1
|
Córdova JA, Palermo JC, Estrin DA, Bari SE, Capece L. Binding mechanism of disulfide species to ferric hemeproteins: The case of metmyoglobin. J Inorg Biochem 2023; 247:112313. [PMID: 37467661 DOI: 10.1016/j.jinorgbio.2023.112313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/15/2023] [Accepted: 07/01/2023] [Indexed: 07/21/2023]
Abstract
The interactions of the heme iron of hemeproteins with sulfide and disulfide compounds are of potential interest as physiological signaling processes. While the interaction with hydrogen sulfide has been described computationally and experimentally, the reaction with disulfide, and specifically the molecular mechanism for ligand binding has not been studied in detail. In this work, we study the association process for disulfane and its conjugate base disulfanide at different pH conditions. Additionally, by means of advanced sampling techniques based on multiple steered molecular dynamics, we provide free energy profiles for ligand migration for both acid/base species, showing a similar behavior to the previously reported for the related H2S/HS¯ pair. Finally, we studied the ligand interchange reaction (H2O/H2S, HS¯ and H2O/HSSH, HSS¯) by means of hybrid quantum mechanics-molecular mechanics calculations. We show that the anionic species are able to displace more efficiently the H2O bound to the iron, and that the H-bond network in the distal cavity can help the neutral species to perform the reaction. Altogether, we provide a molecular explanation for the experimental information and show that the global association process depends on a fine balance between the migration towards the active site and the ligand interchange reaction.
Collapse
Affiliation(s)
- Jonathan Alexis Córdova
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Buenos Aires, Argentina
| | - Juan Cruz Palermo
- CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina
| | - Darío A Estrin
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina
| | - Sara E Bari
- CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina..
| | - Luciana Capece
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina..
| |
Collapse
|
2
|
Maymand VM, Bavi O, Karami A. Probing the mechanical properties of ORF3a protein, a transmembrane channel of SARS-CoV-2 virus: Molecular dynamics study. Chem Phys 2023; 569:111859. [PMID: 36852417 PMCID: PMC9946729 DOI: 10.1016/j.chemphys.2023.111859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/04/2022] [Accepted: 02/19/2023] [Indexed: 02/24/2023]
Abstract
SARS-CoV-2-encoded accessory protein ORF3a was found to be a conserved coronavirus protein that shows crucial roles in apoptosis in cells as well as in virus release and replications. To complete the knowledge and identify the unknown of this protein, further comprehensive research is needed to clarify the leading role of ORF3a in the functioning of the coronavirus. One of the efficient approaches to determining the functionality of this protein is to investigate the mechanical properties and study its structural dynamics in the presence of physical stimuli. Herein, performing all-atom steered molecular dynamics (SMD) simulations, the mechanical properties of the force-bearing components of the ORF3a channel are calculated in different physiological conditions. As variations occurring in ORF3a may lead to alteration in protein structure and function, the G49V mutation was also simulated to clarify the relationship between the mechanical properties and chemical stability of the protein by comparing the behavior of the wild-type and mutant Orf3a. From a physiological conditions point of view, it was observed that in the solvated system, the presence of water molecules reduces Young's modulus of TM1 by ∼30 %. Our results also show that by substitution of Gly49 with valine, Young's modulus of the whole helix increases from 1.61 ± 0.20 to 2.08 ± 0.15 GPa, which is consistent with the calculated difference in free energy of wild-type and mutant helices. In addition to finding a way to fight against Covid-19 disease, understanding the mechanical behavior of these biological nanochannels can lead to the development of the potential applications of the ORF3a protein channel, such as tunable nanovalves in smart drug delivery systems, nanofilters in the new generation of desalination systems, and promising applications in DNA sequencing.
Collapse
Affiliation(s)
| | - Omid Bavi
- Department of Mechanical Engineering, Shiraz University of Technology, Shiraz, Iran
| | - Abbas Karami
- Department of Mechanical Engineering, Shiraz University of Technology, Shiraz, Iran
| |
Collapse
|
3
|
Dhiman A, Purohit R. Profiling the disintegration of BRPs released by massive wasp stings using serratiopeptidase: An in-silico insight. Comput Biol Med 2023; 159:106951. [PMID: 37086660 DOI: 10.1016/j.compbiomed.2023.106951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/10/2023] [Accepted: 04/15/2023] [Indexed: 04/24/2023]
Abstract
Serratiopeptidase is a multifaceted therapeutic enzyme renowned for its anti-inflammatory, analgesic, anti-biofilm, fibrinolytic, and anti-edemic properties. It is vital to uncover more about the assets of such efficacious enzyme in order to facilitate their contribution in all health-related issues, notably inflammatory ailments. The current study sought to determine whether serratiopeptidase would disintegrate bradykinin related peptides (BRPs) from wasp venom in the same manner as it does with human bradykinin. To accomplish this objective, we docked selected BRPs onto the binding pocket of wild and previously identified mutant (N412D) of serratiopeptidase. Based on their docked scores, the top two BRPs were selected, and their conformational behavior was analyzed employing molecular dynamics studies. Additionally, thermodynamics end-state energy analysis reported that both the complexes exhibited higher stability and identical ΔG values when compared to the reference complex. Further, we condemned the external pulling forces on both peptides to observe the force needed in the disassociation process to endorse the binding affinity findings in terms of unbinding mechanism. This analysis suggested that BRP-7 (Wasp kinin PMM1) peptide was tightly anchored and laid out the highest pulling force to get detach from the active pocket of serratiopeptidase in contrast to the BRP-6 peptide. The current study endorses up the present findings and paves the way for serratiopeptidase to be used as an anti-angioedemic peptidase as well as a fixed-dose combination (FDC) in hypotensive drugs.
Collapse
Affiliation(s)
- Ankita Dhiman
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| |
Collapse
|
4
|
Singh R, Purohit R. Computational analysis of protein-ligand interaction by targeting a cell cycle restrainer. Comput Methods Programs Biomed 2023; 231:107367. [PMID: 36716649 DOI: 10.1016/j.cmpb.2023.107367] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/10/2023] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND AND OBJECTIVE The cyclin-dependent kinases 4/6 (CDK4/6) are among the most crucial controllers of the cell cycle, and their abnormal activity may induce uncontrolled cell multiplication, leading to cancers. The FDA currently approved three CDK4/6 inhibitors, however, they are associated with a variety of side effects. Thus it is required to design/develop novel potent and safe CDK4/6 inhibitors. METHODS In the present work, we furnished an integrated in-silico approach followed by steered molecular dynamics (SMD) simulations to identify molecules that can be developed into novel CDK4/6 inhibitors. RESULTS Out of thirty-two 3-methyleneisoindolin-1-one molecules we selected top three M18, M24, and M32 molecules as potential drug candidates based on their respective interaction energies. According to the robust 250 ns MD simulations and thermodynamic free energy, M24 was the best molecule in comparison to palbociclib. In SMD, M24 required ∼205.587 kJ/mol/nm external pulling force, while palbociclib needed ∼160.97 kJ/mol/nm to dissociate from the binding pocket of the CDK4. CONCLUSIONS The high pulling force required for M24 dissociation from the binding site denotes stronger binding with CDK4. Therefore, M24 offers the possibility of a critical starting structure in developing effective CDK4 inhibitors.
Collapse
Affiliation(s)
- Rahul Singh
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India.
| |
Collapse
|
5
|
Kumar S, Bhardwaj VK, Singh R, Purohit R. Structure restoration and aggregate inhibition of V30M mutant transthyretin protein by potential quinoline molecules. Int J Biol Macromol 2023; 231:123318. [PMID: 36681222 DOI: 10.1016/j.ijbiomac.2023.123318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/01/2023] [Accepted: 01/14/2023] [Indexed: 01/20/2023]
Abstract
Transthyretin (TTR) is a tetrameric protein found in human plasma and cerebrospinal fluid that functions as a transporter of thyroxine (T4) and retinol. A mutation resulting in the substitution of valine to methionine at position 30 (V30M) is the most common mutation that destabilizes the tetramer structure of TTR protein resulting in a fatal neuropathy known as TTR amyloidosis. The V30M TTR-induced neuropathy can be inhibited through stabilization of the TTR tetramer by the binding of small molecules. We accessed the potential of in-house synthesized quinoline molecules to stabilize the V30M TTR structure and analyzed the impact of protein-ligand interactions through molecular docking, molecular dynamics (MD) simulations, steered MD, and umbrella sampling simulations. This study revealed that the binding of quinoline molecules reverted back the structural changes including the residual flexibility, changes in secondary structural elements, and also restored the alterations in the electrostatic surface potential induced by the V30M mutation. Further, the top-most 4G and 4R molecules were compared with an FDA-approved drug (Tafamidis) and a reference quinoline molecule 14C. Here, we intend to suggest that the quinoline molecules could revert the structural changes, cease tetramer dissociation, prevent abnormal oligomerization and therefore could be developed as an effective therapeutics against TTR amyloidosis.
