1
|
Sheikhzadeh A, Safaei M, Fadaei Naeini V, Baghani M, Foroutan M, Baniassadi M. Multiscale modeling of unfolding and bond dissociation of rubredoxin metalloprotein. J Mol Graph Model 2024; 129:108749. [PMID: 38442439 DOI: 10.1016/j.jmgm.2024.108749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 03/07/2024]
Abstract
Mechanical properties of proteins that have a crucial effect on their operation. This study used a molecular dynamics simulation package to investigate rubredoxin unfolding on the atomic scale. Different simulation techniques were applied, and due to the dissociation of covalent/hydrogen bonds, this protein demonstrates several intermediate states in force-extension behavior. A conceptual model based on the cohesive finite element method was developed to consider the intermediate damages that occur during unfolding. This model is based on force-displacement curves derived from molecular dynamics results. The proposed conceptual model is designed to accurately identify bond rupture points and determine the associated forces. This is achieved by conducting a thorough comparison between molecular dynamics and cohesive finite element results. The utilization of a viscoelastic cohesive zone model allows for the consideration of loading rate effects. This rate-dependent model can be further developed and integrated into the multiscale modeling of large assemblies of metalloproteins, providing a comprehensive understanding of mechanical behavior while maintaining a reduced computational cost.
Collapse
Affiliation(s)
- Aliakbar Sheikhzadeh
- School of Mechanical Engineering, College of Engineering, University of Tehran, Tehran, Iran; Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, T6G 2V4, Canada
| | - Mohammad Safaei
- School of Mechanical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Vahid Fadaei Naeini
- Division of Machine Elements, Luleå University of Technology, Luleå, SE-97187, Sweden
| | - Mostafa Baghani
- School of Mechanical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Masumeh Foroutan
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran.
| | - Majid Baniassadi
- School of Mechanical Engineering, College of Engineering, University of Tehran, Tehran, Iran; University of Strasbourg, CNRS, ICUBE Laboratory, Strasbourg, France.
| |
Collapse
|
2
|
Maghsoud Y, Dong C, Cisneros GA. Computational Characterization of the Inhibition Mechanism of Xanthine Oxidoreductase by Topiroxostat. ACS Catal 2023; 13:6023-6043. [PMID: 37547543 PMCID: PMC10399974 DOI: 10.1021/acscatal.3c01245] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Xanthine oxidase (XO) is a member of the molybdopterin-containing enzyme family. It interconverts xanthine to uric acid as the last step of purine catabolism in the human body. The high uric acid concentration in the blood directly leads to human diseases like gout and hyperuricemia. Therefore, drugs that inhibit the biosynthesis of uric acid by human XO have been clinically used for many years to decrease the concentration of uric acid in the blood. In this study, the inhibition mechanism of XO and a new promising drug, topiroxostat (code: FYX-051), is investigated by employing molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations. This drug has been reported to act as both a noncovalent and covalent inhibitor and undergoes a stepwise inhibition by all its hydroxylated metabolites, which include 2-hydroxy-FYX-051, dihydroxy-FYX-051, and trihydroxy-FYX-051. However, the detailed mechanism of inhibition of each metabolite remains elusive and can be useful for designing more effective drugs with similar inhibition functions. Hence, herein we present the computational investigation of the structural and dynamical effects of FYX-051 and the calculated reaction mechanism for all of the oxidation steps catalyzed by the molybdopterin center in the active site. Calculated results for the proposed reaction mechanisms for each metabolite's inhibition reaction in the enzyme's active site, binding affinities, and the noncovalent interactions with the surrounding amino acid residues are consistent with previously reported experimental findings. Analysis of the noncovalent interactions via energy decomposition analysis (EDA) and noncovalent interaction (NCI) techniques suggests that residues L648, K771, E802, R839, L873, R880, R912, F914, F1009, L1014, and A1079 can be used as key interacting residues for further hybrid-type inhibitor development.
Collapse
Affiliation(s)
- Yazdan Maghsoud
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Chao Dong
- Department of Chemistry and Physics, The University of Texas Permian Basin, Odessa, Texas 79762, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States; Department of Physics, The University of Texas at Dallas, Richardson, Texas 75080, United States
| |
Collapse
|
3
|
Effects of Active-Center Reduction of Plant-Type Ferredoxin on Its Structure and Dynamics: Computational Analysis Using Molecular Dynamics Simulations. Int J Mol Sci 2022; 23:ijms232415913. [PMID: 36555561 PMCID: PMC9782105 DOI: 10.3390/ijms232415913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
"Plant-type" ferredoxins (Fds) in the thylakoid membranes of plants, algae, and cyanobacteria possess a single [2Fe-2S] cluster in active sites and mediate light-induced electron transfer from Photosystem I reaction centers to various Fd-dependent enzymes. Structural knowledge of plant-type Fds is relatively limited to static structures, and the detailed behavior of oxidized and reduced Fds has not been fully elucidated. It is important that the investigations of the effects of active-center reduction on the structures and dynamics for elucidating electron-transfer mechanisms. In this study, model systems of oxidized and reduced Fds were constructed from the high-resolution crystal structure of Chlamydomonas reinhardtii Fd1, and three 200 ns molecular dynamics simulations were performed for each system. The force field parameters of the oxidized and reduced active centers were independently obtained using quantum chemical calculations. There were no substantial differences in the global conformations of the oxidized and reduced forms. In contrast, active-center reduction affected the hydrogen-bond network and compactness of the surrounding residues, leading to the increased flexibility of the side chain of Phe61, which is essential for the interaction between Fd and the target protein. These computational results will provide insight into the electron-transfer mechanisms in the Fds.
Collapse
|
4
|
Burastero O, Defelipe LA, Gola G, Tateosian NL, Lopez ED, Martinena CB, Arcon JP, Traian MD, Wetzler DE, Bento I, Barril X, Ramirez J, Marti MA, Garcia-Alai MM, Turjanski AG. Cosolvent Sites-Based Discovery of Mycobacterium Tuberculosis Protein Kinase G Inhibitors. J Med Chem 2022; 65:9691-9705. [PMID: 35737472 PMCID: PMC9344462 DOI: 10.1021/acs.jmedchem.1c02012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Computer-aided
drug discovery methods play a major role in the
development of therapeutically important small molecules, but their
performance needs to be improved. Molecular dynamics simulations in
mixed solvents are useful in understanding protein–ligand recognition
and improving molecular docking predictions. In this work, we used
ethanol as a cosolvent to find relevant interactions for ligands toward
protein kinase G, an essential protein of Mycobacterium
tuberculosis (Mtb).
