor blocking agents are able to induce local perturbations affecting particularly the fibrinogen E-region allosteric residues linked to significant changes in the inter-residue communication and flexibility properties of residue network. In this sense, we show that the key biophysical parameters like frequency and collectivity degree may be compromised in different ways by the interaction with acebutolol and propranolol. Isothermal titration calorimetry, zeta potential and small angle X-ray scattering (SAXS) measurements were performed to complete and corroborate computational analysis. The combined experimental results point out that acebutolol acts to a lesser extent to fibrinogen structure than propranolol.
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Affiliation(s)
- Michael González-Durruthy
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; LAQV-REQUIMTE of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Gustavo Scanavachi
- Department of Applied Physics, Institute of Physics, University of São Paulo, SP, Brazil
| | - Ramón Rial
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Zhen Liu
- Department of Physics and Engineering, Frostburg State University, Frostburg, MD 21532, United States
| | - M Natália D S Cordeiro
- LAQV-REQUIMTE of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Rosangela Itri
- Department of Applied Physics, Institute of Physics, University of São Paulo, SP, Brazil
| | - Juan M Ruso
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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23
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Kumbhar BV, Bhandare VV, Panda D, Kunwar A. Delineating the interaction of combretastatin A-4 with αβ tubulin isotypes present in drug resistant human lung carcinoma using a molecular modeling approach. J Biomol Struct Dyn 2019; 38:426-438. [DOI: 10.1080/07391102.2019.1577174] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Bajarang Vasant Kumbhar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Vishwambhar Vishnu Bhandare
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Dulal Panda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Ambarish Kunwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
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24
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Loop dynamics behind the affinity of DARPins towards ERK2: Molecular dynamics simulations (MDs) and elastic network model (ENM). J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.10.157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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25
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Timmons JJ, Preto J, Tuszynski JA, Wong ET. Tubulin's response to external electric fields by molecular dynamics simulations. PLoS One 2018; 13:e0202141. [PMID: 30231050 PMCID: PMC6145594 DOI: 10.1371/journal.pone.0202141] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/27/2018] [Indexed: 02/03/2023] Open
Abstract
Tubulin heterodimers are the building blocks of microtubules and disruption of their dynamics is exploited in the treatment of cancer. Electric fields at certain frequencies and magnitudes are believed to do the same. Here, the tubulin dimer’s response to external electric fields was determined by atomistic simulation. External fields from 50 to 750 kV/cm, applied for 10 ns, caused significant conformational rearrangements that were dependent upon the field’s directionality. Charged and flexible regions, including the α:H1-B2 loop, β:M-loop, and C-termini, were susceptible. Closer inspection of the α:H1-B2 loop in lower strength fields revealed that these effects were consistent and proportional to field strength, and the findings indicate that external electric fields modulate the stability of microtubules through conformational changes to key loops involved in lateral contacts. We also find evidence that tubulin’s curvature and elongation are affected, and external electric fields may bias tubulin towards depolymerization.
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Affiliation(s)
- Joshua J. Timmons
- Brain Tumor Center & Neuro-Oncology Unit, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jordane Preto
- Department of Physics, University of Alberta, Edmonton, Canada
| | - Jack A. Tuszynski
- Department of Physics, University of Alberta, Edmonton, Canada
- Department of Oncology, University of Alberta, Edmonton, Canada
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi, Torino, Italy
| | - Eric T. Wong
- Brain Tumor Center & Neuro-Oncology Unit, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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26
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Ben Imeddourene A, Esque J, André I. Combining multi-scale modelling methods to decipher molecular motions of a branching sucrase from glycoside-hydrolase family 70. PLoS One 2018; 13:e0201323. [PMID: 30067837 PMCID: PMC6070258 DOI: 10.1371/journal.pone.0201323] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/12/2018] [Indexed: 01/23/2023] Open
Abstract
Among α-transglucosylases from Glycoside-Hydrolase family 70, the ΔN123-GB-CD2 enzyme derived from the bifunctional DSR-E from L. citreum NRRL B-1299 is particularly interesting as it was the first described engineered Branching Sucrase, not able to elongate glucan polymers from sucrose substrate. The previously reported overall structural organization of this multi-domain enzyme is an intricate U-shape fold conserved among GH70 enzymes which showed a certain conformational variability of the so-called domain V, assumed to play a role in the control of product structures, in available X-ray structures. Understanding the role of functional dynamics on enzyme reaction and substrate recognition is of utmost interest although it remains a challenge for biophysical methods. By combining long molecular dynamics simulation (1μs) and multiple analyses (NMA, PCA, Morelet Continuous Wavelet Transform and Cross Correlations Dynamics), we investigated here the dynamics of ΔN123-GB-CD2 alone and in interaction with sucrose substrate. Overall, our results provide the detailed picture at atomic level of the hierarchy of motions occurring along different timescales and how they are correlated, in agreement with experimental structural data. In particular, detailed analysis of the different structural domains revealed cooperative dynamic behaviors such as twisting, bending and wobbling through anti- and correlated motions, and also two structural hinge regions, of which one was unreported. Several highly flexible loops surrounding the catalytic pocket were also highlighted, suggesting a potential role in the acceptor promiscuity of ΔN123-GBD-CD2. Normal modes and essential dynamics underlined an interesting two-fold dynamic of the catalytic domain A, pivoting about an axis splitting the catalytic gorge in two parts. The comparison of the conformational free energy landscapes using principal component analysis of the enzyme in absence or in presence of sucrose, also revealed a more harmonic basin when sucrose is bound with a shift population of the bending mode, consistent with the substrate binding event.