Collapse
Affiliation(s)
- Sachin Kumar
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rahul Singh
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India.
| |
Collapse
|
6
|
Sayed AM, Ibrahim AH, Tajuddeen N, Seibel J, Bodem J, Geiger N, Striffler K, Bringmann G, Abdelmohsen UR. Korupensamine A, but not its atropisomer, korupensamine B, inhibits SARS-CoV-2 in vitro by targeting its main protease (M pro). Eur J Med Chem 2023; 251:115226. [PMID: 36893625 PMCID: PMC9972725 DOI: 10.1016/j.ejmech.2023.115226] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/07/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023]
Abstract
By combining docking and molecular dynamics simulations, we explored a library of 65 mostly axially chiral naphthylisoquinoline alkaloids and their analogues, with most different molecular architectures and structural analogues, for their activity against SARS-CoV-2. Although natural biaryls are often regarded without consideration of their axial chirality, they can bind to protein targets in an atroposelective manner. By combining docking results with steered molecular dynamics simulations, we identified one alkaloid, korupensamine A, that atropisomer-specifically inhibited the main protease (Mpro) activity of SARS-CoV-2 significantly in comparison to the reference covalent inhibitor GC376 (IC50 = 2.52 ± 0.14 and 0.88 ± 0.15 μM, respectively) and reduced viral growth by five orders of magnitude in vitro (EC50 = 4.23 ± 1.31 μM). To investigate the binding pathway and mode of interaction of korupensamine A within the active site of the protease, we utilized Gaussian accelerated molecular dynamics simulations, which reproduced the docking pose of korupensamine A inside the active site of the enzyme. The study presents naphthylisoquinoline alkaloids as a new class of potential anti-COVID-19 agents.
Collapse
Affiliation(s)
- Ahmed M Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef, 62513, Egypt
| | - Alyaa Hatem Ibrahim
- Department of Pharmacognosy, Faculty of Pharmacy, Sohag University, Sohag, 82524, Egypt
| | - Nasir Tajuddeen
- Department of Chemistry, Ahmadu Bello University, 15 Sokoto Road Samaru, Zaria, 810107, Nigeria
| | - Jürgen Seibel
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Jochen Bodem
- Institute of Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078, Würzburg, Germany
| | - Nina Geiger
- Institute of Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078, Würzburg, Germany
| | - Kathrin Striffler
- Institute of Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078, Würzburg, Germany
| | - Gerhard Bringmann
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt; Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone, New Minia City, 61111, Egypt.
| |
Collapse
|
7
|
Behmard E, Ghasemian A, Barzegari E, Farjadfar A, Kouhpayeh A, Najafipour S. Advanced simulations and screening to repurposing a 3C protease inhibitor against the rupintrivir-resistant human norovirus-induced gastroenteritis. J Mol Graph Model 2023; 118:108345. [PMID: 36308946 DOI: 10.1016/j.jmgm.2022.108345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/19/2022] [Accepted: 09/23/2022] [Indexed: 11/06/2022]
Abstract
Human norovirus (HuNoV) causes acute viral gastroenteritis in all age groups, and dehydration and severe diarrhea in the elderly. The World Health Organization reports ∼1.45 million deaths from acute gastroenteritis annually in the world. Rupintrivir, an inhibitory medicine against the human rhinovirus C3 protease, has been reported to inhibit HuNoV 3C protease. However, several HuNoV 3C protease mutations have been revealed to reduce the susceptibility of HuNoV to rupintrivir. The structural details behind rupintrivir-resistance of these single-point mutations (A105V and I109V) are not still clear. Hence, in this study, a combination of computational techniques were used to determine the rupintrivir-resistance mechanism and to propose an inhibitor against wild-type and mutant HuNoV 3C protease through structure-based virtual screening. Dynamic structural results indicated the unstable binding of rupintrivir at the cleft binding site of the wild-type and mutant 3C proteases, leading to its detachment. Our findings presented that the domain II of the HuNoV 3C protease had a critical role in binding of inhibitory molecules. Binding energy computations, steered molecular dynamics and umbrella sampling simulations confirmed that amentoflavone, the novel suggested inhibitor, strongly binds to the cleft site of all protease models and has a good structural stability in the complex system along the molecular dynamic simulations. Our in silico study proposed the selected compound as a potential inhibitor against the HuNoV 3C protease. However, additional experimental and clinical studies are required to corroborate the therapeutic efficacy of the compound.
Collapse
Affiliation(s)
- Esmaeil Behmard
- School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran.
| | - Abdolmajid Ghasemian
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Ebrahim Barzegari
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Akbar Farjadfar
- Department of Medical Biotechnology, Fasa University of Medical Sciences, Fasa, Iran
| | - Amin Kouhpayeh
- Department of Pharmacology, Faculty of Medicine, Fasa University of Medical Sciences, Fasa, Iran.
| | - Sohrab Najafipour
- School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran.
| |
Collapse
|
8
|
Iida S, Tomoshi K. Free energy and kinetic rate calculation via non-equilibrium molecular simulation: application to biomolecules. Biophys Rev 2022; 14:1303-1314. [PMID: 36659997 PMCID: PMC9842846 DOI: 10.1007/s12551-022-01036-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/26/2022] [Indexed: 12/30/2022] Open
Abstract
Non-equilibrium molecular dynamics (NEMD) simulation has been recognized as a powerful tool for examining biomolecules and provides fruitful insights into not only non-equilibrium but also equilibrium processes. We review recent advances in NEMD simulation and relevant, fundamental results of non-equilibrium statistical mechanics. We first introduce Crooks fluctuation theorem and Jarzynski equality that relate free energy difference to work done on a physical system during a non-equilibrium process. The theorems are beneficial for the analysis of NEMD trajectories. We then describe rate theory, a framework to calculate molecular kinetics from a non-equilibrium process; this theoretical framework enables us to calculate a reaction time-mean-first passage time-from NEMD trajectories. We, in turn, present recent NEMD techniques that apply an external force to a system to enhance molecular dissociation and introduce their application to biomolecules. Lastly, we show the current status of an appropriate selection of reaction coordinates for NEMD simulation.
Collapse
Affiliation(s)
- Shinji Iida
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-Ku, Tokyo, 135-0064 Japan
| | - Kameda Tomoshi
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-Ku, Tokyo, 135-0064 Japan
| |
Collapse
|
9
|
Dastorani S, Ghasemi RH, Soheilifard R. A Study on the Bending Stiffness of a New DNA Origami Nano-Joint. Mol Biotechnol 2021; 63:1057-1067. [PMID: 34224047 DOI: 10.1007/s12033-021-00367-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 06/28/2021] [Indexed: 11/29/2022]
Abstract
The present article aims to investigate the mechanical properties of a new DNA origami nano-joint using the steered molecular dynamics (SMD) simulation. Since the analysis of mechanical properties is of great importance in bending conditions for a nano-joint, the forces are selected to achieve angular changes in the joint by the resultant torque. In this study, the nano-joint is considered as a beam in order to use mechanical equations to extract the mechanical properties of the designed nano-joint. In addition, the bending stiffness of the beam is investigated in different modes of deflection using the Euler-Bernoulli beam theory. The results revealed that the value of bending stiffness increases with increasing deflection, and the changes in the bending stiffness relative to the deflection is linear. The proposed DNA origami nano-joint can be used as a joint in nanorobots and can be effectively applied in nanorobotic systems to move different components.
Collapse
Affiliation(s)
- Sadegh Dastorani
- Department of Mechanical Engineering, Hakim Sabzevari University, Sabzevar, Iran
| | | | - Reza Soheilifard
- Department of Mechanical Engineering, Hakim Sabzevari University, Sabzevar, Iran
| |
Collapse
|
10
|
Kopp N, Civenni G, Marson D, Laurini E, Pricl S, Catapano CV, Humpf HU, Almansa C, Nieto FR, Schepmann D, Wünsch B. Chemoenzymatic synthesis of 2,6-disubstituted tetrahydropyrans with high σ 1 receptor affinity, antitumor and analgesic activity. Eur J Med Chem 2021; 219:113443. [PMID: 33901806 DOI: 10.1016/j.ejmech.2021.113443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/22/2021] [Accepted: 03/29/2021] [Indexed: 02/06/2023]
Abstract
1,3-Dioxanes 1 and cyclohexanes 2 bearing a phenyl ring and an aminoethyl moiety in 1,3-relationship to each other represent highly potent σ1 receptor antagonists. In order to increase the chemical stability of the acetalic 1,3-dioxanes 1 and the polarity of the cyclohexanes 2, tetrahydropyran derivatives 3 equipped with the same substituents were designed, synthesized and pharmacologically evaluated. The key step of the synthesis was a lipase-catalyzed enantioselective acetylation of the alcohol (R)-5 leading finally to enantiomerically pure test compounds 3a-g. With respect to σ1 receptor affinity and selectivity over a broad range of related (σ2, PCP binding site) and further targets, the enantiomeric benzylamines 3a and cyclohexylmethylamines 3b represent the most promising drug candidates of this series. However, the eudismic ratio for σ1 binding is only in the range of 2.5-3.3. Classical molecular dynamics (MD) simulations confirmed the same binding pose for both the tetrahydropyran 3 and cyclohexane derivatives 2 at the σ1 receptor, according to which: i) the protonated amino moiety of (2S,6R)-3a engages the same key polar interactions with Glu172 (ionic) and Phe107 (π-cation), ii) the lipophilic parts of (2S,6R)-3a are hosted in three hydrophobic regions of the σ1 receptor, and iii) the O-atom of the tetrahydropyran derivatives 3 does not show a relevant interaction with the σ1 receptor. Further in silico evidences obtained by the application of free energy perturbation and steered MD techniques fully supported the experimentally observed difference in receptor/ligand affinities. Tetrahydropyrans 3 require a lower dissociative force peak than cyclohexane analogs 2. Enantiomeric benzylamines 3a and cyclohexylmethylamines 3b were able to inhibit the growth of the androgen negative human prostate cancer cell line DU145. The cyclohexylmethylamine (2S,6R)-3b showed the highest σ1 affinity (Ki(σ1) = 0.95 nM) and the highest analgesic activity in vivo (67%).