We validated the hot spots by screening a database of fragment-like
compounds and another one of known kinase inhibitors. Next, we performed
a pharmacophore-guided docking simulation and found three low micromolar
inhibitors, including one with a novel chemical scaffold that we expanded
to four derivative compounds. Binding affinities were characterized
by intrinsic fluorescence quenching assays, isothermal titration calorimetry,
and the analysis of melting curves. The predicted binding mode was
confirmed by X-ray crystallography. Finally, the compounds significantly
inhibited the viability of Mtb in infected
THP-1 macrophages.
Collapse
Affiliation(s)
- Osvaldo Burastero
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina.,European Molecular Biology Laboratory Hamburg, Notkestrasse 85, Hamburg D-22607, Germany
| | - Lucas A Defelipe
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina.,European Molecular Biology Laboratory Hamburg, Notkestrasse 85, Hamburg D-22607, Germany
| | - Gabriel Gola
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina.,Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica (UMYMFOR), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. CONICET, Buenos Aires C1428EGA, Argentina
| | - Nancy L Tateosian
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina
| | - Elias D Lopez
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina
| | - Camila Belen Martinena
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina
| | - Juan Pablo Arcon
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina
| | - Martín Dodes Traian
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina
| | - Diana E Wetzler
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina
| | - Isabel Bento
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, Hamburg D-22607, Germany
| | - Xavier Barril
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, Barcelona 08010, Spain.,Faculty of Pharmacy and Institute of Biomedicine (IBUB), University of Barcelona, Av.Joan XXIII 27-31, Barcelona 08028, Spain
| | - Javier Ramirez
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina.,Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica (UMYMFOR), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. CONICET, Buenos Aires C1428EGA, Argentina
| | - Marcelo A Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina
| | - Maria M Garcia-Alai
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, Hamburg D-22607, Germany
| | - Adrián G Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EGA, Argentina
| |
Collapse
|
5
|
Burastero O, Cabrera M, Lopez ED, Defelipe LA, Arcon JP, Durán R, Marti MA, Turjanski AG. Specificity and Reactivity of Mycobacterium tuberculosis Serine/Threonine Kinases PknG and PknB. J Chem Inf Model 2022; 62:1723-1733. [PMID: 35319884 DOI: 10.1021/acs.jcim.1c01358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of Tuberculosis, has 11 eukaryotic-like serine/threonine protein kinases, which play essential roles in cell growth, signal transduction, and pathogenesis. Protein kinase G (PknG) regulates the carbon and nitrogen metabolism by phosphorylation of the glycogen accumulation regulator (GarA) protein at Thr21. Protein kinase B (PknB) is involved in cell wall synthesis and cell shape, as well as phosphorylates GarA but at Thr22. While PknG seems to be constitutively activated and recognition of GarA requires phosphorylation in its unstructured tail, PknB activation is triggered by phosphorylation of its activation loop, which allows binding of the forkhead-associated domain of GarA. In the present work, we used molecular dynamics and quantum-mechanics/molecular mechanics simulations of the catalytically competent complex and kinase activity assays to understand PknG/PknB specificity and reactivity toward GarA. Two hydrophobic residues in GarA, Val24 and Phe25, seem essential for PknG binding and allow specificity for Thr21 phosphorylation. On the other hand, phosphorylated residues in PknB bind Arg26 in GarA and regulate its specificity for Thr22. We also provide a detailed analysis of the free energy profile for the phospho-transfer reaction and show why PknG has a constitutively active conformation not requiring priming phosphorylation in contrast to PknB. Our results provide new insights into these two key enzymes relevant for Mtb and the mechanisms of serine/threonine phosphorylation in bacteria.
Collapse
Affiliation(s)
- Osvaldo Burastero
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EGA Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EGA Buenos Aires, Argentina
| | - Marisol Cabrera
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EGA Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EGA Buenos Aires, Argentina
| | - Elias D Lopez
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EGA Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EGA Buenos Aires, Argentina
| | - Lucas A Defelipe
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EGA Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EGA Buenos Aires, Argentina
| | - Juan Pablo Arcon
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EGA Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EGA Buenos Aires, Argentina
| | - Rosario Durán
- Institut Pasteur de Montevideo, 11400 Montevideo, Uruguay.,Instituto de Investigaciones BiológicasClemente Estable, 11600 Montevideo, Uruguay
| | - Marcelo A Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EGA Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EGA Buenos Aires, Argentina
| | - Adrian G Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EGA Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EGA Buenos Aires, Argentina
| |
Collapse
|
6
|
Zuo K, Marjault HB, Bren KL, Rossetti G, Nechushtai R, Carloni P. The two redox states of the human NEET proteins' [2Fe-2S] clusters. J Biol Inorg Chem 2021; 26:763-774. [PMID: 34453614 PMCID: PMC8463382 DOI: 10.1007/s00775-021-01890-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 07/26/2021] [Indexed: 11/04/2022]
Abstract
The NEET proteins constitute a unique class of [2Fe-2S] proteins. The metal ions bind to three cysteines and one histidine. The proteins' clusters exist in two redox states; the oxidized protein (containing two FeIII ions) can transfer the cluster to apo-acceptor protein(s), while the reduced form (containing one ferrous ion) remains bound to the protein frame. Here, we perform in silico and in vitro studies on human NEET proteins in both reduced and oxidized forms. Quantum chemical calculations on all available human NEET proteins structures suggest that reducing the cluster weakens the Fe-NHis and Fe-SCys bonds, similar to what is seen in other Fe-S proteins (e.g., ferredoxin and Rieske protein). We further show that the extra electron in the [2Fe-2S]+ clusters of one of the NEET proteins (mNT) is localized on the His-bound iron ion, consistently with our previous spectroscopic studies. Kinetic measurements demonstrate that the mNT [2Fe-2S]+ is released only by an increase in temperature. Thus, the reduced state of human NEET proteins [2Fe-2S] cluster is kinetically inert. This previously unrecognized kinetic inertness of the reduced state, along with the reactivity of the oxidized state, is unique across all [2Fe-2S] proteins. Finally, using a coevolutionary analysis, along with molecular dynamics simulations, we provide insight on the observed allostery between the loop L2 and the cluster region. Specifically, we show that W75, R76, K78, K79, F82 and G85 in the latter region share similar allosteric characteristics in both redox states.