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Affiliation(s)
- Akli Ben Imeddourene
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Jérémy Esque
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Isabelle André
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- * E-mail:
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27
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Manandhar A, Kang M, Chakraborty K, Loverde SM. Effect of Nucleotide State on the Protofilament Conformation of Tubulin Octamers. J Phys Chem B 2018; 122:6164-6178. [PMID: 29768004 DOI: 10.1021/acs.jpcb.8b02193] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
At the molecular level, the dynamic instability (random growth and shrinkage) of the microtubule (MT) is driven by the nucleotide state (GTP vs GDP) in the β subunit of the tubulin dimers at the MT cap. Here, we use large-scale molecular dynamics (MD) simulations and normal-mode analysis (NMA) to characterize the effect of a single GTP cap layer on tubulin octamers composed of two neighboring protofilaments (PFs). We utilize recently reported high-resolution structures of dynamic MTs to simulate a GDP octamer both with and without a single GTP cap layer. We perform multiple replicas of long-time atomistic MD simulations (3 replicas, 0.3 μs for each replica, 0.9 μs for each octamer system, and 1.8 μs total) of both octamers. We observe that a single GTP cap layer induces structural differences in neighboring PFs, finding that one PF possesses a gradual curvature, compared to the second PF which possesses a kinked conformation. This results in either curling or splaying between these PFs. We suggest that this is due to asymmetric strengths of longitudinal contacts between the two PFs. Furthermore, using NMA, we calculate mechanical properties of these octamer systems and find that octamer system with a single GTP cap layer possesses a lower flexural rigidity.
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Affiliation(s)
- Anjela Manandhar
- Department of Chemistry, College of Staten Island , City University of New York , 2800 Victory Boulevard , Staten Island , New York 10314 , United States.,Ph.D. Program in Biochemistry , The Graduate Center of the City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Myungshim Kang
- Department of Chemistry, College of Staten Island , City University of New York , 2800 Victory Boulevard , Staten Island , New York 10314 , United States
| | - Kaushik Chakraborty
- Department of Chemistry, College of Staten Island , City University of New York , 2800 Victory Boulevard , Staten Island , New York 10314 , United States
| | - Sharon M Loverde
- Department of Chemistry, College of Staten Island , City University of New York , 2800 Victory Boulevard , Staten Island , New York 10314 , United States.,Ph.D. Program in Biochemistry , The Graduate Center of the City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
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28
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Insight into microtubule destabilization mechanism of 3,4,5-trimethoxyphenyl indanone derivatives using molecular dynamics simulation and conformational modes analysis. J Comput Aided Mol Des 2018. [DOI: 10.1007/s10822-018-0109-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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29
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Huzil JT, Chen K, Kurgan L, Tuszynski JA. The Roles of β-Tubulin Mutations and Isotype Expression in Acquired Drug Resistance. Cancer Inform 2017. [DOI: 10.1177/117693510700300028] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The antitumor drug paclitaxel stabilizes microtubules and reduces their dynamicity, promoting mitotic arrest and eventually apoptosis. Upon assembly of the α/β-tubulin heterodimer, GTP becomes bound to both the α and β-tubulin monomers. During microtubule assembly, the GTP bound to β-tubulin is hydrolyzed to GDP, eventually reaching steady-state equilibrium between free tubulin dimers and those polymerized into microtubules. Tubulin-binding drugs such as paclitaxel interact with β-tubulin, resulting in the disruption of this equilibrium. In spite of several crystal structures of tubulin, there is little biochemical insight into the mechanism by which anti-tubulin drugs target microtubules and alter their normal behavior. The mechanism of drug action is further complicated, as the description of altered β-tubulin isotype expression and/or mutations in tubulin genes may lead to drug resistance as has been described in the literature. Because of the relationship between β-tubulin isotype expression and mutations within β-tubulin, both leading to resistance, we examined the properties of altered residues within the taxane, colchicine and Vinca binding sites. The amount of data now available, allows us to investigate common patterns that lead to microtubule disruption and may provide a guide to the rational design of novel compounds that can inhibit microtubule dynamics for specific tubulin isotypes or, indeed resistant cell lines. Because of the vast amount of data published to date, we will only provide a broad overview of the mutational results and how these correlate with differences between tubulin isotypes. We also note that clinical studies describe a number of predictive factors for the response to anti-tubulin drugs and attempt to develop an understanding of the features within tubulin that may help explain how they may affect both microtubule assembly and stability.