Collapse
Affiliation(s)
- Nicole Kopp
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149, Münster, Germany
| | - Gianluca Civenni
- Institute of Oncology Research, Università della Svizzera Italiana (USI), Via Vincenzo Vela 6, CH-6500, Bellinzona, Switzerland
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127, Trieste, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, 34127, Trieste, Italy; Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Carlo V Catapano
- Institute of Oncology Research, Università della Svizzera Italiana (USI), Via Vincenzo Vela 6, CH-6500, Bellinzona, Switzerland
| | - Hans-Ulrich Humpf
- Institut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149, Münster, Germany
| | - Carmen Almansa
- Esteve Pharmaceuticals S.A., Baldiri Reixach 4-8, 08028, Barcelona, Spain
| | - Francisco Rafael Nieto
- Department of Pharmacology and Neurosciences Institute (Biomedical Research Center), University of Granada and Biosanitary Research Institute, 18010, Granada, Spain
| | - Dirk Schepmann
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149, Münster, Germany
| | - Bernhard Wünsch
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149, Münster, Germany; GRK 2515, Chemical Biology of Ion Channels (Chembion), Westfälische Wilhelms-Universität Münster, Germany.
| |
Collapse
|
11
|
Harder-Viddal C, Heide F, Roshko RM, Stetefeld J. Molecular dynamics simulations of ortho-carborane nano-diamond storage within the nonpolar channel cavities of a right-handed coiled-coil tetrabrachion nanotube. Comput Struct Biotechnol J 2021; 19:3531-3541. [PMID: 34194676 PMCID: PMC8220585 DOI: 10.1016/j.csbj.2021.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 10/26/2022] Open
Abstract
Molecular dynamics simulations have been performed on a complex in which clusters of boron in the form of molecules of the nanodiamond ortho-carborane ( C 2 B 10 H 12 ) have been inserted into the four large nonpolar cavities of a nanotube of the right-handed coiled-coil ( R H C C ) t e t r a b r a c h i o n . The techniques of multi-configurational thermodynamic integration, steered molecular dynamics and umbrella sampling have been combined to investigate the energetics of storage of ortho-carborane in the cavities and to map out the free energy landscape of the RHCC - t e t r a b r a c h i o n - o r t h o - c a r b o r a n e complex along the central channel and along directions transverse to the central channel. The purpose of the study was to explore potential pathways for the diffusion of ortho-carborane between the cavities and the solvent and to assess the stability of the complex as a possible drug delivery system for boron neutron capture therapy (BNCT). The investigation reveals a complex free energy landscape with a multitude of peaks and valleys, all of which can be related to specific architectural elements of the RHCC - n a n o t u b e , and the activation barriers for ortho-carborane capture and release support the requirements for rapid cargo uptake coupled with tight binding to the cavities.
Collapse
Affiliation(s)
- C Harder-Viddal
- Department of Chemistry and Physics, Canadian Mennonite University, 500 Shaftesbury Blvd, Winnipeg, Manitoba, Canada
| | - F Heide
- Department of Chemistry, University of Manitoba, 144 Dysart Rd, Winnipeg, Manitoba, Canada
| | - R M Roshko
- Department of Physics and Astronomy, University of Manitoba, 30A Sifton Rd, Winnipeg, Manitoba, Canada
| | - J Stetefeld
- Department of Chemistry, University of Manitoba, 144 Dysart Rd, Winnipeg, Manitoba, Canada.,Center for Oil and Gas Research and Development (COGRAD), Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, Canada.,Department of Human Anatomy and Cell Science, University of Manitoba, Canada
| |
Collapse
|
12
|
Cao TM, King MR. Stabilization of the Hinge Region of Human E-selectin Enhances Binding Affinity to Ligands Under Force. Cell Mol Bioeng 2021; 14:65-74. [PMID: 33633813 DOI: 10.1007/s12195-021-00666-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 01/04/2021] [Indexed: 12/30/2022] Open
Abstract
Introduction E-selectin is a member of the selectin family of cell adhesion molecules expressed on the plasma membrane of inflamed endothelium and facilitates initial leukocyte tethering and subsequent cell rolling during the early stages of the inflammatory response via binding to glycoproteins expressing sialyl LewisX and sialyl LewisA (sLeX/A). Existing crystal structures of the extracellular lectin/EGF-like domain of E-selectin complexed with sLeX have revealed that E-selectin can exist in two conformation states, a low affinity (bent) conformation, and a high affinity (extended) conformation. The differentiating characteristic of the two conformations is the interdomain angle between the lectin and the EGF-like domain. Methods Using molecular dynamics (MD) simulations we observed that in the absence of tensile force E-selectin undergoes spontaneous switching between the two conformational states at equilibrium. A single amino acid substitution at residue 2 (serine to tyrosine) on the lectin domain favors the extended conformation. Results Steered molecular dynamics (SMD) simulations of E-selectin and PSGL-1 in conjunction with experimental cell adhesion assays show a longer binding lifetime of E-selectin (S2Y) to PSGL-1 compared to wildtype protein. Conclusions The findings in this study advance our understanding into how the structural makeup of E-selectin allosterically influences its adhesive dynamics.
Collapse
|
13
|
Hacisuleyman A, Erman B. ModiBodies: A computational method for modifying nanobodies in nanobody-antigen complexes to improve binding affinity and specificity. J Biol Phys 2020; 46:189-208. [PMID: 32418062 DOI: 10.1007/s10867-020-09548-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/28/2020] [Indexed: 11/26/2022] Open
Abstract
Nanobodies are special derivatives of antibodies, which consist of single domain fragments. They have become of considerable interest as next-generation biotechnological tools for antigen recognition. They can be easily engineered due to their high stability and compact size. Nanobodies have three complementarity-determining regions, CDRs, which are enlarged to provide a similar binding surface to that of human immunoglobulins. Here, we propose a benchmark testing algorithm that uses 3D structures of already existing protein-nanobody complexes as initial structures followed by successive mutations on the CDR domains. The aim is to find optimum binding amino acids for hypervariable residues of CDRs. We use molecular dynamics simulations to compare the binding energies of the resulting complexes with that of the known complex and accept those that are improved by mutations. We use the MDM4-VH9 complex, (PDB id 2VYR), fructose-bisphosphate aldolase from Trypanosoma congolense (PDB id 5O0W) and human lysozyme (PDB id 4I0C) as benchmark complexes. By using this algorithm, better binding nanobodies can be generated in a short amount of time. We suggest that this method can complement existing immune and synthetic library-based methods, without a need for extensive experimentation or large libraries.
Collapse
Affiliation(s)
- Aysima Hacisuleyman
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey.
| | - Burak Erman
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| |
Collapse
|
14
|
Abstract
Molecular dynamics simulation is a powerful computational technique to study biomolecular systems, which complements experiments by providing insights into the structural dynamics relevant to biological functions at atomic scale. It can also be used to calculate the free energy landscapes of the conformational transitions to better understand the functions of the biomolecules. However, the sampling of biomolecular configurations is limited by the free energy barriers that need to be overcome, leading to considerable gaps between the timescales reached by MD simulation and those governing biological processes. To address this issue, many enhanced sampling methodologies have been developed to increase the sampling efficiency of molecular dynamics simulations and free energy calculations. Usually, enhanced sampling algorithms can be classified into methods based on collective variables (CV-based) and approaches which do not require predefined CVs (CV-free). In this chapter, the theoretical basis of free energy estimation is briefly reviewed first, followed by the reviews of the most common CV-based and CV-free methods including the presentation of some examples and recent developments. Finally, the combination of different enhanced sampling methods is discussed.