Collapse
Affiliation(s)
- Ke Zuo
- The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, 91904, Jerusalem, Israel
- Department of Physics, RWTH Aachen University, 52074, Aachen, Germany
| | - Henri-Baptiste Marjault
- The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, 91904, Jerusalem, Israel
- Department of Physics, RWTH Aachen University, 52074, Aachen, Germany
| | - Kara L Bren
- Department of Chemistry, University of Rochester, Rochester, NY, 14627-0216, USA
| | - Giulia Rossetti
- Computational Biomedicine, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Jülich Supercomputing Center (JSC), Forschungszentrum Jülich GmbH, Jülich, Germany
- Department of Neurology, Faculty of Medicine, RWTH Aachen University, 52074, Aachen, Germany
| | - Rachel Nechushtai
- The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, 91904, Jerusalem, Israel.
| | - Paolo Carloni
- Department of Physics, RWTH Aachen University, 52074, Aachen, Germany.
- Computational Biomedicine, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
- JARA Institute: Molecular Neuroscience and Imaging, Institute of Neuroscience and Medicine INM-11, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
| |
Collapse
|
7
|
Willow SY, Yuan M, Juárez O, Minh DDL. Electrostatics and water occlusion regulate covalently-bound flavin mononucleotide cofactors of Vibrio cholerae respiratory complex NQR. Proteins 2021; 89:1376-1385. [PMID: 34091964 DOI: 10.1002/prot.26158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/20/2021] [Accepted: 06/01/2021] [Indexed: 12/20/2022]
Abstract
Proteins like NADH:ubiquinone oxidoreductase (NQR), an essential enzyme and ion pump in the physiology of several pathogenic bacteria, tightly regulate the redox properties of their cofactors. Although flavin mononucleotide (FMN) is fully reduced in aqueous solution, FMN in subunits B and C of NQR exclusively undergo one-electron transitions during its catalytic cycle. Here, we perform ab initio calculations and molecular dynamics simulations to elucidate the mechanisms that regulate the redox state of FMN in NQR. QM/MM calculations show that binding site electrostatics disfavor anionic forms of FMNH2 , but permit a neutral form of the fully reduced flavin. The potential energy surface is unaffected by covalent bonding between FMN and threonine. Molecular dynamics simulations show that the FMN binding sites are inaccessible by water, suggesting that further reductions of the cofactors are limited or prohibited by the availability of water and other proton donors. These findings provide a deeper understanding of the mechanisms used by NQR to regulate electron transfer through the cofactors and perform its physiologic role. They also provide the first, to our knowledge, evidence of the simple concept that proteins regulate flavin redox states via water occlusion.
Collapse
Affiliation(s)
- Soohaeng Yoo Willow
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Ming Yuan
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Oscar Juárez
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois, USA
| | - David D L Minh
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois, USA
| |
Collapse
|
8
|
Proteins maintain hydration at high [KCl] concentration regardless of content in acidic amino acids. Biophys J 2021; 120:2746-2762. [PMID: 34087206 PMCID: PMC8390907 DOI: 10.1016/j.bpj.2021.05.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/22/2021] [Accepted: 05/19/2021] [Indexed: 11/23/2022] Open
Abstract
Proteins of halophilic organisms, which accumulate molar concentrations of KCl in their cytoplasm, have a much higher content in acidic amino acids than proteins of mesophilic organisms. It has been proposed that this excess is necessary to maintain proteins hydrated in an environment with low water activity, either via direct interactions between water and the carboxylate groups of acidic amino acids or via cooperative interactions between acidic amino acids and hydrated cations. Our simulation study of five halophilic proteins and five mesophilic counterparts does not support either possibility. The simulations use the AMBER ff14SB force field with newly optimized Lennard-Jones parameters for the interactions between carboxylate groups and potassium ions. We find that proteins with a larger fraction of acidic amino acids indeed have higher hydration levels, as measured by the concentration of water in their hydration shell and the number of water/protein hydrogen bonds. However, the hydration level of each protein is identical at low (bKCl = 0.15 mol/kg) and high (bKCl = 2 mol/kg) KCl concentrations; excess acidic amino acids are clearly not necessary to maintain proteins hydrated at high salt concentration. It has also been proposed that cooperative interactions between acidic amino acids in halophilic proteins and hydrated cations stabilize the folded protein structure and would lead to slower dynamics of the solvation shell. We find that the translational dynamics of the solvation shell is barely distinguishable between halophilic and mesophilic proteins; if such a cooperative effect exists, it does not have that entropic signature.
Collapse
|
9
|
Force Field Parameters for Fe 2+4S 2-4 Clusters of Dihydropyrimidine Dehydrogenase, the 5-Fluorouracil Cancer Drug Deactivation Protein: A Step towards In Silico Pharmacogenomics Studies. Molecules 2021; 26:molecules26102929. [PMID: 34069161 PMCID: PMC8156676 DOI: 10.3390/molecules26102929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 12/01/2022] Open
Abstract
The dimeric dihydropyrimidine dehydrogenase (DPD), metalloenzyme, an adjunct anti-cancer drug target, contains highly specialized 4 × Fe2+4S2−4 clusters per chain. These clusters facilitate the catalysis of the rate-limiting step in the pyrimidine degradation pathway through a harmonized electron transfer cascade that triggers a redox catabolic reaction. In the process, the bulk of the administered 5-fluorouracil (5-FU) cancer drug is inactivated, while a small proportion is activated to nucleic acid antimetabolites. The occurrence of missense mutations in DPD protein within the general population, including those of African descent, has adverse toxicity effects due to altered 5-FU metabolism. Thus, deciphering mutation effects on protein structure and function is vital, especially for precision medicine purposes. We previously proposed combining molecular dynamics (MD) and dynamic residue network (DRN) analysis to decipher the molecular mechanisms of missense mutations in other proteins. However, the presence of Fe2+4S2−4 clusters in DPD poses a challenge for such in silico studies. The existing AMBER force field parameters cannot accurately describe the Fe2+ center coordination exhibited by this enzyme. Therefore, this study aimed to derive AMBER force field parameters for DPD enzyme Fe2+ centers, using the original Seminario method and the collation features Visual Force Field Derivation Toolkit as a supportive approach. All-atom MD simulations were performed to validate the results. Both approaches generated similar force field parameters, which accurately described the human DPD protein Fe2+4S2−4 cluster architecture. This information is crucial and opens new avenues for in silico cancer pharmacogenomics and drug discovery related research on 5-FU drug efficacy and toxicity issues.