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Affiliation(s)
- J. Torin Huzil
- Department of Oncology, University of Alberta, Edmonton, Alberta
| | - Ke Chen
- Department of Computer and Electrical Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Lukasz Kurgan
- Department of Computer and Electrical Engineering, University of Alberta, Edmonton, Alberta, Canada
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Deformation pattern in vibrating microtubule: Structural mechanics study based on an atomistic approach. Sci Rep 2017; 7:4227. [PMID: 28652626 PMCID: PMC5484714 DOI: 10.1038/s41598-017-04272-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 05/12/2017] [Indexed: 12/27/2022] Open
Abstract
The mechanical properties of microtubules are of great importance for understanding their biological function and for applications in artificial devices. Although microtubule mechanics has been extensively studied both theoretically and experimentally, the relation to its molecular structure is understood only partially. Here, we report on the structural analysis of microtubule vibration modes calculated by an atomistic approach. Molecular dynamics was applied to refine the atomic structure of a microtubule and a Cα elastic network model was analyzed for its normal modes. We mapped fluctuations and local deformations up to the level of individual aminoacid residues. The deformation is mode-shape dependent and principally different in α-tubulins and β-tubulins. Parts of the tubulin dimer sequence responding specifically to longitudinal and radial stress are identified. We show that substantial strain within a microtubule is located both in the regions of contact between adjacent dimers and in the body of tubulins. Our results provide supportive evidence for the generally accepted assumption that the mechanics of microtubules, including its anisotropy, is determined by the bonds between tubulins.
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31
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Ozgur B, Ozdemir ES, Gursoy A, Keskin O. Relation between Protein Intrinsic Normal Mode Weights and Pre-Existing Conformer Populations. J Phys Chem B 2017; 121:3686-3700. [DOI: 10.1021/acs.jpcb.6b10401] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Beytullah Ozgur
- Center for Computational Biology and Bioinformatics, ‡Chemical and Biological
Engineering, and §Computer Engineering,
College of Engineering, Koc University, 34450 Istanbul, Turkey
| | - E. Sila Ozdemir
- Center for Computational Biology and Bioinformatics, ‡Chemical and Biological
Engineering, and §Computer Engineering,
College of Engineering, Koc University, 34450 Istanbul, Turkey
| | - Attila Gursoy
- Center for Computational Biology and Bioinformatics, ‡Chemical and Biological
Engineering, and §Computer Engineering,
College of Engineering, Koc University, 34450 Istanbul, Turkey
| | - Ozlem Keskin
- Center for Computational Biology and Bioinformatics, ‡Chemical and Biological
Engineering, and §Computer Engineering,
College of Engineering, Koc University, 34450 Istanbul, Turkey
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32
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Molecular modeling and molecular dynamic simulation of the effects of variants in the TGFBR2 kinase domain as a paradigm for interpretation of variants obtained by next generation sequencing. PLoS One 2017; 12:e0170822. [PMID: 28182693 PMCID: PMC5300139 DOI: 10.1371/journal.pone.0170822] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/11/2017] [Indexed: 01/01/2023] Open
Abstract
Variants in the TGFBR2 kinase domain cause several human diseases and can increase propensity for cancer. The widespread application of next generation sequencing within the setting of Individualized Medicine (IM) is increasing the rate at which TGFBR2 kinase domain variants are being identified. However, their clinical relevance is often uncertain. Consequently, we sought to evaluate the use of molecular modeling and molecular dynamics (MD) simulations for assessing the potential impact of variants within this domain. We documented the structural differences revealed by these models across 57 variants using independent MD simulations for each. Our simulations revealed various mechanisms by which variants may lead to functional alteration; some are revealed energetically, while others structurally or dynamically. We found that the ATP binding site and activation loop dynamics may be affected by variants at positions throughout the structure. This prediction cannot be made from the linear sequence alone. We present our structure-based analyses alongside those obtained using several commonly used genomics-based predictive algorithms. We believe the further mechanistic information revealed by molecular modeling will be useful in guiding the examination of clinically observed variants throughout the exome, as well as those likely to be discovered in the near future by clinical tests leveraging next-generation sequencing through IM efforts.