Collapse
Affiliation(s)
- Qinghua Liao
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden.
| |
Collapse
|
15
|
Garcia PS, Brum DG, Oliveira ON, Higa AM, Ierich JCM, Moraes ADS, Shimizu FM, Okuda-Shinagawa NM, Peroni LA, da Gama PD, Machini MT, Leite FL. Nanoimmunosensor based on atomic force spectroscopy to detect anti-myelin basic protein related to early-stage multiple sclerosis. Ultramicroscopy 2020; 211:112946. [PMID: 32028099 DOI: 10.1016/j.ultramic.2020.112946] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 12/02/2019] [Accepted: 01/21/2020] [Indexed: 02/06/2023]
Abstract
Multiple Sclerosis (MS) is a chronic inflammatory disorder in the central nervous system for which biomarkers for diagnosis still remain unknown. One potential biomarker is the myelin basic protein. Here, a nanoimmunosensor based on atomic force spectroscopy (AFS) successfully detected autoantibodies against the MBP85-99 peptide from myelin basic protein. The nanoimmunosensor consisted of an atomic force microscope tip functionalization with MBP85-99 peptide, which was made to interact with a mica surface coated either with a layer of anti-MBP85-99 (positive control) or samples of cerebrospinal fluid (CSF) from five multiple sclerosis (MS) patients at different stages of the disease and five non-MS subjects. The adhesion forces obtained from AFS pointed to a high concentration of anti-MBP85-99 for the two patients at early stages of relapsing-remitting multiple sclerosis (RRMS), which were indistinguishable from the positive control. In contrast, considerably lower adhesion forces were measured for all the other eight subjects, including three MS patients with longer history of the disease and under treatment, without episodes of acute MS activity. We have also shown that the average adhesion force between MBP85-99 and anti-MBP85-99 is compatible with the value estimated using steered molecular dynamics. Though further tests will be required with a larger cohort of patients, the present results indicate that the nanoimmunosensor may be a simple tool to detect early-stage MS patients and be useful to understand the molecular mechanisms behind MS.
Collapse
Affiliation(s)
- Pâmela Soto Garcia
- Department of Physics, Chemistry and Mathematics, Nanoneurobiophysics Research Group, Federal University of São Carlos, Sorocaba, São Paulo 18052780, Brazil; Institute of Tropical Medicine, University of São Paulo, 05403-000, São Paulo, SP, Brazil
| | - Doralina Guimarães Brum
- Department of Neurology, Psychology and Psychiatry, São Paulo State University, 18618-687, Botucatu, SP, Brazil
| | - Osvaldo N Oliveira
- São Carlos Institute of Physics, University of São Paulo, 13560-970, São Carlos, SP, Brazil
| | - Akemi Martins Higa
- Department of Physics, Chemistry and Mathematics, Nanoneurobiophysics Research Group, Federal University of São Carlos, Sorocaba, São Paulo 18052780, Brazil; Institute of Tropical Medicine, University of São Paulo, 05403-000, São Paulo, SP, Brazil
| | - Jéssica Cristiane Magalhães Ierich
- Department of Physics, Chemistry and Mathematics, Nanoneurobiophysics Research Group, Federal University of São Carlos, Sorocaba, São Paulo 18052780, Brazil; Institute of Tropical Medicine, University of São Paulo, 05403-000, São Paulo, SP, Brazil
| | - Ariana de Souza Moraes
- Department of Physics, Chemistry and Mathematics, Nanoneurobiophysics Research Group, Federal University of São Carlos, Sorocaba, São Paulo 18052780, Brazil; Institute of Tropical Medicine, University of São Paulo, 05403-000, São Paulo, SP, Brazil
| | - Flávio Makoto Shimizu
- São Carlos Institute of Physics, University of São Paulo, 13560-970, São Carlos, SP, Brazil
| | - Nancy M Okuda-Shinagawa
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000, São Paulo, SP, Brazil
| | - Luís Antonio Peroni
- Rheabiotech Laboratory Research and Development, 13084-791, Campinas, SP, Brazil
| | | | - M Teresa Machini
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000, São Paulo, SP, Brazil
| | - Fabio Lima Leite
- Department of Physics, Chemistry and Mathematics, Nanoneurobiophysics Research Group, Federal University of São Carlos, Sorocaba, São Paulo 18052780, Brazil.
| |
Collapse
|
16
|
Harder-Viddal C, McDougall M, Roshko RM, Stetefeld J. Energetics of Storage and Diffusion of Water and Cyclo-Octasulfur for a Nonpolar Cavity of RHCC Tetrabrachion by Molecular Dynamics Simulations. Comput Struct Biotechnol J 2019; 17:675-683. [PMID: 31198494 PMCID: PMC6555900 DOI: 10.1016/j.csbj.2019.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/11/2019] [Accepted: 05/13/2019] [Indexed: 02/07/2023] Open
Abstract
Tetrabrachion forms the key component of the S-layer of Staphylothermus marinus. Molecular dynamics simulations have been used to study the energetics of occupancy of cavity 3 of the right-handed coiled-coil stalk of tetrabrachion by both water molecules and cyclooctasulfur S8 crowns, as well as to determine possible pathways and free energy barriers for the diffusion of both water and cyclooctasulfur through the peptide walls of RHCC tetrabrachion between cavity 3 and bulk solvent. Calculations of the transfer free energy from solvent to cavity show that clusters of six, seven and eight water molecules are marginally stable in cavity 3, but that occupancy of the cavity by a cyclooctasulfur ring is favoured significantly over water clusters of all sizes. Thermal activation simulations at T = 400K revealed that water molecules diffusing through the wall pass through a sequence of metastable configurations where they are temporarily immobilized by forming networks of hydrogen bonds with specific wall residues. Calculations of the free energy of these metastable configurations using multi-configurational thermodynamic integration yielded a free energy profile with a principal free energy maximum ∆G~50 kJ/mol and a slight activation asymmetry in favour of the direction from cavity to solvent. Potential exit pathways for cyclooctasulfur were investigated with the methods of steered molecular dynamics and umbrella sampling. The cyclooctasulfur was steered through a gap in the tetrabrachion wall along a linear path from cavity 3 into the solvent and the resulting trajectory was subdivided into 22 sampling windows. The free energy profile created for the trajectory by umbrella sampling showed a sharp principal maximum as a function of the reaction coordinate with asymmetric free energy barriers ∆Gexit~220 kJ/mol and ∆Gentrance~100 kJ/mol for cavity exit and entrance, respectively.
Collapse
Affiliation(s)
- C Harder-Viddal
- Department of Chemistry and Physics, Canadian Mennonite University, 500 Shaftesbury Blvd, Winnipeg, Manitoba, Canada
| | - M McDougall
- Department of Chemistry, University of Manitoba, 144 Dysart Rd, Winnipeg, Manitoba, Canada.,Center for Oil and Gas Research and Development (COGRAD), Canada
| | - R M Roshko
- Department of Physics and Astronomy, University of Manitoba, 30A Sifton Rd, Winnipeg, Manitoba, Canada
| | - J Stetefeld
- Department of Chemistry, University of Manitoba, 144 Dysart Rd, Winnipeg, Manitoba, Canada.,Center for Oil and Gas Research and Development (COGRAD), Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, Canada.,Department of Human Anatomy and Cell Science, University of Manitoba, Canada
| |
Collapse
|
17
|
Salehi Mojarrad MH, Goodarzi V, Taheri RA. Force Sensing in Nanoscale: Integration of Virtual Spring for Sensing the Interactions of β-Amyloid Grabbed by Prefoldin. Appl Biochem Biotechnol 2019; 188:1108-16. [PMID: 30806943 DOI: 10.1007/s12010-019-02975-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/01/2019] [Indexed: 10/27/2022]
Abstract
Analysis of atomic forces in molecular scale including the reciprocal internal force directions, quantity, and Young's modulus, and more detailed analysis via diagrams, is one of the most current research topics. This research aims to analyze the bilateral forces applied between a nano-actuator and a cargo from a new perspective. While virtual springs have been used as a tool to convey forces in the previous steered molecular dynamics simulations, this study uses the spring as a sensor for measuring the internal forces. This study introduces atomic sensing via the steered molecular dynamics method. Following the previous studies, the protein employed in this study is the mutated Archetype Prefoldin being used to control the pathogenic cargo beta-amyloid (Alzheimer's). The powerful Gromacs software carries out the simulations for the calculation of the total force and force for each branch. The simulation results illustrate the total force between the cargo and nano-actuator is ~ 2.8 nN, while each branch needs a force of ~ 1.2-1.5 nN to release the cargo. The results demonstrate the validity of the method and applicability of the virtual sensor for assessing the microscopic forces. This investigation is a pioneer study for the advent of the sensor as an assessment tool for the mechanical analysis and precise atomic force studies.