Collapse
|
10
|
da Silva TU, Pougy KDC, Albuquerque MG, da Silva Lima CH, Machado SDP. Development of parameters compatible with the CHARMM36 force field for [Fe 4S 4] 2+ clusters and molecular dynamics simulations of adenosine-5'-phosphosulfate reductase in GROMACS 2019. J Biomol Struct Dyn 2020; 40:3481-3491. [PMID: 33183173 DOI: 10.1080/07391102.2020.1847687] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
DFT calculations were used to obtain parameters compatible with the CHARMM36 force field for iron-sulfur clusters (Fe-S) of the type [Fe4S4]2+ that are coordinated to dissimilatory adenosine-5'-phosphosulfate reductase (APSrAB). Classical molecular dynamics (MD) simulations were performed on two APSrAB systems to validate the parameters and verify the stability of the studied systems. The time analysis of the parameters inserted into the force field was in reasonable agreement with the experimental X-ray diffraction data. The analysis of the time evolution of the studied systems indicated that these systems and, in particular, the clusters in their respective cavities had a good stability and were in agreement with what was observed in previous works. The parameters obtained provide the basis for the study of APSrAB as well as other systems that contain [Fe4S4]2+ through the CHARMM36 force field.
Collapse
|
11
|
Mestizo PD, Narváez DM, Pinzón-Ulloa JA, Di Bello DT, Franco-Ulloa S, Macías MA, Groot H, Miscione GP, Suescun L, Hurtado JJ. Novel complexes with ONNO tetradentate coumarin schiff-base donor ligands: x-ray structures, DFT calculations, molecular dynamics and potential anticarcinogenic activity. Biometals 2020; 34:119-140. [PMID: 33185808 DOI: 10.1007/s10534-020-00268-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/04/2020] [Indexed: 12/24/2022]
Abstract
The synthesis of eight novel Zn(II), Co(II), Cu(II), Ni(II) and Pt(II) complexes (2-9) derived from the ONNO tetradentate coumarin Schiff-Base donor ligands, L1 and the novel L2, was performed. All compounds were characterized by analytical, spectrometry and spectroscopy techniques. Complexes 2-4 were also characterized by DFT calculations and the structures of 5 and 6 were determined by single-crystal X-ray diffraction analysis. A cytotoxicity study was carried out through an MTT assay in the carcinogenic cell line HeLa and the noncarcinogenic cell lines HFF-1 and HaCaT. The results indicated that among all the evaluated compounds, 2 and 6 presented the best anticarcinogenic potential against HeLa cells with an IC50 of 3.5 and 4.1 µM, respectively. In addition, classical molecular dynamics simulations were performed on the synthesized coordination compounds bound to G4 DNA architectures in the scope of shedding light on their inhibition mode and the most conserved interactions that may lead to the biological activity of the compounds.
Collapse
Affiliation(s)
- Paula Daniela Mestizo
- Departamento de Química, Universidad de Los Andes, Carrera 1 No. 18A-12, 111711, Bogotá, Colombia
| | - Diana M Narváez
- Human Genetics Laboratory, Universidad de Los Andes, Carrera 1 No. 18A-12, 111711, Bogotá, Colombia
| | | | - Daniela Torres Di Bello
- Human Genetics Laboratory, Universidad de Los Andes, Carrera 1 No. 18A-12, 111711, Bogotá, Colombia
| | - Sebastian Franco-Ulloa
- COBO Computational Bio-Organic Chemistry, Chemistry Department, Universidad de Los Andes, Carrera 1 No. 18A-12, 111711, Bogotá, Colombia
| | - Mario A Macías
- Departamento de Química, Universidad de Los Andes, Carrera 1 No. 18A-12, 111711, Bogotá, Colombia
| | - Helena Groot
- Human Genetics Laboratory, Universidad de Los Andes, Carrera 1 No. 18A-12, 111711, Bogotá, Colombia
| | - Gian Pietro Miscione
- COBO Computational Bio-Organic Chemistry, Chemistry Department, Universidad de Los Andes, Carrera 1 No. 18A-12, 111711, Bogotá, Colombia
| | - Leopoldo Suescun
- Cryssmat-Lab/Cátedra de Física/DETEMA, Facultad de Química, Universidad de La República, Montevideo, Uruguay
| | - John J Hurtado
- Departamento de Química, Universidad de Los Andes, Carrera 1 No. 18A-12, 111711, Bogotá, Colombia.
| |
Collapse
|
12
|
Ferreira P, Cerqueira NMFSA, Fernandes PA, Romão MJ, Ramos MJ. Catalytic Mechanism of Human Aldehyde Oxidase. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02627] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Pedro Ferreira
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Nuno M. F. Sousa A. Cerqueira
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro Alexandrino Fernandes
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria João Romão
- UCIBIO@REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Maria João Ramos
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| |
Collapse
|
13
|
Haghshenas H, Tavakol H, Kaviani B, Mohammadnezhad G. AMBER Force Field Parameters for Cobalt-Containing Biological Systems: A Systematic Derivation Study. J Phys Chem B 2020; 124:777-787. [PMID: 31912730 DOI: 10.1021/acs.jpcb.9b10739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the present work, the parameterization of a set of cobalt-containing systems has been performed to create a comprehensive library for bonding parameters of biological Co-containing systems. A standard process for the extraction and validation of parameters was employed, which could be used to create force field parameters for the other metal-containing systems. All protein data banks were searched to extract common chemical groups in bonding with cobalt, and finally, 16 structures were designed to represent the binding model of the chemical moieties with cobalt. The Hessian matrix of each structure was computed at the B3LYP/6-311++G(2d,2p) level of theory and the Seminario method was employed to compute cobalt bond stretching and angle bending parameters. Validation of the derived parameters was performed using structural minimization and molecular dynamics (MD) simulations of four models. Further validation was performed using an extensive MD simulation on carbonic anhydrase II as a common cobalt-containing metalloprotein. The results demonstrated that among models, the bonded model in combination with the RESP charges can produce the most reliable and accurate structural conformations for the metal site of cobalt-containing systems.