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33
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Majumdar S, Ghosh Dastidar S. Ligand Binding Swaps between Soft Internal Modes of α,β-Tubulin and Alters Its Accessible Conformational Space. J Phys Chem B 2016; 121:118-128. [DOI: 10.1021/acs.jpcb.6b11322] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sarmistha Majumdar
- Bioinformatics Centre, Bose Institute, P-1/12 C.I.T. Scheme VII M, Kolkata 700054, India
| | - Shubhra Ghosh Dastidar
- Bioinformatics Centre, Bose Institute, P-1/12 C.I.T. Scheme VII M, Kolkata 700054, India
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34
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Bending-Twisting Motions and Main Interactions in Nucleoplasmin Nuclear Import. PLoS One 2016; 11:e0157162. [PMID: 27258022 PMCID: PMC4892583 DOI: 10.1371/journal.pone.0157162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 05/25/2016] [Indexed: 01/11/2023] Open
Abstract
Alpha solenoid proteins play a key role in regulating the classical nuclear import pathway, recognizing a target protein and transporting it into the nucleus. Importin-α (Impα) is the solenoid responsible for cargo protein recognition, and it has been extensively studied by X-ray crystallography to understand the binding specificity. To comprehend the main motions of Impα and to extend the information about the critical interactions during carrier-cargo recognition, we surveyed different conformational states based on molecular dynamics (MD) and normal mode (NM) analyses. Our model of study was a crystallographic structure of Impα complexed with the classical nuclear localization sequence (cNLS) from nucleoplasmin (Npl), which was submitted to multiple 100 ns of MD simulations. Representative conformations were selected for calculating the 87 lowest frequencies NMs of vibration, and a displacement approach was applied along each NM. Based on geometric criteria, using the radius of curvature and inter-repeat angles as the reference metrics, the main motions of Impα were described. Moreover, we determined the salt bridges, hydrogen bonds and hydrophobic interactions in the Impα-NplNLS interface. Our results show the bending and twisting motions participating in the recognition of nuclear proteins, allowing the accommodation and adjustment of a classical bipartite NLS sequence. The essential contacts for the nuclear import were also described and were mostly in agreement with previous studies, suggesting that the residues in the cNLS linker region establish important contacts with Impα adjusting the cNLS backbone. The MD simulations combined with NM analysis can be applied to the Impα-NLS system to help understand interactions between Impα and cNLSs and the analysis of non-classic NLSs.
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35
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Natarajan K, Mohan J, Senapati S. Relating nucleotide-dependent conformational changes in free tubulin dimers to tubulin assembly. Biopolymers 2016; 99:282-91. [PMID: 23426572 DOI: 10.1002/bip.22153] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 08/29/2012] [Indexed: 11/07/2022]
Abstract
The complex dynamic behavior of microtubules (MTs) is believed to be primarily due to the αβ-tubulin dimer architecture and its intrinsic GTPase activity. Hence, a detailed knowledge of the conformational variations of isolated α-GTP-β-GTP- and α-GTP-β-GDP-tubulin dimers in solution and their implications to interdimer interactions and stability is directly relevant to understand the MT dynamics. An attempt has been made here by combining molecular dynamics (MD) simulations and protein-protein docking studies that unravels key structural features of tubulin dimer in different nucleotide states and correlates their association to tubulin assembly. Results from simulations suggest that tubulin dimers and oligomers attain curved conformations in both GTP and GDP states. Results also indicate that the tubulin C-terminal domain and the nucleotide state are closely linked. Protein-protein docking in combination with MD simulations suggest that the GTP-tubulin dimers engage in relatively stronger interdimer interactions even though the interdimer interfaces are bent in both GTP and GDP tubulin complexes, providing valuable insights on in vitro finding that GTP-tubulin is a better assembly candidate than GDP-tubulin during the MT nucleation and elongation processes.
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Affiliation(s)
- Kathiresan Natarajan
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
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36
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Hamacher K, McCammon JA. Computing the Amino Acid Specificity of Fluctuations in Biomolecular Systems. J Chem Theory Comput 2015; 2:873-8. [PMID: 26626694 DOI: 10.1021/ct050247s] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We developed a new amino acid specific method for the computation of spatial fluctuations of proteins around their native structures. We show the consistency with experimental values and the increased performance in comparison to an established model, based on statistical estimates for a set of test proteins. We apply the new method to HIV-1 protease in its wild-type form and to a V82F-I84V mutant that shows resistance to protease inhibitors. We further show how the method can be successfully used to explain the molecular biophysics of drug resistance of the mutant.
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Affiliation(s)
- K Hamacher
- Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, Department of Pharmacology, and Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California 92093-0365
| | - J A McCammon
- Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, Department of Pharmacology, and Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California 92093-0365
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37
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Tripathi S, Kumar A, Kumar BS, Negi AS, Sharma A. Structural investigations into the binding mode of novel neolignans Cmp10 and Cmp19 microtubule stabilizers byin silicomolecular docking, molecular dynamics, and binding free energy calculations. J Biomol Struct Dyn 2015. [DOI: 10.1080/07391102.2015.1074941] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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38
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Churchill CDM, Klobukowski M, Tuszynski JA. Elucidating the mechanism of action of the clinically approved taxanes: a comprehensive comparison of local and allosteric effects. Chem Biol Drug Des 2015; 86:1253-66. [PMID: 26032329 DOI: 10.1111/cbdd.12595] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/29/2015] [Accepted: 05/14/2015] [Indexed: 12/26/2022]
Abstract
The clinically approved taxanes (paclitaxel, docetaxel and cabazitaxel) target the tubulin protein in microtubules. Despite the clinical success of these agents, the mechanism of action of this class of drugs remains elusive, making rational design of taxanes difficult. Molecular dynamics simulations of these three taxanes with the αβ-tubulin heterodimer examine the similarities and differences in the effects of the drugs on tubulin, probing both local and allosteric effects. Despite their structural similarity, the drugs adopt different conformations in the binding site on β-tubulin. The taxanes similarly increase the helical character of α- and β-tubulins. No correlations are found between microtubule assembly and (i) binding affinity or (ii) the role of the M-loop in enhancing lateral contacts. Instead, changes in intra- and interdimer longitudinal contacts are indicative of the mechanism of action of the taxanes. We find β:H1-S1', and more importantly β:H9 and β:H10, play a role translating the effect of local drug binding in β-tubulin to an allosteric effect in α-tubulin and propose that the displacement of these secondary structures towards α-tubulin may be used as a predictor of the effect of taxanes on the tubulin heterodimers in rational drug design approaches.
