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Gupta MK, Vemula S, Donde R, Gouda G, Behera L, Vadde R. In-silico approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel. J Biomol Struct Dyn 2020; 39:2617-2627. [PMID: 32238078 PMCID: PMC7171389 DOI: 10.1080/07391102.2020.1751300] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent outbreak of Coronavirus disease (COVID-19) pandemic around the world is associated with ‘severe acute respiratory syndrome’ (SARS-CoV2) in humans. SARS-CoV2 is an enveloped virus and E proteins present in them are reported to form ion channels, which is mainly associated with pathogenesis. Thus, there is always a quest to inhibit these ion channels, which in turn may help in controlling diseases caused by SARS-CoV2 in humans. Considering this, in the present study, authors employed computational approaches for studying the structure as well as function of the human ‘SARS-CoV2 E’ protein as well as its interaction with various phytochemicals. Result obtained revealed that α-helix and loops present in this protein experience random movement under optimal condition, which in turn modulate ion channel activity; thereby aiding the pathogenesis caused via SARS-CoV2 in human and other vertebrates. However, after binding with Belachinal, Macaflavanone E, and Vibsanol B, the random motion of the human ‘SARS-CoV2 E’ protein gets reduced, this, in turn, inhibits the function of the ‘SARS-CoV2 E’ protein. It is pertinent to note that two amino acids, namely VAL25 and PHE26, play a key role while interacting with these three phytochemicals. As these three phytochemicals, namely, Belachinal, Macaflavanone E & Vibsanol B, have passed the ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) property as well as ‘Lipinski’s Rule of 5s’, they may be utilized as drugs in controlling disease caused via SARS-COV2, after further investigation. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Manoj Kumar Gupta
- Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh, India
| | - Sarojamma Vemula
- Department of Microbiology, Government Medical College, Anantapur, Andhra Pradesh, India
| | - Ravindra Donde
- ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Gayatri Gouda
- ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Lambodar Behera
- ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Ramakrishna Vadde
- Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh, India
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Gupta MK, Vadde R. A computational structural biology study to understand the impact of mutation on structure-function relationship of inward-rectifier potassium ion channel Kir6.2 in human. J Biomol Struct Dyn 2020; 39:1447-1460. [PMID: 32089084 DOI: 10.1080/07391102.2020.1733666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Type 2 diabetes (T2D) is clinically characterized via hyperglycemia. Polymorphism rs5219 in the KCNJ11 gene is a risk factor for developing T2D in humans. KCNJ11 encodes the 'inward-rectifier potassium ion channel (Kir6.2)'. However, because of the absence of the complete crystal/NMR structures of Kir6.2 proteins, insight into its structure and function and its interaction with diverse ligands remain elusive to date. Therefore, a computational approach was employed for predicting the best plausible 'three-dimensional' structure of Kir6.2 as well as for studying the influence of mutation (p. GLU23LYS) on both architectures as well as the function of Kir6.2 employing simulation studies. Results obtained revealed that though, with increased time, 'Gibbs free energy' becomes positive, residues in wild type Kir6.2 experiences less random movement as compared to mutant Kir6.2. The less random movement of residues in wild type Kir6.2 represents the standard coupling between open and closing of 'KATP channel' and thus the normal secretion of insulin. The more dispersed motion of mutant Kir6.2 residues represents 'overactivity' of the 'KATP channel' and thus insulin 'under-secretion'. Further, molecular docking and simulation studies identified two phytochemicals/drugs, namely, A-348441 and chushizisin I, which retains the wild type property of Kir6.2 after binding with mutant protein. Unlike A-348441, this is for the first time, the present study is reporting about the plausible anti-diabetic property of chushizisin I. As these two phytochemicals/drugs, namely, A-348441 and chushizisin I, have passed ADMET test, in the near future, they may be utilized as anti-diabetic drugs after further investigation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manoj Kumar Gupta
- Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh, India
| | - Ramakrishna Vadde
- Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh, India
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Solution NMR structure and inhibitory effect against amyloid-β fibrillation of Humanin containing a d-isomerized serine residue. Biochem Biophys Res Commun 2016; 477:647-653. [PMID: 27349871 DOI: 10.1016/j.bbrc.2016.06.114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 06/23/2016] [Indexed: 11/24/2022]
Abstract
Humanin comprising 24 amino acid residues is a bioactive peptide that has been isolated from the brain tissue of patients with Alzheimer's disease. Humanin reportedly suppressed aging-related death of various cells due to amyloid fibrils and oxidative stress. There are reports that the cytoprotective activity of Humanin was remarkably enhanced by optical isomerization of the Ser14 residue from l to d form, but details of the molecular mechanism remained unclear. Here we demonstrated that Humanin d-Ser14 exhibited potent inhibitory activity against fibrillation of amyloid-β and remarkably higher binding affinity for amyloid-β than that of the Humanin wild-type and S14G mutant. In addition, we determined the solution structure of Humanin d-Ser14 by nuclear magnetic resonance (NMR) and showed that d-isomerization of the Ser14 residue enables drastic conformational rearrangement of Humanin. Furthermore, we identified an amyloid-β-binding site on Humanin d-Ser14 at atomic resolution by NMR. These biophysical and high-resolution structural analyses clearly revealed structure-function relationships of Humanin and explained the driving force of the drastic conformational change and molecular basis of the potent anti-amyloid-β fibrillation activity of Humanin caused by d-isomerization of the Ser14 residue. This is the first study to show correlations between the functional activity, tertiary structure, and partner recognition mode of Humanin and may lead to elucidation of the molecular mechanisms of the cytoprotective activity of Humanin.