Collapse
Affiliation(s)
- Hamed Haghshenas
- Division of Biochemistry, Department of Biology, Faculty of Sciences , Shahrekord University , Shahrekord 038 , Iran
| | - Hossein Tavakol
- Department of Chemistry , Isfahan University of Technology , Isfahan 84156-83111 , Iran
| | - Bita Kaviani
- Division of Genetics, Department of Biology, Faculty of Sciences , Islamic Azad University , Shahrekord Branch , Shahrekord 65234-98712 , Iran
| | | |
Collapse
|
14
|
Ferreira P, Cerqueira NMFSA, Coelho C, Fernandes PA, Romão MJ, Ramos MJ. New insights about the monomer and homodimer structures of the human AOX1. Phys Chem Chem Phys 2019; 21:13545-13554. [DOI: 10.1039/c9cp01040h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We conducted MD simulations to provide a comprehensive study on the human aldehyde oxidase and on the impact that the allosteric inhibitor thioridazine and malonate ions have on its structure, particularly on the catalytic tunnel.
Collapse
Affiliation(s)
- P. Ferreira
- UCIBIO@REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
- 4169-007 Porto
| | - N. M. F. S. A. Cerqueira
- UCIBIO@REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
- 4169-007 Porto
| | - C. Coelho
- UCIBIO@REQUIMTE
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade Nova de Lisboa
- 2829-516 Caparica
| | - P. A. Fernandes
- UCIBIO@REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
- 4169-007 Porto
| | - M. J. Romão
- UCIBIO@REQUIMTE
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade Nova de Lisboa
- 2829-516 Caparica
| | - M. J. Ramos
- UCIBIO@REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
- 4169-007 Porto
| |
Collapse
|
15
|
Juncosa JI, Takaya K, Le HV, Moschitto MJ, Weerawarna PM, Mascarenhas R, Liu D, Dewey SL, Silverman RB. Design and Mechanism of (S)-3-Amino-4-(difluoromethylenyl)cyclopent-1-ene-1-carboxylic Acid, a Highly Potent γ-Aminobutyric Acid Aminotransferase Inactivator for the Treatment of Addiction. J Am Chem Soc 2018; 140:2151-2164. [PMID: 29381352 PMCID: PMC5812813 DOI: 10.1021/jacs.7b10965] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
γ-Aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the central nervous system. Inhibition of GABA aminotransferase (GABA-AT), a pyridoxal 5'-phosphate (PLP)-dependent enzyme that degrades GABA, has been established as a possible strategy for the treatment of substance abuse. The raised GABA levels that occur as a consequence of this inhibition have been found to antagonize the rapid release of dopamine in the ventral striatum (nucleus accumbens) that follows an acute challenge by an addictive substance. In addition, increased GABA levels are also known to elicit an anticonvulsant effect in patients with epilepsy. We previously designed the mechanism-based inactivator (1S,3S)-3-amino-4-difluoromethylenyl-1-cyclopentanoic acid (2), now called CPP-115, that is 186 times more efficient in inactivating GABA-AT than vigabatrin, the only FDA-approved drug that is an inactivator of GABA-AT. CPP-115 was found to have high therapeutic potential for the treatment of cocaine addiction and for a variety of epilepsies, has successfully completed a Phase I safety clinical trial, and was found to be effective in the treatment of infantile spasms (West syndrome). Herein we report the design, using molecular dynamics simulations, synthesis, and biological evaluation of a new mechanism-based inactivator, (S)-3-amino-4-(difluoromethylenyl)cyclopent-1-ene-1-carboxylic acid (5), which was found to be almost 10 times more efficient as an inactivator of GABA-AT than CPP-115. We also present the unexpected crystal structure of 5 bound to GABA-AT, as well as computational analyses used to assist the structure elucidation process. Furthermore, 5 was found to have favorable pharmacokinetic properties and low off-target activities. In vivo studies in freely moving rats showed that 5 was dramatically superior to CPP-115 in suppressing the release of dopamine in the corpus striatum, which occurs subsequent to either an acute cocaine or nicotine challenge. Compound 5 also attenuated increased metabolic demands (neuronal glucose metabolism) in the hippocampus, a brain region that encodes spatial information concerning the environment in which an animal receives a reinforcing or aversive drug. This multidisciplinary computational design to preclinical efficacy approach should be applicable to the design and improvement of mechanism-based inhibitors of other enzymes whose crystal structures and inactivation mechanisms are known.
Collapse
Affiliation(s)
- Jose I. Juncosa
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Kenji Takaya
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Hoang V. Le
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Matthew J. Moschitto
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Pathum M. Weerawarna
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Romila Mascarenhas
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Stephen L. Dewey
- Center for Neurosciences, Laboratory for Behavioral and Molecular Neuroimaging, Feinstein Institute for Medical Research, North Shore-LIJ Health System, Manhasset, New York 11030, United States
| | - Richard B. Silverman
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
16
|
Sala D, Giachetti A, Rosato A. Molecular dynamics simulations of metalloproteins: A folding study of rubredoxin from <em>Pyrococcus furiosus</em>. AIMS BIOPHYSICS 2018. [DOI: 10.3934/biophy.2018.1.77] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
17
|
Nunes-Alves A, Arantes GM. Mechanical Unfolding of Macromolecules Coupled to Bond Dissociation. J Chem Theory Comput 2017; 14:282-290. [DOI: 10.1021/acs.jctc.7b00805] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ariane Nunes-Alves
- Department of Biochemistry,
Instituto de Quı́mica, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
| | - Guilherme Menegon Arantes
- Department of Biochemistry,
Instituto de Quı́mica, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
| |
Collapse
|
18
|
Pesce L, Calandrini V, Marjault HB, Lipper CH, Rossetti G, Mittler R, Jennings PA, Bauer A, Nechushtai R, Carloni P. Molecular Dynamics Simulations of the [2Fe-2S] Cluster-Binding Domain of NEET Proteins Reveal Key Molecular Determinants That Induce Their Cluster Transfer/Release. J Phys Chem B 2017; 121:10648-10656. [PMID: 29086562 PMCID: PMC5713697 DOI: 10.1021/acs.jpcb.7b10584] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The NEET proteins are a novel family of iron-sulfur proteins characterized by an unusual three cysteine and one histidine coordinated [2Fe-2S] cluster. Aberrant cluster release, facilitated by the breakage of the Fe-N bond, is implicated in a variety of human diseases, including cancer. Here, the molecular dynamics in the multi-microsecond timescale, along with quantum chemical calculations, on two representative members of the family (the human NAF-1 and mitoNEET proteins), show that the loss of the cluster is associated with a dramatic decrease in secondary and tertiary structure. In addition, the calculations provide a mechanism for cluster release and clarify, for the first time, crucial differences existing between the two proteins, which are reflected in the experimentally observed difference in the pH-dependent cluster reactivity. The reliability of our conclusions is established by an extensive comparison with the NMR data of the solution proteins, in part measured in this work.