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Affiliation(s)
- Cassandra D M Churchill
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, T6G 2G2, Canada
| | - Mariusz Klobukowski
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, T6G 2G2, Canada
| | - Jack A Tuszynski
- Department of Oncology, University of Alberta, Cross Cancer Institute 11560 University Avenue, Edmonton, AB, T6G 1Z2, Canada.,Department of Physics, University of Alberta, 4-181 CCIS, Edmonton, AB, T6G 2E1, Canada
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39
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Wieninger SA, Ullmann GM. CoMoDo: Identifying Dynamic Protein Domains Based on Covariances of Motion. J Chem Theory Comput 2015; 11:2841-54. [DOI: 10.1021/acs.jctc.5b00150] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Silke A. Wieninger
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstrasse 30, BGI, 95447 Bayreuth, Germany
| | - G. Matthias Ullmann
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstrasse 30, BGI, 95447 Bayreuth, Germany
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40
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Selvaa Kumar C, Gadewal N, Mohammed SM. Seminal role of deletion of amino acid residues in H1-S2 and S-loop regions in eukaryotic β-tubulin investigated from docking and dynamics perspective. J Theor Biol 2015; 378:79-88. [PMID: 25956360 DOI: 10.1016/j.jtbi.2015.04.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 04/20/2015] [Accepted: 04/24/2015] [Indexed: 11/16/2022]
Abstract
Tubulin is the fundamental unit of microtubules. It is reported to effect different functions like cell division, chromosomal segregation, motility and intracellular transportation. α- and β-tubulin associate laterally and longitudinally to form protofilaments. Both the subunits are structurally identical to each other except for the deletions reported in H1-S2 and S loop regions in eukaryotic β-tubulin. These deletions mimic the ancestral tubulin protein named Latest Common FtsZ-Tubulin Ancestor (LCFTA) with a shorter S-loop region resulting in weak dimerization. However, in eukaryotic beta tubulin, the significance of this shorter region remains elusive till date. The main objective of this study was to model variants of beta tubulin (βmut1, βmut2 and βmut3) with inserts that lengthened the loop, and to compare them with the native α- and β-subunits to understand their biological significance. Further, one more mutant was modeled with the intention of understanding the counter effect of additional deletion of amino acid residues from both H1-S2 and S-loop regions; this mutant was designated as βmut4. Our study confirms that the insertion of amino acid residues considerably increases the protein-protein interactions in βmut1-βmut1, βmut2-βmut2 and βmut3-βmut3 compared to their native β-subunit. Similarly, the binding affinity of GTP also increases in βmut2 and βmut3 as compared to the wild type. However, these deletions result in decreased protein-protein and ligand interactions in wild beta tubulin and βmut4, as compared to βmut1, βmut2,and βmut3. Therefore, we conclude here that residual inserts in the H1-S2 and S loop sub segments bring about conformational changes in regions critically involved in lateral interactions and in the nucleotide binding site, thus altering the binding affinities between the dimers and the ligands. Regarding the biological importance of such deletions in wild beta tubulin, these deletions result in flexible M-loop leading to weak protein-protein interaction. This could be an adaptive feature playing a crucial role in protofilament dissociation during GTP hydrolysis, because of weak dimerization.
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Affiliation(s)
- C Selvaa Kumar
- School of Biotechnology and Bioinformatics, D.Y. Patil University, CBD Belapur, Navi Mumbai, India.
| | - Nikhil Gadewal
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, India.
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41
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Li Z, Alisaraie L. Microtubules dual chemo and thermo-responsive depolymerization. Proteins 2015; 83:970-81. [PMID: 25739855 DOI: 10.1002/prot.24793] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 02/14/2015] [Accepted: 02/24/2015] [Indexed: 02/01/2023]
Abstract
The effects of chemotherapeutic agent vinblastine versus low temperature of 277 K were investigated on the structure of αβ-tubulin heterodimer by means of molecular dynamics simulations. Individual experiments have shown that the vinblastine-bound heterodimer, and its apo structure under low temperature of 277 K, both undergo conformational changes toward destabilization of the dimer as compared to the apo tubulin at 300 K. Both factors exhibited weakening of the longitudinal interactions of tubulin heterodimer through displacing dimer interfacial segments, resulting in dominant electrostatic repulsion at the interface of the subunits. The two independent factors of temperature and anti-mitotic agent facilitate alteration of secondary structure in functional segments such as H1-S2 loop, H3, H10 helices, and T7 loop, which are known to be important in either longitudinal or lateral contacts among αβ-heterodimers in MTs protofilaments and their depolymerization mechanism.