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Conformational changes of Aβ (1-42) monomers in different solvents. J Mol Graph Model 2016; 65:8-14. [PMID: 26896721 DOI: 10.1016/j.jmgm.2016.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 01/16/2016] [Accepted: 02/06/2016] [Indexed: 11/21/2022]
Abstract
Amyloid proteins are known to be the main cause of numerous degenerative and neurodegenerative diseases. In general, amyloids are misfolded from monomers and they tend to have β-strand formations. These misfolded monomers are then transformed into oligomers, fibrils, and plaques. It is important to understand the forming mechanism of amyloids in order to prevent degenerative diseases to occur. Aβ protein is a highly noticeable protein which causes Alzheimer's disease. It is reported that solvents affect the forming mechanism of Aβ amyloids. In this research, Aβ1-42 was analyzed using an all-atom MD simulation with the consideration of effects induced by two disparate solvents: water and DMSO. As a result, two different conformation changes of Aβ1-42 were exhibited in each solvent. It was found that salt-bridge of Asp23 and Lys28 in Aβ1-42 was the key for amyloid folding based on the various analysis including hydrogen bond, electrostatic interaction energy and salt-bridge distance. Since this salt-bridge region plays a crucial role in initiating the misfolding of Aβ1-42, this research may shed a light for studies related in amyloid folding and misfolding.
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Gong Z, Tas E, Muzumdar R. Humanin and age-related diseases: a new link? Front Endocrinol (Lausanne) 2014; 5:210. [PMID: 25538685 PMCID: PMC4255622 DOI: 10.3389/fendo.2014.00210] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 11/22/2014] [Indexed: 12/16/2022] Open
Abstract
Humanin (HN) is 24-amino acid mitochondria-associated peptide. Since its initial discovery over a decade ago, a role for HN has been reported in many biological processes such as apoptosis, cell survival, substrate metabolism, inflammatory response, and response to stressors such as oxidative stress, ischemia, and starvation. HN and its potent analogs have been shown to have beneficial effects in many age-related diseases including Alzheimer's disease, stroke, diabetes, myocardial ischemia and reperfusion, atherosclerosis, amyotrophic lateral sclerosis, and certain types of cancer both in vitro and in vivo. More recently, an association between HN levels, growth hormone/insulin-like growth factor-1 (GH/IGF axis), and life span was demonstrated using various mouse models with mutations in the GH/IGF axis. The goal of this review is to summarize the current understanding of the role of HN in aging and age-related diseases.