Collapse
|
18
|
Mao S, Wang JW, Liu F, Zhu Z, Gao D, Guo Q, Xu P, Ma Z, Hou Y, Cheng X, Sun D, Lu F, Qin HM. Engineering of 3-ketosteroid-∆ 1-dehydrogenase based site-directed saturation mutagenesis for efficient biotransformation of steroidal substrates. Microb Cell Fact 2018; 17:141. [PMID: 30200975 PMCID: PMC6130075 DOI: 10.1186/s12934-018-0981-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/24/2018] [Indexed: 12/17/2022] Open
Abstract
Background Biosynthesis of steroidal drugs is of great benefit in pharmaceutical manufacturing as the process involves efficient enzymatic catalysis at ambient temperature and atmospheric pressure compared to chemical synthesis. 3-ketosteroid-∆1-dehydrogenase from Arthrobacter simplex (KsdD3) catalyzes 1,2-desaturation of steroidal substrates with FAD as a cofactor. Results Recombinant KsdD3 exhibited organic solvent tolerance. W117, F296, W299, et al., which were located in substrate-binding cavity, were predicted to form hydrophobic interaction with the substrate. Structure-based site-directed saturation mutagenesis of KsdD3 was performed with W299 mutants, which resulted in improved catalytic activities toward various steroidal substrates. W299A showed the highest increase in catalytic efficiency (kcat/Km) compared with the wild-type enzyme. Homology modelling revealed that the mutants enlarged the active site cavity and relieved the steric interference facilitating recognition of C17 hydroxyl/carbonyl steroidal substrates. Steered molecular dynamics simulations revealed that W299A/G decreased the potential energy barrier of association of substrates and dissociation of the corresponding products. The biotransformation of AD with enzymatic catalysis and resting cells harbouring KsdD3 WT/mutants revealed that W299A catalyzed the maximum ADD yields of 71 and 95% by enzymatic catalysis and resting cell conversion respectively, compared with the wild type (38 and 75%, respectively). Conclusions The successful rational design of functional KsdD3 greatly advanced our understanding of KsdD family enzymes. Structure-based site-directed saturation mutagenesis and biochemical data were used to design KsdD3 mutants with a higher catalytic activity and broader selectivity. ![]() Electronic supplementary material The online version of this article (10.1186/s12934-018-0981-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Shuhong Mao
- State Key Laboratory of Food Nutrition and Safety, Tianjin, People's Republic of China.,Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, People's Republic of China.,Tianjin Key Laboratory of Industrial Microbiology, Tianjin, People's Republic of China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Jian-Wen Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Fufeng Liu
- State Key Laboratory of Food Nutrition and Safety, Tianjin, People's Republic of China.,Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, People's Republic of China.,Tianjin Key Laboratory of Industrial Microbiology, Tianjin, People's Republic of China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Zhangliang Zhu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Dengke Gao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Qianqian Guo
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Panpan Xu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Zheng Ma
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Yali Hou
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Xiaotao Cheng
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Dengyue Sun
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Fuping Lu
- State Key Laboratory of Food Nutrition and Safety, Tianjin, People's Republic of China. .,Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, People's Republic of China. .,Tianjin Key Laboratory of Industrial Microbiology, Tianjin, People's Republic of China. .,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People's Republic of China. .,National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, People's Republic of China.
| | - Hui-Min Qin
- State Key Laboratory of Food Nutrition and Safety, Tianjin, People's Republic of China. .,Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, People's Republic of China. .,Tianjin Key Laboratory of Industrial Microbiology, Tianjin, People's Republic of China. .,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People's Republic of China. .,National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, People's Republic of China.
| |
Collapse
|
19
|
Tang M, Li T, Pickering E, Gandhi NS, Burrage K, Gu Y. Steered molecular dynamics characterization of the elastic modulus and deformation mechanisms of single natural tropocollagen molecules. J Mech Behav Biomed Mater 2018; 86:359-67. [PMID: 30015207 DOI: 10.1016/j.jmbbm.2018.07.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 06/30/2018] [Accepted: 07/04/2018] [Indexed: 11/21/2022]
Abstract
Collagen is a common structural protein, providing mechanical integrity for various vertebrate connective tissues such as cartilage and bone. The mechanical behaviours of these tissues under physical stimulations are controlled by the hierarchical structure of collagen and its interactions with other extracellular matrix molecules. However, the mechanical properties and deformation mechanisms of natural collagen under physiological loading rates at the molecular level are not fully understood. In this study, comprehensive steered molecular dynamics (SMD) simulations were performed on the 2nd intact overlap region (d2ol) and the 2nd intact D-period (d2olgp) of an in-situ characterized collagen molecule, under a large range of strain rates (6.5 × 106% s-1 to 1.3 × 1012% s-1). The results show that, depending on the applied strain rates, tropocollagen molecules unfold in different ways. Particularly, at high and intermediate strain rates, the number of inter-chain hydrogen bonds decreases rapidly even at small deformations, leading to a dramatic increase in the force. This results in an increase in the estimated Young's modulus of collagen triple helices as the deformation rate goes up, which, together with the nonlinear mechanical behaviour, explains the broad range of the Young's modulus for collagen model peptides reported in earlier SMD studies. Atomistic-level analyses indicate that the elastic modulus of single tropocollagen molecules decreases as the strain rate becomes smaller. However, for strain rates below 1.3 × 108% s-1, the tangent Young's modulus of d2ol (d2olgp) converges to approximately 3.2 GPa (3.4 GPa), at the strain of 10.5% (12%) when the segment is fully uncrimped. Furthermore, for strain rates under 1.3 × 108% s-1, d2ol and d2olgp show identical deformation mechanisms (unwinding, uncoiling and backbone stretching), but the corresponding strain ranges are different. This study will aid in future studies on characterizing the mechanical properties of collagen molecules and collagen-like peptides by indicating the proper pulling strain rates and how to determine the suitable strain range used for evaluating the elastic modulus.
Collapse
|
20
|
Lee M, Choi H, Yoon G, Na S. Loading-device effects on the protein-unfolding mechanisms using molecular-dynamic simulations. J Mol Graph Model 2018; 81:162-167. [PMID: 29554493 DOI: 10.1016/j.jmgm.2018.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/12/2018] [Accepted: 03/10/2018] [Indexed: 10/17/2022]
Abstract
Experimental force spectroscopy has been effectively utilized for measuring structural characterization of biomolecules and mechanical properties of biomaterials. Specifically, atomic force microscopy (AFM) has been widely used to portray biomolecular characterization in single-molecule experiment by observing the unfolding behavior of the proteins. Not only the experimental techniques enable us to characterize globular protein, but computational methods like molecular dynamics (MD) also gives insight into understanding biomolecular structures. To better comprehend the behavior of biomolecules, conditions such as pulling velocities and loading rates are put to the test, yet there are still limitations in understanding the unfolding behavior of biomolecules with the effect of different loading devices. In this study, we performed an all-atom MD and steered molecular dynamics (SMD) simulations considering different loading device effects such as "soft" and "stiff" to characterize the anisotropic unfolding behavior of ubiquitin protein. We found out the anisotropic unfolding pathways of the protein through the broken number of hydrogen bonds and geometric secondary structures of the biomolecule. Our study provides the importance for usage of various loading-devices on biomolecules when analyzing the structural compositions and the characteristics of globular biomolecules.
Collapse
Affiliation(s)
- Myeongsang Lee
- Institute of Advanced Machinery Design Technology, Korea University, 02841, Seoul, Republic of Korea
| | - Hyunsung Choi
- Department of Mechanical Engineering, Korea University, 02841, Seoul, Republic of Korea
| | - Gwonchan Yoon
- Department of Mechanical Engineering, Korea University, 02841, Seoul, Republic of Korea; Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, TX, 79409, USA
| | - Sungsoo Na
- Department of Mechanical Engineering, Korea University, 02841, Seoul, Republic of Korea.
| |
Collapse
|
21
|
Xue YL, Zhou L, Sun Y, Li H, Jones GW, Song Y. Steered molecular dynamics simulation of the binding of the bovine auxilin J domain to the Hsc70 nucleotide-binding domain. J Mol Model 2017; 23:320. [PMID: 29063205 DOI: 10.1007/s00894-017-3453-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 09/05/2017] [Indexed: 11/25/2022]
Abstract
The Hsp70 and Hsp40 chaperone machine plays critical roles in protein folding, membrane translocation, and protein degradation by binding and releasing protein substrates in a process that utilizes ATP. The activities of the Hsp70 family of chaperones are recruited and stimulated by the J domains of Hsp40 chaperones. However, structural information on the Hsp40-Hsp70 complex is lacking, and the molecular details of this interaction are yet to be elucidated. Here we used steered molecular dynamics (SMD) simulations to investigate the molecular interactions that occur during the dissociation of the auxilin J domain from the Hsc70 nucleotide-binding domain (NBD). The changes in energy observed during the SMD simulation suggest that electrostatic interactions are the dominant type of interaction. Additionally, we found that Hsp70 mainly interacts with auxilin through the surface residues Tyr866, Arg867, and Lys868 of helix II, His874, Asp876, Lys877, Thr879, and Gln881 of the HPD loop, and Phe891, Asn895, Asp896, and Asn903 of helix III. The conservative residues Tyr866, Arg867, Lys868, His874, Asp876, Lys877, and Phe891 were also found in a previous study to be indispensable to the catalytic activity of the DnaJ J domain and the binding of it with the NBD of DnaK. The in silico identification of the importance of auxilin residues Asn895, Asp896, and Asn903 agrees with previous mutagenesis and NMR data suggesting that helix III of the J domain of the T antigen interacts with Hsp70. Furthermore, our data indicate that Thr879 and Gln881 from the HPD loop are also important as they mediate the interaction between the bovine auxilin J domain and Hsc70.