Collapse
Affiliation(s)
- Luca Pesce
- Computational Biomedicine Section, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH , 52425 Jülich, Germany
| | - Vania Calandrini
- Computational Biomedicine Section, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH , 52425 Jülich, Germany
| | - Henri-Baptiste Marjault
- The Alexander Silberman Life Science Institute and the Wolfson Center for Applied Structural Biology, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram , 91904 Jerusalem, Israel
| | - Colin H Lipper
- Departments of Chemistry and Biochemistry, University of California San Diego , La Jolla, 92093 San Diego, California, United States of America
| | - Gulia Rossetti
- Computational Biomedicine Section, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH , 52425 Jülich, Germany.,Division Computational Science - Simulation Laboratory Biology, Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH , 52428 Jülich, Germany.,Department of Oncology, Hematology and Stem Cell Transplantation, University Hospital Aachen, RWTH Aachen University , 52074 Aachen, Germany
| | - Ron Mittler
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas , 76203 Denton, Texas, United States of America
| | - Patricia A Jennings
- Departments of Chemistry and Biochemistry, University of California San Diego , La Jolla, 92093 San Diego, California, United States of America
| | - Andreas Bauer
- Molecular Organisation of the Brain Molecular Neuroimaging, Institute of Neuroscience and Medicine INM-2, Forschungszentrum Jülich GmbH , 52428 Jülich, Germany
| | - Rachel Nechushtai
- The Alexander Silberman Life Science Institute and the Wolfson Center for Applied Structural Biology, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram , 91904 Jerusalem, Israel
| | - Paolo Carloni
- Computational Biomedicine Section, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH , 52425 Jülich, Germany.,JARA-HPC , 52428 Jülich, Germany
| |
Collapse
|
19
|
Wang R, Ozhgibesov M, Hirao H. Analytical hessian fitting schemes for efficient determination of force-constant parameters in molecular mechanics. J Comput Chem 2017; 39:307-318. [DOI: 10.1002/jcc.25100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 09/21/2017] [Accepted: 10/12/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Ruixing Wang
- Department of Chemistry; City University of Hong Kong, Tat Chee Avenue; Kowloon Hong Kong China
| | - Mikhail Ozhgibesov
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University, 21 Nanyang Link; 637371 Singapore
| | - Hajime Hirao
- Department of Chemistry; City University of Hong Kong, Tat Chee Avenue; Kowloon Hong Kong China
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University, 21 Nanyang Link; 637371 Singapore
| |
Collapse
|
20
|
David R, Jamet H, Nivière V, Moreau Y, Milet A. Iron Hydroperoxide Intermediate in Superoxide Reductase: Protonation or Dissociation First? MM Dynamics and QM/MM Metadynamics Study. J Chem Theory Comput 2017; 13:2987-3004. [DOI: 10.1021/acs.jctc.7b00126] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rolf David
- DCM, Univ. Grenoble Alpes, F-38000 Grenoble, France
- CNRS, DCM, F-38000, Grenoble, France
- Laboratoire
de Chimie et Biologie des Métaux, CEA/DRF/BIG/CBM/MCT, CNRS
UMR 5249, Université Grenoble Alpes, Grenoble, France
| | - Hélène Jamet
- DCM, Univ. Grenoble Alpes, F-38000 Grenoble, France
- CNRS, DCM, F-38000, Grenoble, France
| | - Vincent Nivière
- Laboratoire
de Chimie et Biologie des Métaux, CEA/DRF/BIG/CBM/BioCat, CNRS
UMR 5249, Université Grenoble Alpes, Grenoble, France
| | - Yohann Moreau
- Laboratoire
de Chimie et Biologie des Métaux, CEA/DRF/BIG/CBM/MCT, CNRS
UMR 5249, Université Grenoble Alpes, Grenoble, France
| | - Anne Milet
- DCM, Univ. Grenoble Alpes, F-38000 Grenoble, France
- CNRS, DCM, F-38000, Grenoble, France
| |
Collapse
|
21
|
Dourado DFAR, Pohle S, Carvalho ATP, Dheeman DS, Caswell JM, Skvortsov T, Miskelly I, Brown RT, Quinn DJ, Allen CCR, Kulakov L, Huang M, Moody TS. Rational Design of a (S)-Selective-Transaminase for Asymmetric Synthesis of (1S)-1-(1,1′-biphenyl-2-yl)ethanamine. ACS Catal 2016. [DOI: 10.1021/acscatal.6b02380] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daniel F. A. R. Dourado
- School
of Chemistry and Chemical Engineering, Queen’s University Belfast, David
Keir Building, Stranmillis Road, Belfast BT9 5AG, Northern Ireland, United Kingdom
- Department
of Biocatalysis and Isotope Chemistry, Almac Sciences, 20 Seagoe Industrial
Estate, Craigavon BT63
5QD, Northern Ireland, United Kingdom
| | - Stefan Pohle
- Department
of Biocatalysis and Isotope Chemistry, Almac Sciences, 20 Seagoe Industrial
Estate, Craigavon BT63
5QD, Northern Ireland, United Kingdom
| | - Alexandra T. P. Carvalho
- School
of Chemistry and Chemical Engineering, Queen’s University Belfast, David
Keir Building, Stranmillis Road, Belfast BT9 5AG, Northern Ireland, United Kingdom
- Department
of Biocatalysis and Isotope Chemistry, Almac Sciences, 20 Seagoe Industrial
Estate, Craigavon BT63
5QD, Northern Ireland, United Kingdom
| | - Dharmendra S. Dheeman
- Department
of Biocatalysis and Isotope Chemistry, Almac Sciences, 20 Seagoe Industrial
Estate, Craigavon BT63
5QD, Northern Ireland, United Kingdom
| | - Jill M. Caswell
- Department
of Biocatalysis and Isotope Chemistry, Almac Sciences, 20 Seagoe Industrial
Estate, Craigavon BT63