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Affiliation(s)
- Zhenwei Gong
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Pediatrics, Division of Pediatric Endocrinology, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Emir Tas
- Department of Pediatrics, Division of Pediatric Endocrinology, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Radhika Muzumdar
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Pediatrics, Division of Pediatric Endocrinology, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- *Correspondence: Radhika Muzumdar, Department of Pediatrics, Children’s Hospital of Pittsburgh of UPMC, University of Pittsburgh School of Medicine, One Children’s Hospital Drive, 4401 Penn Avenue, Pittsburgh, PA 15224, USA e-mail:
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Equilibrium and folding simulations of NS4B H2 in pure water and water/2,2,2-trifluoroethanol mixed solvent: examination of solvation models. J Mol Model 2013; 19:3931-9. [DOI: 10.1007/s00894-013-1933-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 06/23/2013] [Indexed: 10/26/2022]
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Xu Z, Lazim R, Sun T, Mei Y, Zhang D. Solvent effect on the folding dynamics and structure of E6-associated protein characterized from ab initio protein folding simulations. J Chem Phys 2012; 136:135102. [PMID: 22482589 DOI: 10.1063/1.3698164] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Solvent effect on protein conformation and folding mechanism of E6-associated protein (E6ap) peptide are investigated using a recently developed charge update scheme termed as adaptive hydrogen bond-specific charge (AHBC). On the basis of the close agreement between the calculated helix contents from AHBC simulations and experimental results, we observed based on the presented simulations that the two ends of the peptide may simultaneously take part in the formation of the helical structure at the early stage of folding and finally merge to form a helix with lowest backbone RMSD of about 0.9 Å in 40% 2,2,2-trifluoroethanol solution. However, in pure water, the folding may start at the center of the peptide sequence instead of at the two opposite ends. The analysis of the free energy landscape indicates that the solvent may determine the folding clusters of E6ap, which subsequently leads to the different final folded structure. The current study demonstrates new insight to the role of solvent in the determination of protein structure and folding dynamics.
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Affiliation(s)
- Zhijun Xu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
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Lee HM, Jin B, Han SW, Kim SK. Conformational analysis of genotoxic benzo[a]pyrene-7,8-dione-duplex DNA adducts using a molecular dynamics method (II). J Biomol Struct Dyn 2011; 28:421-30. [PMID: 20919757 DOI: 10.1080/07391102.2010.10507371] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The conformations of the benzo[a]pyrene-7,8-quinone (BPQ) modified oligonucleotide were investigated using molecular dynamic simulation. In the initial structures, the central guanine base was modified with BPQ resulting in the formation of four structurally distinguishable 10-(N2-deoxyguanosyl)-9,10-dihydro-9-hydroxy benzo[a]pyrene-7,8-dione adducts (BPQ-G3,4). Each of the oligonucleotide adduct consisted of two conformers, namely syn and anti conformations, depending on the rotation around the glycosidic bond between BPQ and the guanine base. The results revealed that the BPQ moiety was located in the major groove for all four syn conformers. The relative energies of these conformers were high, and the backbone largely deviated from the B-form. On the other hand, BPQ was located in the minor groove with relatively low energies, and backbone was retained in all of the anti conformer cases. The most conceivable BPQ-modified double stranded oligonucleotide structure was proposed from the energy calculation and the structural analysis.
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Affiliation(s)
- Hyun Mee Lee
- Department of Chemistry, Yeungnam University, Daedong, Gyeongsan City, Gyeong-buk, 712-749, Republic of Korea
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Gong Z, Xiao Y, Xiao Y. RNA stability under different combinations of amber force fields and solvation models. J Biomol Struct Dyn 2011; 28:431-41. [PMID: 20919758 DOI: 10.1080/07391102.2010.10507372] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The proper matching of force field and solvent is critical to obtain correct result in molecular dynamics simulation of bio-molecules. This problem has been intensively investigated for protein but not for RNA yet. In this paper, we use standard molecular dynamics and replica exchange molecular dynamics to take a series of tests on the RNA stability under different combinations of Amber force field parameters (ff98, ff99 and ff99bsc0) and the general Born implicit solvent models (igb1, igb2 and igb5). It is found that only ff98 and ff99bsc0 with igb1 can keep the native conformations of RNA hairpin and duplex. Our results suggest that ff98 plus igb1 may be reasonable choice for molecular dynamics simulation of RNA dynamics.