Collapse
Affiliation(s)
- You-Lin Xue
- School of Environmental Science, Liaoning University, Shenyang, 110036, China.,College of Light Industry, Liaoning University, Shenyang, 110036, China
| | - Lei Zhou
- School of Environmental Science, Liaoning University, Shenyang, 110036, China
| | - Yuna Sun
- Province Key Laboratory of Animal Resource and Epidemic Disease Prevention, College of Life Science, Liaoning University, Shenyang, 110036, China
| | - Hui Li
- Province Key Laboratory of Animal Resource and Epidemic Disease Prevention, College of Life Science, Liaoning University, Shenyang, 110036, China
| | - Gary W Jones
- Centre for Biomedical Science Research, School of Clinical and Applied Sciences, Leeds Beckett University, Leeds, LS1 3HE, UK
| | - Youtao Song
- School of Environmental Science, Liaoning University, Shenyang, 110036, China. .,Province Key Laboratory of Animal Resource and Epidemic Disease Prevention, College of Life Science, Liaoning University, Shenyang, 110036, China.
| |
Collapse
|
22
|
Thai NQ, Nguyen HL, Linh HQ, Li MS. Protocol for fast screening of multi-target drug candidates: Application to Alzheimer's disease. J Mol Graph Model 2017; 77:121-129. [PMID: 28850894 DOI: 10.1016/j.jmgm.2017.08.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/03/2017] [Accepted: 08/04/2017] [Indexed: 01/08/2023]
Abstract
The treatment of many diseases may require drugs that are capable to attack multiple targets simultaneously. Obviously, the virtual screening of multi-target drug candidates is much more time consuming compared to the single-target case. This, in particular, concerns the last step of virtual screening where the binding free energy is computed by conventional molecular dynamics simulation. To overcome this difficulty we propose a simple protocol which is relied on the fast steered molecular dynamics simulation and on available experimental data on binding affinity of reference ligand to a given target. Namely, first we compute non-equilibrium works generated during pulling ligands from the binding site using the steered molecular dynamics method. Then as top leads we choose only those compounds that have the non-equilibrium work larger than that of a reference compound for which the binding free energy has been already known from experiment. Despite many efforts no cures for AD (Alzheimer's disease) have been found. One of possible reasons for this failure is that drug candidates were developed for a single target, while there are exist many possible pathways to AD. Applying our new protocol to five targets including amyloid beta fibril, peroxisome proliferator-activated receptor γ, retinoic X receptor α, β- and γ-secretases, we have found two potential drugs (CID 16040294 and CID 9998128) for AD from the large PubChem database. We have also shown that these two ligands can interfere with the activity of popular Acetylcholinesterase target through strong binding towards it.
Collapse
Affiliation(s)
- Nguyen Quoc Thai
- Institute for Computational Sciences and Technology,SBI building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Viet Nam; Dong Thap University,783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Viet Nam; Biomedical Engineering Department, University of Technology -VNU HCM, 268 Ly Thuong Kiet Str., Distr. 10, Ho Chi Minh City, Viet Nam
| | - Hoang Linh Nguyen
- Institute for Computational Sciences and Technology,SBI building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Viet Nam
| | - Huynh Quang Linh
- Biomedical Engineering Department, University of Technology -VNU HCM, 268 Ly Thuong Kiet Str., Distr. 10, Ho Chi Minh City, Viet Nam
| | - Mai Suan Li
- Institute for Computational Sciences and Technology,SBI building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Viet Nam; Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| |
Collapse
|
23
|
Ghosh S, Chandar NB, Jana K, Ganguly B. Revealing the importance of linkers in K-series oxime reactivators for tabun-inhibited AChE using quantum chemical, docking and SMD studies. J Comput Aided Mol Des 2017. [PMID: 28646405 DOI: 10.1007/s10822-017-0036-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Inhibition of acetylcholinesterase (AChE) with organophosphorus compounds has a detrimental effect on human life. Oxime K203 seems to be one of the promising reactivators for tabun-inhibited AChE than (K027, K127, and K628). These reactivators differ only in the linker units between the two pyridinium rings. The conformational analyses performed with quantum chemical RHF/6-31G* level for K027, K127, K203 and K628 showed that the minimum energy conformers have different orientations of the active and peripheral pyridinium rings for these reactivator molecules. K203 with (-CH2-CH=CH-CH2-) linker unit possesses more open conformation compared to the other reactivators. Such orientation of K203 experiences favorable interaction with the surrounding residues of catalytic anionic site (CAS) and peripheral anionic site (PAS) of tabun-inhibited AChE. From the steered molecular dynamics simulations, it has been observed that the oxygen atom of the oxime group of K203 reactivator approaches nearest to the P-atom of the SUN203 (3.75 Å) at lower time scales (less than ~1000 ps) as compared to the other reactivators. K203 experiences less number of hydrophobic interaction with the PAS residues which is suggested to be an important factor for the efficient reactivation process. In addition, K203 crates large number of H-bonding with CAS residues SUN203, Phe295, Tyr337, Phe338 and His447. K203 barely changes its conformation during the SMD simulation process and hence the energy penalty to adopt any other conformation is minimal in this case as compared to the other reactivators. The molecular mechanics and Poisson-Boltzmann surface area binding energies obtained for the interaction of K203 inside the gorge of tabun inhibited AChE is substantially higher (-290.2 kcal/mol) than the corresponding K628 reactivator (-260.4 kcal/mol), which also possess unsaturated aromatic linker unit.
Collapse
Affiliation(s)
- Shibaji Ghosh
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364 002, India.,Academy of Scientific and Innovative Research, CSIR-CSMCRI, Bhavnagar, Gujarat, 364 002, India
| | - Nellore Bhanu Chandar
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364 002, India.,Academy of Scientific and Innovative Research, CSIR-CSMCRI, Bhavnagar, Gujarat, 364 002, India
| | - Kalyanashis Jana
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364 002, India.,Academy of Scientific and Innovative Research, CSIR-CSMCRI, Bhavnagar, Gujarat, 364 002, India
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364 002, India. .,Academy of Scientific and Innovative Research, CSIR-CSMCRI, Bhavnagar, Gujarat, 364 002, India.
| |
Collapse
|
24
|
Zhao X, Liu Y, Guo Z, Zhang Y, Li Y, Liu W. Mechanical response and deformation mechanics of Type IV pili investigated using steered coarse-grained molecular dynamics simulation. J Biomech 2017; 56:97-101. [PMID: 28365063 DOI: 10.1016/j.jbiomech.2017.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/09/2017] [Accepted: 03/11/2017] [Indexed: 12/20/2022]
Abstract
Type IV pili are long filamentous structures on the surface of bacteria, which can be rapidly assembled or disassembled with pilin subunits by molecular motors. They can generate force during retraction and are involved in many bacterial functions. Steered molecular dynamics simulations with coarse-grained MARTINI models are carried out to investigate the mechanical behaviors of pili under tension. Our study is the first to report a Young's modulus of 0.80±0.07GPa and a spring constant of 1294.6±116.5kJmol-1nm-2 for pilus. Our results show the mechanical responses of pili are different from those described by the worm-like chain model and the van der Waal's interactions play a critical role in the mechanical responses. Moreover, the effects of pulling rates and virtual spring constants of pilus on Young's modulus are studied and two distinct morphological stages with the conformational changes appear during the extension of pilus are observed. This work provide insight into the mechanics and the deformation mechanism of pilus assembly.
Collapse
Affiliation(s)
- Xiaoxi Zhao
- School of Water Conservancy and Environmental Engineering, Zhengzhou University, Zhengzhou 450001, China; Department of Modern Mechanics, University of Science and Technology of China, Hefei 230026, China
| | - Yankai Liu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhouhang Guo
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yizhe Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yongchi Li
- Department of Modern Mechanics, University of Science and Technology of China, Hefei 230026, China
| | - Wei Liu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China.
| |
Collapse
|
25
|
Kitao A, Nishihara Y. Structure of the MotA/B Proton Channel. Methods Mol Biol 2017; 1593:133-45. [PMID: 28389950 DOI: 10.1007/978-1-4939-6927-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Flagellar motors utilize the motive force of protons and other ions as an energy source. To elucidate the mechanisms of ion permeation and torque generation, it is essential to investigate the structure of the motor stator complex; however, the atomic structure of the transmembrane region of the stator has not been determined experimentally. We recently constructed an atomic model structure of the transmembrane region of the Escherichia coli MotA/B stator complex based on previously published disulfide cross-linking and tryptophan scanning mutations. Dynamic permeation by hydronium ions, sodium ions, and water molecules was then observed using steered molecular dynamics simulations, and free energy profiles for ion/water permeation were calculated using umbrella sampling. We also examined the possible ratchet motion of the cytoplasmic domain induced by the protonation/deprotonation cycle of the MotB proton binding site, Asp32. In this chapter, we describe the methods used to conduct these analyses, including atomic structure modeling of the transmembrane region of the MotA/B complex; molecular dynamics simulations in equilibrium and in ion permeation processes; and ion permeation-free energy profile calculations.
Collapse
|
26
|
Ferreira MF, Franca EF, Leite FL. Unbinding pathway energy of glyphosate from the EPSPs enzyme binding site characterized by Steered Molecular Dynamics and Potential of Mean Force. J Mol Graph Model 2017; 72:43-49. [PMID: 28033555 DOI: 10.1016/j.jmgm.2016.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/13/2016] [Accepted: 11/14/2016] [Indexed: 10/20/2022]
Abstract
The quantification of herbicides in the environment, like glyphosate, is extremely important to prevent contamination. Nanobiosensors stands out in the quantization process, because of the high selectivity, sensitivity and short response time of the method. In order to emulate the detection of glyphosate using a specific nanobiossensor through an Atomic Force Microscope (AFM), this work carried out Steered Molecular Dynamics simulations (SMD) in which the herbicide was unbinded from the active site of the enzyme 5- enolpyruvylshikimate 3 phosphate synthase (EPSPS) along three different directions.After the simulations, Potential of Mean Force calculations were carried, from a cumulant expansion of Jarzynski's equation to obtain the profile of free energy of interaction between the herbicide and the active site of the enzyme in the presence of shikimate-3 substrate phosphate (S3P). The set of values for external work, had a Gaussian distribution. The PMF values ranged according to the directions of the unbindong pahway of each simulation, displaying energy values of 10.7, 14.7 and 19.5KJmol-1. The results provide a theoretical support in order to assist the construction of a specific nanobiossensor to quantify the glyphosate herbicide.