5QD, Northern Ireland, United Kingdom
| | - Timofey Skvortsov
- Department
of Biocatalysis and Isotope Chemistry, Almac Sciences, 20 Seagoe Industrial
Estate, Craigavon BT63
5QD, Northern Ireland, United Kingdom
- School
of Biological Sciences, Queen’s University Belfast, Medical Biology
Centre, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, United Kingdom
| | - Iain Miskelly
- Department
of Biocatalysis and Isotope Chemistry, Almac Sciences, 20 Seagoe Industrial
Estate, Craigavon BT63
5QD, Northern Ireland, United Kingdom
| | - Rodney T. Brown
- Department
of Biocatalysis and Isotope Chemistry, Almac Sciences, 20 Seagoe Industrial
Estate, Craigavon BT63
5QD, Northern Ireland, United Kingdom
| | - Derek J. Quinn
- Department
of Biocatalysis and Isotope Chemistry, Almac Sciences, 20 Seagoe Industrial
Estate, Craigavon BT63
5QD, Northern Ireland, United Kingdom
| | - Christopher C. R. Allen
- School
of Biological Sciences, Queen’s University Belfast, Medical Biology
Centre, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, United Kingdom
| | - Leonid Kulakov
- School
of Biological Sciences, Queen’s University Belfast, Medical Biology
Centre, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, United Kingdom
| | - Meilan Huang
- School
of Chemistry and Chemical Engineering, Queen’s University Belfast, David
Keir Building, Stranmillis Road, Belfast BT9 5AG, Northern Ireland, United Kingdom
| | - Thomas S. Moody
- Department
of Biocatalysis and Isotope Chemistry, Almac Sciences, 20 Seagoe Industrial
Estate, Craigavon BT63
5QD, Northern Ireland, United Kingdom
| |
Collapse
|
22
|
Olubiyi OO, Strodel B. Topology and parameter data of thirteen non-natural amino acids for molecular simulations with CHARMM22. Data Brief 2016; 9:642-647. [PMID: 27766295 PMCID: PMC5067094 DOI: 10.1016/j.dib.2016.09.051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 09/27/2016] [Accepted: 09/30/2016] [Indexed: 11/16/2022] Open
Abstract
In this article we provide a data package containing the topology files and parameters compatible with the CHARMM22 force field for thirteen non-natural amino acids. The force field parameters were derived based on quantum mechanical (QM) calculations involving geometry optimization and potential energy surface scanning at the HF 6-31G(d) and HF 6-311G(d,p) levels of theory. The resulting energy data points were fitted to mathematical functions representing each component of the CHARMM22 force field. Further fine-tuning of the parameters utilized molecular mechanics energies, which were iteratively calculated and compared to the corresponding QM values until the latter were satisfactorily reproduced. The final force field data were validated with molecular dynamics simulations in explicit solvent conditions.
Collapse
Affiliation(s)
- Olujide O Olubiyi
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| |
Collapse
|
23
|
Wang R, Ozhgibesov M, Hirao H. Partial hessian fitting for determining force constant parameters in molecular mechanics. J Comput Chem 2016; 37:2349-59. [DOI: 10.1002/jcc.24457] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/28/2016] [Accepted: 07/06/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Ruixing Wang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical SciencesNanyang Technological University21 Nanyang Link637371 Singapore
| | - Mikhail Ozhgibesov
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical SciencesNanyang Technological University21 Nanyang Link637371 Singapore
| | - Hajime Hirao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical SciencesNanyang Technological University21 Nanyang Link637371 Singapore
| |
Collapse
|
24
|
Liu JY, Chen XE, Zhang YL. Insights into the key interactions between human protein phosphatase 5 and cantharidin using molecular dynamics and site-directed mutagenesis bioassays. Sci Rep 2015; 5:12359. [PMID: 26190207 PMCID: PMC4507179 DOI: 10.1038/srep12359] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 05/05/2015] [Indexed: 01/23/2023] Open
Abstract
Serine/threonine protein phosphatase 5 (PP5) is a promising novel target for anticancer therapies. This work aims to uncover the key interactions at the atomic level between PP5 and three inhibitors (cantharidin, norcantharidin and endothall). We found that, unlike previous report, Arg 100 contributes less to PP5-inhibitor binding, and the residues His 69, Asn 128, His 129, Arg 225, His 252 and Arg 250 are of importance to PP5-inhibitor binding. The hydrophobic interactions established between the residues Val 254, Phe 271 and Tyr 276, especially Glu 253, are very important to enhance the inhibitive interaction. We suggested that, to increase the inhibitory activity, the interactions of inhibitor with three negatively charged unfavorable interaction residues, Asp 99, Glu 130 and Asp 213, should be avoided. However, the interactions of inhibitor with favorable interaction residue Arg 250 could enhance the inhibitory activity. The Manganese ion 2 (MN2) unfavorably contribute to the total interaction free energies. The coordination between MN2 and chemical group of inhibitor should be eliminated. This work provides insight into how cantharidin and its analogs bind to PP5c at the atomic level and will facilitate modification of cantharidin-like chemicals to rationally develop more specific and less cytotoxic anti-cancer drugs.