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Affiliation(s)
- Zhou Gong
- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
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Wiesner J, Kříž Z, Kuča K, Jun D, Koča J. Influence of the acetylcholinesterase active site protonation on omega loop and active site dynamics. J Biomol Struct Dyn 2011; 28:393-403. [PMID: 20919754 DOI: 10.1080/07391102.2010.10507368] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Existence of alternative entrances in acetylcholinesterase (AChE) could explain the contrast between the very high AChE catalytic efficiency and the narrow and long access path to the active site revealed by X-ray crystallography. Alternative entrances could facilitate diffusion of the reaction products or at least water and ions from the active site. Previous molecular dynamics simulations identified side door and back door as the most probable alternative entrances. The simulations of non-inhibited AChE suggested that the back door opening events occur only rarely (0.8% of the time in the 10ns trajectory). Here we present a molecular dynamics simulation of non-inhibited AChE, where the back door opening appears much more often (14% of the time in the 12ns trajectory) and where the side door opening was observed quite frequently (78% of trajectory time). We also present molecular dynamics, where the back door does not open at all, or where large conformational changes of the AChE omega loop occur together with alternative passage opening events. All these differences in AChE dynamical behavior are caused by different protonation states of two glutamate residues located on bottom of the active site gorge (Glu202 and G450 in Mus musculus AChE). Our results confirm the results of previous molecular dynamics simulations, expand the view and suggest the probable reasons for the overall conformational behavior of AChE omega loop.
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Affiliation(s)
- Jiří Wiesner
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic
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Zhong L. Exposure of Hydrophobic Core in Human Prion Protein Pathogenic Mutant H187R. J Biomol Struct Dyn 2010; 28:355-61. [DOI: 10.1080/07391102.2010.10507365] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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12
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Chang TT, Huang HJ, Lee KJ, Yu HW, Chen HY, Tsai FJ, Sun MF, Chen CYC. Key Features for Designing Phosphodiesterase-5 Inhibitors. J Biomol Struct Dyn 2010; 28:309-21. [DOI: 10.1080/07391102.2010.10507361] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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13
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Poddar NK, Ansari ZA, Singh RKB, Movahedi AAM, Ahmad F. Effect of Oligosaccharides and their Monosaccharide Mixtures on the Stability of Proteins: A Scaled Particle Study. J Biomol Struct Dyn 2010; 28:331-41. [DOI: 10.1080/07391102.2010.10507363] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Cao Z, Liu L, Wang J. Effects of pH and Temperature on the Structural and Thermodynamic Character of a-syn12 Peptide in Aqueous Solution. J Biomol Struct Dyn 2010; 28:343-53. [DOI: 10.1080/07391102.2010.10507364] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Nasiri R, Bahrami H, Zahedi M, Moosavi-Movahedi AA, Sattarahmady N. A theoretical elucidation of glucose interaction with HSA's domains. J Biomol Struct Dyn 2010; 28:211-26. [PMID: 20645654 DOI: 10.1080/07391102.2010.10507354] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The interaction of different domains belonging to Human Serum Albumin (HSA) with open form of glucose have been investigated using molecular dynamics simulation methods. Applying docking, primary structures involving interaction of some residues with glucose have been obtained. Subsequently, equilibrium geometries at 300 K and minimum geometries have been determined for each of aforementioned structures by employing MD simulation and simulated annealing. The stability of species has been evaluated using a SAWSA v2.0 model. Ultimately, NBO analysis has been carried out to specify possible hydrogen bonding regarding the HSA interaction with glucose. Results obtained show that glucose can interact with Lys195, Lys199, and Glu153. In these interactions, each lysine forms an H-bonding with glucose. The H-bonding is obtained by stretching of N-H bond belonging to NH(3)(+) group of lysine along an oxygen atom of glucose. In addition, the above mentioned lysines are protonated, and there is an electrostatic interaction between glucose with Lys195 or Lys199. In addition, an H-bonding is formed between O atom of -COO group belonging to Glu153 and H atom of OH group belonging to glucose. Because, the N-H group of Lys195 interacts with the O atom of latter OH group, reaction of Lys195 is more desirable than that of Lys199. In fact, glucose is placed in the vicinity of Lys195 along with electrostatic interaction and H-bonding to Lys195 and Lys199 as well as H-bonding with Glu153, which subsequently reacts with Lys195. Thus, Lys195 is the primary site in reaction of glucose with HSA.