Collapse
Affiliation(s)
- Moacir F Ferreira
- Instituto de Química, Universidade Federal de Uberlândia, 38408-100, Uberlândia, MG, Brazil.
| | - Eduardo F Franca
- Instituto de Química, Universidade Federal de Uberlândia, 38408-100, Uberlândia, MG, Brazil
| | - Fábio L Leite
- Universidade Federal de São Carlos, 18052-780, Sorocaba, SP, Brazil
| |
Collapse
|
27
|
Meshach Paul D, Rajasekaran R. In silico approach to explore the disruption in the molecular mechanism of human hyaluronidase 1 by mutant E268K that directs Natowicz syndrome. Eur Biophys J 2016; 46:157-169. [PMID: 27424109 DOI: 10.1007/s00249-016-1151-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/02/2016] [Accepted: 07/01/2016] [Indexed: 01/27/2023]
Abstract
Natowicz syndrome (mucopolysaccharidoses type 9) is a lysosomal storage disorder caused by deficient or defective human hyaluronidase 1. The disorder is not well studied at the molecular level. Therefore, a new in silico approach was proposed to study the molecular basis on which one clinically observed mutation, Glu268Lys, results in a defective enzyme. The native and mutant structures were subjected to comparative analyses using a conformational sampling approach for geometrical variables viz, RMSF, RMSD, and Ramachandran plot. In addition, the strength of a Cys207-Cys221 disulfide bond and electrostatic interaction between Arg265 and Asp206 were studied, as they are known to be involved in the catalytic activity of the enzyme. Native and mutant E268K showed statistically significant variations with p < 0.05 in RMSD, Ramachandran plot, strengths of disulfide bond, and electrostatic interactions. Further, single model analysis showed variations between native and mutant structures in terms of intra-protein interactions, hydrogen bond dilution, secondary structure, and dihedral angles. Docking analysis predicted the mutant to have a less favorable substrate binding energy compared to the native protein. Additionally, steered MD analysis indicated that the substrate should have more affinity to the native than mutant enzymes. The observed changes theoretically explain the less favorable binding energy of substrate towards mutant E268K, thereby providing a structural basis for its reduced catalytic activity. Hence, our study provides a basis for understanding the disruption in the molecular mechanism of human hyaluronidase 1 by mutation E268K, which may prove useful for the development of synthetic chaperones as a treatment option for Natowicz syndrome.
Collapse
Affiliation(s)
- D Meshach Paul
- Computational Biology Lab, Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - R Rajasekaran
- Computational Biology Lab, Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India.
| |
Collapse
|
28
|
Rocheleau AD, Cao TM, Takitani T, King MR. Comparison of human and mouse E-selectin binding to Sialyl-Lewis(x). BMC Struct Biol 2016; 16:10. [PMID: 27368167 PMCID: PMC4930595 DOI: 10.1186/s12900-016-0060-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/21/2016] [Indexed: 12/22/2022]
Abstract
Background During inflammation, leukocytes are captured by the selectin family of adhesion receptors lining blood vessels to facilitate exit from the bloodstream. E-selectin is upregulated on stimulated endothelial cells and binds to several ligands on the surface of leukocytes. Selectin:ligand interactions are mediated in part by the interaction between the lectin domain and Sialyl-Lewis x (sLex), a tetrasaccharide common to selectin ligands. There is a high degree of homology between selectins of various species: about 72 and 60 % in the lectin and EGF domains, respectively. In this study, molecular dynamics, docking, and steered molecular dynamics simulations were used to compare the binding and dissociation mechanisms of sLex with mouse and human E-selectin. First, a mouse E-selectin homology model was generated using the human E-selectin crystal structure as a template. Results Mouse E-selectin was found to have a greater interdomain angle, which has been previously shown to correlate with stronger binding among selectins. sLex was docked onto human and mouse E-selectin, and the mouse complex was found to have a higher free energy of binding and a lower dissociation constant, suggesting stronger binding. The mouse complex had higher flexibility in a few key residues. Finally, steered molecular dynamics was used to dissociate the complexes at force loading rates of 2000–5000 pm/ps2. The mouse complex took longer to dissociate at every force loading rate and the difference was statistically significant at 3000 pm/ps2. When sLex-coated microspheres were perfused through microtubes coated with human or mouse E-selectin, the particles rolled more slowly on mouse E-selectin. Conclusions Both molecular dynamics simulations and microsphere adhesion experiments show that mouse E-selectin protein binds more strongly to sialyl Lewis x ligand than human E-selectin. This difference was explained by a greater interdomain angle for mouse E-selectin, and greater flexibility in key residues. Future work could introduce similar amino acid substitutions into the human E-selectin sequence to further modulate adhesion behavior.
Collapse
Affiliation(s)
- Anne D Rocheleau
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Thong M Cao
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Tait Takitani
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Michael R King
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
29
|
Nguyen TT, Tran DP, Hoang Z, Carloni P, Van Pham P, Nguyen C, Li MS. Ligand binding to anti-cancer target CD44 investigated by molecular simulations. J Mol Model 2016; 22:165. [PMID: 27342250 DOI: 10.1007/s00894-016-3029-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/31/2016] [Indexed: 12/31/2022]
Abstract
CD44 is a cell-surface glycoprotein and receptor for hyaluronan, one of the major components of the tumor extracellular matrix. There is evidence that the interaction between CD44 and hyaluronan promotes breast cancer metastasis. Recently, the molecule F-19848A was shown to inhibit hyaluronan binding to receptor CD44 in a cell-based assay. In this study, we investigated the mechanism and energetics of F-19848A binding to CD44 using molecular simulation. Using the molecular mechanics/Poisson Boltzmann surface area (MM-PBSA) method, we obtained the binding free energy and inhibition constant of the complex. The van der Waals (vdW) interaction and the extended portion of F-19848A play key roles in the binding affinity. We screened natural products from a traditional Chinese medicine database to search for CD44 inhibitors. From combining pharmaceutical requirements with docking and molecular dynamics simulations, we found ten compounds that are potentially better or equal to the F-19848A ligand at binding to CD44 receptor. Therefore, we have identified new candidates of CD44 inhibitors, based on molecular simulation, which may be effective small molecules for the therapy of breast cancer.
Collapse
Affiliation(s)
- Tin Trung Nguyen
- Institute for Computational Sciences and Technology, SBI building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Duy Phuoc Tran
- University of Technology, Vietnam National University-Ho Chi Minh City, 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City, Vietnam
| | - Zung Hoang
- Center for Molecular and NanoArchitecture (MANAR), Vietnam National University-Ho Chi Minh City, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Juelich, Juelich, Germany.
| | - Phuc Van Pham
- Stem Cell Research and Application Laboratory, University of Science, Vietnam National University, Ho Chi Minh City, Vietnam.
| | - Chuong Nguyen
- Theoretical Physics Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668, Warsaw, Poland.
| |
Collapse
|
30
|
Ghodsi H, Darvish K. Characterization of the viscoelastic behavior of a simplified collagen micro-fibril based on molecular dynamics simulations. J Mech Behav Biomed Mater 2016; 63:26-34. [PMID: 27341288 DOI: 10.1016/j.jmbbm.2016.06.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/31/2016] [Accepted: 06/04/2016] [Indexed: 10/21/2022]
Abstract
Collagen fibril is a major component of connective tissues such as bone, tendon, blood vessels, and skin. The mechanical properties of this highly hierarchical structure are greatly influenced by the presence of covalent cross-links between individual collagen molecules. This study investigates the viscoelastic behavior of a collagen lysine-lysine cross-link based on creep simulations with applied forces in the range or 10 to 2000pN using steered molecular dynamics (SMD). The viscoelastic model of the cross-link was combined with a system composed by two segments of adjacent collagen molecules hence representing a reduced viscoelastic model for a simplified micro-fibril. It was found that the collagen micro-fibril assembly had a steady-state Young׳s modulus ranging from 2.24 to 3.27GPa, which is in agreement with reported experimental measurements. The propagation of longitudinal force wave along the molecule was implemented by adding a delay element to the model. The force wave speed was found to be correlated with the speed of one-dimensional elastic waves in rods. The presented reduced model with three degrees of freedom can serve as a building block for developing models of the next level of hierarchy, i.e., a collagen fibril.