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Affiliation(s)
- Z Li
- School of Pharmacy, Memorial University of Newfoundland, 300 Prince Philip Dr, St. John's, Newfoundland, A1B 3V6, Canada
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42
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Amirmostofian M, Kobarfard F, Reihanfard H, Mashayekhi V, Zarghi A. Design, Synthesis and Cytotoxicity Evaluationof New 1,2-diaryl-4, 5, 6, 7-Tetrahydro-1H-benzo[d] Imidazolesas Tubulin Inhibitors. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2015; 14:59-65. [PMID: 25561912 PMCID: PMC4277619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A new series of 1,2-diaryl-4,5,6,7-tetrahydro-1H-benzo[d]imidazoles, possessing trimethoxyphenyl pharmacophore, were synthesized to evaluate their biological activities as tubulin inhibitors. Cytotoxic activity of the synthesized compounds 7a-f was assessed against several human cancer cell lines, including MCF-7 (breast cancer cell), HEPG2 (liver hepatocellular cells), A549 (adenocarcinomic human alveolar basal epithelial cells), T47D (Human ductal breast epithelial tumor cell line) and fibroblast. According to our results, HEPG2 seems to be the most sensitive, while MCF7 was the most resistant cell line to the compounds. All the compounds expect 7b, possessed satisfactory activity against HEPG2 with mean IC50 values ranging from 15.60 to 43.81 µM.
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Affiliation(s)
- Marzieh Amirmostofian
- Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Farzad Kobarfard
- Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Hamed Reihanfard
- Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Vida Mashayekhi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, Iran.
| | - Afshin Zarghi
- Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran. ,
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43
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Ma CW, Lüddecke J, Forchhammer K, Zeng AP. Population shift of binding pocket size and dynamic correlation analysis shed new light on the anticooperative mechanism of PII protein. Proteins 2014; 82:1048-59. [PMID: 24218085 PMCID: PMC4282546 DOI: 10.1002/prot.24477] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 10/24/2013] [Accepted: 11/04/2013] [Indexed: 12/03/2022]
Abstract
PII protein is one of the largest families of signal transduction proteins in archaea, bacteria, and plants, controlling key processes of nitrogen assimilation. An intriguing characteristic for many PII proteins is that the three ligand binding sites exhibit anticooperative allosteric regulation. In this work, PII protein from Synechococcus elongatus, a model for cyanobacteria and plant PII proteins, is utilized to reveal the anticooperative mechanism upon binding of 2-oxoglutarate (2-OG). To this end, a method is proposed to define the binding pocket size by identifying residues that contribute greatly to the binding of 2-OG. It is found that the anticooperativity is realized through population shift of the binding pocket size in an asymmetric manner. Furthermore, a new algorithm based on the dynamic correlation analysis is developed and utilized to discover residues that mediate the anticooperative process with high probability. It is surprising to find that the T-loop, which is believed to be responsible for mediating the binding of PII with its target proteins, also takes part in the intersubunit signal transduction process. Experimental results of PII variants further confirmed the influence of T-loop on the anticooperative regulation, especially on binding of the third 2-OG. These discoveries extend our understanding of the PII T-loop from being essential in versatile binding of target protein to signal-mediating in the anticooperative allosteric regulation.
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Affiliation(s)
- Cheng-Wei Ma
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of TechnologyD-21073, Hamburg, Germany
| | - Jan Lüddecke
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin der Eberhard-Karls-Universität Tübingen72076, Tübingen, Germany
| | - Karl Forchhammer
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin der Eberhard-Karls-Universität Tübingen72076, Tübingen, Germany
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of TechnologyD-21073, Hamburg, Germany
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44
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Theisen KE, Desai NJ, Volski AM, Dima RI. Mechanics of severing for large microtubule complexes revealed by coarse-grained simulations. J Chem Phys 2014; 139:121926. [PMID: 24089738 DOI: 10.1063/1.4819817] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We investigate the mechanical behavior of microtubule (MT) protofilaments under the action of bending forces, ramped up linearly in time, to provide insight into the severing of MTs by microtubule associated proteins (MAPs). We used the self-organized polymer model which employs a coarse-grained description of the protein chain and ran Brownian dynamics simulations accelerated on graphics processing units that allow us to follow the dynamics of a MT system on experimental timescales. Our study focused on the role played in the MT depolymerization dynamics by the inter-tubulin contacts a protofilament experiences when embedded in the MT lattice, and the number of binding sites of MAPs on MTs. We found that proteins inducing breaking of MTs must have at least three attachment points on any tubulin dimer from an isolated protofilament. In contrast, two points of contact would suffice when dimers are located in an intact MT lattice, in accord with experimental findings on MT severing proteins. Our results show that confinement of a protofilament in the MT lattice leads to a drastic reduction in the energy required for the removal of tubulin dimers, due to the drastic reduction in entropy. We further showed that there are differences in the energetic requirements based on the location of the dimer to be removed by severing. Comparing the energy of tubulin dimers removal revealed by our simulations with the amount of energy resulting from one ATP hydrolysis, which is the source of energy for all MAPs, we provided strong evidence for the experimental finding that severing proteins do not bind uniformly along the MT wall.