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Affiliation(s)
- Rasoul Nasiri
- Department of Chemistry, Faculty of Sciences, Shahid Beheshti University, Evin, 19839-63113, Tehran, Iran
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Tao Y, Rao ZH, Liu SQ. Insight derived from molecular dynamics simulation into substrate-induced changes in protein motions of proteinase K. J Biomol Struct Dyn 2010; 28:143-58. [PMID: 20645649 DOI: 10.1080/073911010010524953] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Because of the significant industrial, agricultural and biotechnological importance of serine protease proteinase K, it has been extensively investigated using experimental approaches such as X-ray crystallography, site-directed mutagenesis and kinetic measurement. However, detailed aspects of enzymatic mechanism such as substrate binding, release and relevant regulation remain unstudied. Molecular dynamics (MD) simulations of the proteinase K alone and in complex with the peptide substrate AAPA were performed to investigate the effect of substrate binding on the dynamics/molecular motions of proteinase K. The results indicate that during simulations the substrate-complexed proteinase K adopt a more compact and stable conformation than the substrate-free form. Further essential dynamics (ED) analysis reveals that the major internal motions are confined within a subspace of very small dimension. Upon substrate binding, the overall flexibility of the protease is reduced; and the noticeable displacements are observed not only in substrate-binding regions but also in regions opposite the substrate-binding groove/pockets. The dynamic pockets caused by the large concerted motions are proposed to be linked to the substrate recognition, binding, orientation and product release; and the significant displacements in regions opposite the binding groove/pockets are considered to play a role in modulating the dynamics of enzyme-substrate interaction. Our simulation results complement the biochemical and structural studies, highlighting the dynamic mechanism of the functional properties of proteinase K.
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Affiliation(s)
- Yan Tao
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, Yunnan, P R China
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Varughese JF, Chalovich JM, Li Y. Molecular dynamics studies on troponin (TnI-TnT-TnC) complexes: insight into the regulation of muscle contraction. J Biomol Struct Dyn 2010; 28:159-74. [PMID: 20645650 DOI: 10.1080/07391102.2010.10507350] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Mutations of any subunit of the troponin complex may lead to serious disorders. Rational approaches to managing these disorders require knowledge of the complex interactions among the three subunits that are required for proper function. Molecular dynamics (MD) simulations were performed for both skeletal (sTn) and cardiac (cTn) troponin. The interactions and correlated motions among the three components of the troponin complex were analyzed using both Molecular Mechanics-Generalized Born Surface Area (MMGBSA) and cross-correlation techniques. The TnTH2 helix was strongly positively correlated with the two long helices of TnI. The C domain of TnC was positively correlated with TnI and TnT. The N domain of TnC was negatively correlated with TnI and TnT in cTn, but not in sTn. The two C-domain calcium-binding sites of TnC were dynamically correlated. The two regulatory N-domain calcium-binding sites of TnC were dynamically correlated, even though the calcium-binding site I is dysfunctional. The strong interaction residue pairs and the strong dynamically correlated residues pairs among the three components of troponin complexes were identified. These correlated motions are consistent with the idea that there is a high degree of cooperativity among the components of the regulatory complex in response to Ca(2+) and other effectors. This approach may give insight into the mechanism by which mutations of troponin cause disease. It is interesting that some observed disease causing mutations fall within regions of troponin that are strongly correlated or interacted.
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Affiliation(s)
- Jayson F Varughese
- Department of Chemistry, Brody School of Medicine, East Carolina University, Greenville, NC 27858, USA
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Mangels C, Kellner R, Einsiedel J, Weiglmeier PR, Rosch P, Gmeiner P, Schwarzinger S. The therapeutically anti-prion active antibody-fragment scFv-W226: paramagnetic relaxation-enhanced NMR spectroscopy aided structure elucidation of the paratope-epitope interface. J Biomol Struct Dyn 2010; 28:13-22. [PMID: 20476792 DOI: 10.1080/07391102.2010.10507340] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Antibodies have become indispensable reagents with numerous applications in biological and biotechnical analysis, in diagnostics as well as in therapy. In all cases, selective interaction with an epitope is crucial and depends on the conformation of the paratope. While epitopes are routinely mapped at high throughput, methods revealing structural insights on a rather short timescale are rare. We here demonstrate paramagnetic relaxation-enhanced (PRE) NMR spectroscopy to be a powerful tool unraveling structural information about epitope-orientation in a groove spanned by the complementary determining regions. In particular, we utilize the spin label TOAC, which is fused to the peptidic epitope using standard solid-phase chemistry and which is characterized by a reduced mobility compared to, e.g., spin labels attached to the side-chain functionalities of cysteine or lysine residues. We apply the method to determine the orientation of helix 1 of the prion protein, which is the epitope for the therapeutically anti-prion active scF(v) fragment W226.