Collapse
Affiliation(s)
- Hossein Ghodsi
- Department of Mechanical Engineering, College of Engineering, Temple University, 1947N. 12th street, Philadelphia, PA 19122, USA.
| | - Kurosh Darvish
- Department of Mechanical Engineering, College of Engineering, Temple University, 1947N. 12th street, Philadelphia, PA 19122, USA.
| |
Collapse
|
31
|
Qu T, Verma D, Alucozai M, Tomar V. Influence of interfacial interactions on deformation mechanism and interface viscosity in α-chitin-calcite interfaces. Acta Biomater 2015; 25:325-38. [PMID: 26143601 DOI: 10.1016/j.actbio.2015.06.034] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 06/16/2015] [Accepted: 06/30/2015] [Indexed: 11/16/2022]
Abstract
The interfaces between organic and inorganic phases in natural materials have a significant effect on their mechanical properties. This work presents a quantification of the interface stress as a function of interface chemical changes (water, organic molecules) in chitin-calcite (CHI-CAL) interfaces using classical non-equilibrium molecular dynamics (NEMD) simulations and steered molecular dynamics (SMD) simulations. NEMD is used to investigate interface stress as a function of applied strain based on the virial stress formulation. SMD is used to understand interface separation mechanism and to calculate interfacial shear stress based on a viscoplastic interfacial sliding model. Analyses indicate that interfacial shear stress combined with shear viscosity can result in variations to the mechanical properties of the examined interfacial material systems. It is further verified with Kelvin-Voigt and Maxwell viscoelastic analytical models representing viscous interfaces and outer matrix. Further analyses show that overall mechanical deformation depends on maximization of interface shear strength in such materials. This work establishes lower and upper bounds of interface strength in the interfaces examined.
Collapse
Affiliation(s)
- Tao Qu
- School of Aeronautics and Astronautics, Purdue University, IN 47907, USA
| | - Devendra Verma
- School of Aeronautics and Astronautics, Purdue University, IN 47907, USA
| | - Milad Alucozai
- School of Aeronautics and Astronautics, Purdue University, IN 47907, USA
| | - Vikas Tomar
- School of Aeronautics and Astronautics, Purdue University, IN 47907, USA.
| |
Collapse
|
32
|
Ghodsi H, Darvish K. Investigation of mechanisms of viscoelastic behavior of collagen molecule. J Mech Behav Biomed Mater 2015; 51:194-204. [PMID: 26256473 DOI: 10.1016/j.jmbbm.2015.07.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 07/06/2015] [Accepted: 07/16/2015] [Indexed: 11/18/2022]
Abstract
Unique mechanical properties of collagen molecule make it one of the most important and abundant proteins in animals. Many tissues such as connective tissues rely on these properties to function properly. In the past decade, molecular dynamics (MD) simulations have been used extensively to study the mechanical behavior of molecules. For collagen, MD simulations were primarily used to determine its elastic properties. In this study, constant force steered MD simulations were used to perform creep tests on collagen molecule segments. The mechanical behavior of the segments, with lengths of approximately 20 (1X), 38 (2X), 74 (4X), and 290 nm (16X), was characterized using a quasi-linear model to describe the observed viscoelastic responses. To investigate the mechanisms of the viscoelastic behavior, hydrogen bonds (H-bonds) rupture/formation time history of the segments were analyzed and it was shown that the formation growth rate of H-bonds in the system is correlated with the creep growth rate of the segment (β=2.41βH). In addition, a linear relationship between H-bonds formation growth rate and the length of the segment was quantified. Based on these findings, a general viscoelastic model was developed and verified here, using the smallest segment as a building block, the viscoelastic properties of larger segments could be predicted. In addition, the effect of temperature control methods on the mechanical properties were studied, and it was shown that application of Langevin Dynamics had adverse effect on these properties while the Lowe-Anderson method was shown to be more appropriate for this application. This study provides information that is essential for multi-scale modeling of collagen fibrils using a bottom-up approach.
Collapse
Affiliation(s)
- Hossein Ghodsi
- Department of Mechanical Engineering, College of Engineering, Temple University, 1947N. 12th Street, Philadelphia, PA 19122, USA.
| | - Kurosh Darvish
- Department of Mechanical Engineering, College of Engineering, Temple University, 1947N. 12th Street, Philadelphia, PA 19122, USA.
| |
Collapse
|
33
|
Chinnadurai RK, Saravanaraman P, Boopathy R. Understanding the molecular mechanism of aryl acylamidase activity of acetylcholinesterase - An in silico study. Arch Biochem Biophys 2015; 580:1-13. [PMID: 26072115 DOI: 10.1016/j.abb.2015.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 06/03/2015] [Accepted: 06/04/2015] [Indexed: 11/30/2022]
Abstract
Acetylcholinesterase (AChE) exhibits two different activities, namely esterase and aryl acylamidase (AAA). Unlike esterase, AAA activity of AChE is inhibited by the active site inhibitors while remaining unaffected by the peripheral anionic site inhibitors. This differential inhibitory pattern of active and peripheral anionic site inhibitors on the AAA activity remains unanswered. To answer this, we investigated the mechanism of binding and trafficking of AAA substrates using in silico tools. Molecular docking of serotonin and AAA substrates (o-nitroacetanilide, and o-nitrotrifluoroacetanilide,) onto AChE shows that these compounds bind at the side door of AChE. Thus, we conceived that the AAA substrates prefer the side door to reach the active site for their catalysis. Further, steered molecular dynamics simulations show that the force required for binding and trafficking of the AAA substrate through the side door is comparatively lesser than their dissociation (900kJ/mol/nm). Among the two substrates, o-nitrotrifluoroacetanilide required lesser force (380kJ/mol/nm) than o-nitroacetanilide the (550kJ/mol/nm) for its binding, thus validating o-nitrotrifluoroacetanilide as a better substrate. With these observations, we resolve that the AAA activity of AChE is mediated through its side door. Therefore, binding of PAS inhibitors at the main door of AChE remain ineffective against AAA activity.
Collapse
Affiliation(s)
- Raj Kumar Chinnadurai
- Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu 641046, India
| | - Ponne Saravanaraman
- Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu 641046, India
| | - Rathanam Boopathy
- Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu 641046, India.
| |
Collapse
|
34
|
Lee M, Chang HJ, Kim D, Lee Y, Suh H, Ahn N, Yoon G, Na S. Relationship between structural composition and material properties of polymorphic hIAPP fibrils. Biophys Chem 2015; 199:1-8. [PMID: 25682214 DOI: 10.1016/j.bpc.2015.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/14/2015] [Accepted: 02/02/2015] [Indexed: 01/21/2023]
Abstract
Amyloid proteins are misfolded, denatured proteins that are responsible for causing several degenerative and neuro-degenerative diseases. Determining the mechanical stability of these amyloids is crucial for understanding the disease mechanisms, which will guide us in treatment. Furthermore, many research groups recognized amyloid proteins as functional biological materials that can be used in nanosensors, bacterial biofilms, coatings, etc. Many in vitro studies have been carried out to determine the characteristics of amyloid proteins via force spectroscopy methods, atomic force microscopy, and optical tweezers. However, computational methods (e.g. molecular dynamics and elastic network model) not only reveal the mechanical properties of the amyloid proteins, but also provide more in-depth information about the amyloids by presenting a visualization of their conformational changes. In this study, we evaluated the various material properties and behaviors of four different polymorphic structures of human islet amyloid polypeptide (hIAPP) by using steered molecular dynamics (SMD) simulations under tensile conditions. From our results, we examined how these mechanical properties may differ with respect to the structural formation of amyloid proteins.
Collapse
|
35
|
Abstract
Riboswitches are RNA sequences located in noncoding portions of mRNA that can sense specific ligands and subsequently control gene expression. The ligand-binding event induces conformational changes in the riboswitch that are then transmitted to the gene expression apparatus. Probing the mechanisms of such a fine regulation at atomic resolution is very difficult experimentally and molecular dynamics (MD) could be used to quantify the ligand-dependent behavior of a riboswitch. However, since the accessible time scale of fully atomistic simulations is limited, this can only be done using enhanced sampling techniques. Here, we discuss the application of steered MD to the characterization of the ligand-dependent stability of the aptamer terminal helix in the add adenine-sensing riboswitch. The employed techniques are discussed in detail and sample input files are provided. We show that with a limited computational effort it is possible to quantify, in terms of free energy, the stacking interaction between the ligand and the terminal helix, obtaining results in agreement with thermodynamic experiments.
Collapse
Affiliation(s)
- Francesco Di Palma
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Francesco Colizzi
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.
| |
Collapse
|
36
|
Wagner C, Olbrich C, Brutzer H, Salomo M, Kleinekathöfer U, Keyser UF, Kremer F. DNA condensation by TmHU studied by optical tweezers, AFM and molecular dynamics simulations. J Biol Phys 2010; 37:117-31. [PMID: 22210966 DOI: 10.1007/s10867-010-9203-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 09/20/2010] [Indexed: 11/24/2022] Open
Abstract
The compaction of DNA by the HU protein from Thermotoga maritima (TmHU) is analysed on a single-molecule level by the usage of an optical tweezers-assisted force clamp. The condensation reaction is investigated at forces between 2 and 40 pN applied to the ends of the DNA as well as in dependence on the TmHU concentration. At 2 and 5 pN, the DNA compaction down to 30% of the initial end-to-end distance takes place in two regimes. Increasing the force changes the progression of the reaction until almost nothing is observed at 40 pN. Based on the results of steered molecular dynamics simulations, the first regime of the length reduction is assigned to a primary level of DNA compaction by TmHU. The second one is supposed to correspond to the formation of higher levels of structural organisation. These findings are supported by results obtained by atomic force microscopy.
Collapse
|