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Affiliation(s)
- Kelly E Theisen
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, USA
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45
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Katebi AR, Jernigan RL. The critical role of the loops of triosephosphate isomerase for its oligomerization, dynamics, and functionality. Protein Sci 2013; 23:213-28. [PMID: 24318986 DOI: 10.1002/pro.2407] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 12/01/2013] [Accepted: 12/03/2013] [Indexed: 11/11/2022]
Abstract
Triosephosphate isomerase (TIM) catalyzes the reaction to convert dihydroxyacetone phosphate into glyceraldehyde 3-phosphate, and vice versa. In most organisms, its functional oligomeric state is a homodimer; however, tetramer formation in hyperthermophiles is required for functional activity. The tetrameric TIM structure also provides added stability to the structure, enabling it to function at more extreme temperatures. We apply Principal Component Analysis to find that the TIM structure space is clearly divided into two groups--the open and the closed TIM structures. The distribution of the structures in the open set is much sparser than that in the closed set, showing a greater conformational diversity of the open structures. We also apply the Elastic Network Model to four different TIM structures--an engineered monomeric structure, a dimeric structure from a mesophile--Trypanosoma brucei, and two tetrameric structures from hyperthermophiles Thermotoga maritima and Pyrococcus woesei. We find that dimerization not only stabilizes the structures, it also enhances their functional dynamics. Moreover, tetramerization of the hyperthermophilic structures increases their functional loop dynamics, enabling them to function in the destabilizing environment of extreme temperatures. Computations also show that the functional loop motions, especially loops 6 and 7, are highly coordinated. In summary, our computations reveal the underlying mechanism of the allosteric regulation of the functional loops of the TIM structures, and show that tetramerization of the structure as found in the hyperthermophilic organisms is required to maintain the coordination of the functional loops at a level similar to that in the dimeric mesophilic structure.
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Affiliation(s)
- Ataur R Katebi
- Department of Biochemistry, Biophysics and Molecular Biology, LH Baker Center for Bioinformatics and Biological Statistics, Interdepartmental Program for Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa, 50011-3020
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46
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Prokop A. The intricate relationship between microtubules and their associated motor proteins during axon growth and maintenance. Neural Dev 2013; 8:17. [PMID: 24010872 PMCID: PMC3846809 DOI: 10.1186/1749-8104-8-17] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 08/14/2013] [Indexed: 12/15/2022] Open
Abstract
The hallmarks of neurons are their slender axons which represent the longest cellular processes of animals and which act as the cables that electrically wire the brain, and the brain to the body. Axons extend along reproducible paths during development and regeneration, and they have to be maintained for the lifetime of an organism. Both axon extension and maintenance essentially depend on the microtubule (MT) cytoskeleton. For this, MTs organize into parallel bundles that are established through extension at the leading axon tips within growth cones, and these bundles then form the architectural backbones, as well as the highways for axonal transport essential for supply and intracellular communication. Axon transport over these enormous distances takes days or even weeks and is a substantial logistical challenge. It is performed by kinesins and dynein/dynactin, which are molecular motors that form close functional links to the MTs they walk along. The intricate machinery which regulates MT dynamics, axonal transport and the motors is essential for nervous system development and function, and its investigation has huge potential to bring urgently required progress in understanding the causes of many developmental and degenerative brain disorders. During the last years new explanations for the highly specific properties of axonal MTs and for their close functional links to motor proteins have emerged, and it has become increasingly clear that motors play active roles also in regulating axonal MT networks. Here, I will provide an overview of these new developments.
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Affiliation(s)
- Andreas Prokop
- Faculty of Life Sciences, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.
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Seckler JM, Leioatts N, Miao H, Grossfield A. The interplay of structure and dynamics: insights from a survey of HIV-1 reverse transcriptase crystal structures. Proteins 2013; 81:1792-801. [PMID: 23720322 DOI: 10.1002/prot.24325] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 04/12/2013] [Accepted: 04/19/2013] [Indexed: 11/07/2022]
Abstract
HIV-1 reverse transcriptase (RT) is a critical drug target for HIV treatment, and understanding the exact mechanisms of its function and inhibition would significantly accelerate the development of new anti-HIV drugs. It is well known that structure plays a critical role in protein function, but for RT, structural information has proven to be insufficient-despite enormous effort-to explain the mechanism of inhibition and drug resistance of non-nucleoside RT inhibitors. We hypothesize that the missing link is dynamics, information about the motions of the system. However, many of the techniques that give the best information about dynamics, such as solution nuclear magnetic resonance and molecular dynamics simulations, cannot be easily applied to a protein as large as RT. As an alternative, we combine elastic network modeling with simultaneous hierarchical clustering of structural and dynamic data. We present an extensive survey of the dynamics of RT bound to a variety of ligands and with a number of mutations, revealing a novel mechanism for drug resistance to non-nucleoside RT inhibitors. Hydrophobic core mutations restore active-state motion to multiple functionally significant regions of HIV-1 RT. This model arises out of a combination of structural and dynamic information, rather than exclusively from one or the other.