Collapse
Affiliation(s)
- Ji-Yuan Liu
- Key Laboratory of Plant Protection Resources &Pest Management of the Ministry of Education, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xi-En Chen
- Key Laboratory of Plant Protection Resources &Pest Management of the Ministry of Education, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Ya-Lin Zhang
- Key Laboratory of Plant Protection Resources &Pest Management of the Ministry of Education, Northwest A&F University, Yangling 712100, Shaanxi, China
| |
Collapse
|
25
|
Lee KL, Singh AK, Heo L, Seok C, Roe JH. Factors affecting redox potential and differential sensitivity of SoxR to redox-active compounds. Mol Microbiol 2015; 97:808-21. [DOI: 10.1111/mmi.13068] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2015] [Indexed: 12/27/2022]
Affiliation(s)
- Kang-Lok Lee
- Laboratory of Molecular Microbiology; School of Biological Sciences, and Institute of Microbiology; Seoul National University; Seoul 151-742 Korea
| | - Atul K. Singh
- Laboratory of Molecular Microbiology; School of Biological Sciences, and Institute of Microbiology; Seoul National University; Seoul 151-742 Korea
| | - Lim Heo
- Department of Chemistry; Seoul National University; Seoul 151-747 Korea
| | - Chaok Seok
- Department of Chemistry; Seoul National University; Seoul 151-747 Korea
| | - Jung-Hye Roe
- Laboratory of Molecular Microbiology; School of Biological Sciences, and Institute of Microbiology; Seoul National University; Seoul 151-742 Korea
| |
Collapse
|
26
|
Mera-Adasme R, Sadeghian K, Sundholm D, Ochsenfeld C. Effect of including torsional parameters for histidine-metal interactions in classical force fields for metalloproteins. J Phys Chem B 2014; 118:13106-11. [PMID: 25410708 DOI: 10.1021/jp5078906] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Classical force-field parameters of the metal site of metalloproteins usually comprise only the partial charges of the involved atoms, as well as the bond-stretching and bending parameters of the metal-ligand interactions. Although for certain metal ligands such as histidine residues, the torsional motions at the metal site play an important role for the dynamics of the protein, no such terms have been considered to be crucial in the parametrization of the force fields, and they have therefore been omitted in the parametrization. In this work, we have optimized AMBER-compatible force-field parameters for the reduced state of the metal site of copper, zinc superoxide dismutase (SOD1) and assessed the effect of including torsional parameters for the histidine-metal interactions in molecular dynamics simulations. On the basis of the obtained results, we recommend that torsion parameters of the metal site are included when processes at the metal site are investigated or when free-energy calculations are performed. As the torsion parameters mainly affect the structure of the metal site, other kinds of structural studies can be performed without considering the torsional parameters of the metal site.
Collapse
Affiliation(s)
- Raúl Mera-Adasme
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , München 80539, Germany
| | | | | | | |
Collapse
|
27
|
Cerqueira NMFSA, Coelho C, Brás NF, Fernandes PA, Garattini E, Terao M, Romão MJ, Ramos MJ. Insights into the structural determinants of substrate specificity and activity in mouse aldehyde oxidases. J Biol Inorg Chem 2014; 20:209-17. [PMID: 25287365 DOI: 10.1007/s00775-014-1198-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/19/2014] [Indexed: 01/07/2023]
Abstract
In this work, a combination of homology modeling and molecular dynamics (MD) simulations was used to investigate the factors that modulate substrate specificity and activity of the mouse AOX isoforms: mAOX1, mAOX2 (previously mAOX3l1), mAOX3 and mAOX4. The results indicate that the AOX isoform structures are highly preserved and even more conserved than the corresponding amino acid sequences. The only differences are at the protein surface and substrate-binding site region. The substrate-binding site of all isoforms consists of two regions: the active site, which is highly conserved among all isoforms, and a isoform-specific region located above. We predict that mAOX1 accepts a broader range of substrates of different shape, size and nature relative to the other isoforms. In contrast, mAOX4 appears to accept a more restricted range of substrates. Its narrow and hydrophobic binding site indicates that it only accepts small hydrophobic substrates. Although mAOX2 and mAOX3 are very similar to each other, we propose the following pairs of overlapping substrate specificities: mAOX2/mAOX4 and mAOX3/mAXO1. Based on these considerations, we propose that the catalytic activity between all isoforms should be similar but the differences observed in the binding site might influence the substrate specificity of each enzyme. These results also suggest that the presence of several AOX isoforms in mouse allows them to oxidize more efficiently a wider range of substrates. This contrasts with the same or other organisms that only express one isoform and are less efficient or incapable of oxidizing the same type of substrates.
Collapse
Affiliation(s)
- Nuno M F S A Cerqueira
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Díaz A, Martínez E, Puerta L, Méndez D, Rodríguez E, Fang L, Wnuk S, Vivas-Reyes R. A CoMSIA study to design antagonist ligands for the LuxS protein. NEW J CHEM 2014. [DOI: 10.1039/c3nj01162c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
29
|
Mahro M, Brás NF, Cerqueira NMFSA, Teutloff C, Coelho C, Romão MJ, Leimkühler S. Identification of crucial amino acids in mouse aldehyde oxidase 3 that determine substrate specificity. PLoS One 2013; 8:e82285. [PMID: 24358164 PMCID: PMC3864932 DOI: 10.1371/journal.pone.0082285] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 11/01/2013] [Indexed: 01/23/2023] Open
Abstract
In order to elucidate factors that determine substrate specificity and activity of mammalian molybdo-flavoproteins we performed site directed mutagenesis of mouse aldehyde oxidase 3 (mAOX3). The sequence alignment of different aldehyde oxidase (AOX) isoforms identified variations in the active site of mAOX3 in comparison to other AOX proteins and xanthine oxidoreductases (XOR). Based on the structural alignment of mAOX3 and bovine XOR, differences in amino acid residues involved in substrate binding in XORs in comparison to AOXs were identified. We exchanged several residues in the active site to the ones found in other AOX homologues in mouse or to residues present in bovine XOR in order to examine their influence on substrate selectivity and catalytic activity. Additionally we analyzed the influence of the [2Fe-2S] domains of mAOX3 on its kinetic properties and cofactor saturation. We applied UV-VIS and EPR monitored redox-titrations to determine the redox potentials of wild type mAOX3 and mAOX3 variants containing the iron-sulfur centers of mAOX1. In addition, a combination of molecular docking and molecular dynamic simulations (MD) was used to investigate factors that modulate the substrate specificity and activity of wild type and AOX variants. The successful conversion of an AOX enzyme to an XOR enzyme was achieved exchanging eight residues in the active site of mAOX3. It was observed that the absence of the K889H exchange substantially decreased the activity of the enzyme towards all substrates analyzed, revealing that this residue has an important role in catalysis.
Collapse
Affiliation(s)
- Martin Mahro
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Natércia F. Brás
- REQUIMTE, Departamento de Quimica, Faculdade de Ciencias, Universidade do Porto, Porto, Portugal
| | | | - Christian Teutloff
- Institute for Experimentalphysics, Free University of Berlin, Berlin, Germany
| | - Catarina Coelho
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Maria João Romão
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| |
Collapse
|