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Affiliation(s)
- James M Seckler
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, New York
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Breviario D, Gianì S, Morello L. Multiple tubulins: evolutionary aspects and biological implications. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:202-18. [PMID: 23662651 DOI: 10.1111/tpj.12243] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 05/03/2013] [Accepted: 05/09/2013] [Indexed: 05/05/2023]
Abstract
Plant tubulin is a dimeric protein that contributes to formation of microtubules, major intracellular structures that are involved in the control of fundamental processes such as cell division, polarity of growth, cell-wall deposition, intracellular trafficking and communications. Because it is a structural protein whose function is confined to the role of microtubule formation, tubulin may be perceived as an uninteresting gene product, but such a perception is incorrect. In fact, tubulin represents a key molecule for studying fundamental biological issues such as (i) microtubule evolution (also with reference to prokaryotic precursors and the formation of cytomotive filaments), (ii) protein structure with reference to the various biochemical features of members of the FstZ/tubulin superfamily, (iii) isoform variations contributed by the existence of multi-gene families and various kinds of post-translational modifications, (iv) anti-mitotic drug interactions and mode of action, (v) plant and cell symmetry, as determined using a series of tubulin mutants, (vi) multiple and sophisticated mechanisms of gene regulation, and (vii) intron molecular evolution. In this review, we present and discuss many of these issues, and offer an updated interpretation of the multi-tubulin hypothesis.
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Affiliation(s)
- Diego Breviario
- Istituto Biologia e Biotecnologia Agraria, Via Bassini 15, 20133 Milano, Italy.
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Kim MH, Seo S, Jeong JI, Kim BJ, Liu WK, Lim BS, Choi JB, Kim MK. A mass weighted chemical elastic network model elucidates closed form domain motions in proteins. Protein Sci 2013; 22:605-13. [PMID: 23456820 DOI: 10.1002/pro.2244] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 02/15/2013] [Accepted: 02/24/2013] [Indexed: 12/18/2022]
Abstract
An elastic network model (ENM), usually Cα coarse-grained one, has been widely used to study protein dynamics as an alternative to classical molecular dynamics simulation. This simple approach dramatically saves the computational cost, but sometimes fails to describe a feasible conformational change due to unrealistically excessive spring connections. To overcome this limitation, we propose a mass-weighted chemical elastic network model (MWCENM) in which the total mass of each residue is assumed to be concentrated on the representative alpha carbon atom and various stiffness values are precisely assigned according to the types of chemical interactions. We test MWCENM on several well-known proteins of which both closed and open conformations are available as well as three α-helix rich proteins. Their normal mode analysis reveals that MWCENM not only generates more plausible conformational changes, especially for closed forms of proteins, but also preserves protein secondary structures thus distinguishing MWCENM from traditional ENMs. In addition, MWCENM also reduces computational burden by using a more sparse stiffness matrix.
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Affiliation(s)
- Min Hyeok Kim
- SKKU Advanced Institute of Nanotechnology-SAINT, Sungkyunkwan University, Suwon 440-746, Korea
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GhattyVenkataKrishna PK, Carri GA. The effect of complex solvents on the structure and dynamics of protein solutions: The case of Lysozyme in trehalose/water mixtures. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2013; 36:14. [PMID: 23404569 DOI: 10.1140/epje/i2013-13014-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 10/15/2012] [Accepted: 01/17/2013] [Indexed: 06/01/2023]
Abstract
We present a Molecular Dynamics simulation study of the effect of trehalose concentration on the structure and dynamics of individual proteins immersed in trehalose/water mixtures. Hen egg-white Lysozyme is used in this study and trehalose concentrations of 0%, 10%, 20%, 30% and 100% by weight are explored. Surprisingly, we have found that changes in trehalose concentration do not change the global structural characteristics of the protein as measured by standard quantities like the mean square deviation, radius of gyration, solvent accessible surface area, inertia tensor and asphericity. Only in the limit of pure trehalose these metrics change significantly. Specifically, we found that the protein is compressed by 2% when immersed in pure trehalose. At the amino acid level there is noticeable rearrangement of the surface residues due to the change in polarity of the surrounding environment with the addition of trehalose. From a dynamic perspective, our computation of the Incoherent Intermediate Scattering Function shows that the protein slows down with increasing trehalose concentration; however, this slowdown is not monotonic. Finally, we also report in-depth results for the hydration layer around the protein including its structure, hydrogen-bonding characteristics and dynamic behavior at different length scales.
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