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Affiliation(s)
- Christian Mangels
- Department of Biopolymers, Universitat Bayreuth, Universitatsstrasse 30, 95440 Bayreuth, Germany
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Yuan Y, Knaggs MH, Poole LB, Fetrow JS, Salsbury FR. Conformational and oligomeric effects on the cysteine pK(a) of tryparedoxin peroxidase. J Biomol Struct Dyn 2010; 28:51-70. [PMID: 20476795 DOI: 10.1080/07391102.2010.10507343] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Typical 2-Cys peroxiredoxins (Prxs) are peroxidases which regulate cell signaling pathways, apoptosis, and differentiation. These enzymes are obligate homodimers, and can form decamers in solution. During catalysis, Prxs exhibit cysteine-dependent reactivity which requires the deprotonation of the peroxidatic cysteine (C(p)) supported by a lowered pK(a) in the initial step. We present the results of molecular dynamics simulations combined with pKa calculations on the monomeric, dimeric and decameric forms of one typical 2-Cys Prx, the tryparedoxin peroxidase from Trypanosoma cruzi (PDB id, 1uul). The calculations indicate that C(p) (C52) pK(a) values are highly affected by oligomeric state; an unshifted C(p) pK(a) (approximately 8.3, comparable to the pK(a) of isolated cysteine) is calculated for the monomer. In the dimers, starting with essentially identical structures, the C(p)s evolve dynamically asymmetric pK(a)s during the simulations; one subunit's C(p) pK(a) is shifted downward at a time, while the other is unshifted. However, when averaged over time, or multiple simulations, the two subunits within a dimer exhibit the same C(p), showing no preference for a lowered pK(a) in either subunit. Two conserved pathways that communicate the asymmetric pK(a)s between C(p)s of different subunits can be identified. In the decamer, all the C(p) pK(a)s are shifted downward, with slight asymmetry in the dimers which form the decamers. Structural analyses implicate oligomerization effects as responsible for these oligomeric state-dependent C(p) pK(a) shifts. The intra-dimer and the inter-dimer subunit contacts in the decamer restrict the conformations of the side chains of several residues (T49, T54 and E55) calculated to be key in shifting the C(p) pK(a). In addition, the backbone fluctuations of a few residues (M46, D47 and F48) result in a different electrostatic environment for the C(p) in dimers relative to the monomers. These side chain and backbone interactions which contribute to pK(a) modulation indicate the importance of oligomerization to the function of the typical 2-Cys Prxs.
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Affiliation(s)
- Ye Yuan
- Departments of Physics and Wake Forest University, 1834 Reynold Road, Winston-Salem, North Carolina 27106, USA
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Mehrnejad F, Khadem-Maaref M, Ghahremanpour MM, Doustdar F. Mechanisms of amphipathic helical peptide denaturation by guanidinium chloride and urea: a molecular dynamics simulation study. J Comput Aided Mol Des 2010; 24:829-41. [DOI: 10.1007/s10822-010-9377-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Accepted: 07/29/2010] [Indexed: 10/19/2022]
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Koshy C, Parthiban M, Sowdhamini R. 100 ns Molecular Dynamics Simulations to Study Intramolecular Conformational Changes in Bax. J Biomol Struct Dyn 2010; 28:71-83. [DOI: 10.1080/07391102.2010.10507344] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Chang LK, Zhao JH, Liu HL, Wu JW, Chuang CK, Liu KT, Chen JT, Tsai WB, Ho Y. The Importance of Steric Zipper on the Aggregation of the MVGGVV Peptide Derived from the Amyloid β Peptide. J Biomol Struct Dyn 2010; 28:39-50. [DOI: 10.1080/07391102.2010.10507342] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Yu Y, Wang Y, He J, Liu Y, Li H, Zhang H, Song Y. Structural and Dynamic properties of a new Amyloidogenic chicken cystatin Mutant I108T. J Biomol Struct Dyn 2010; 27:641-9. [DOI: 10.1080/07391102.2010.10508578] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Sharma S, Sonavane UB, Joshi RR. Molecular dynamics simulations of cyclohexyl modified peptide nucleic acids (PNA). J Biomol Struct Dyn 2010; 27:663-76. [PMID: 20085383 DOI: 10.1080/07391102.2010.10508580] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Peptide Nucleic Acids (PNA) that bind sequence specifically to DNA/RNA are of major interest in the field of molecular biology and could form the basis for gene-targeted drugs. Molecular dynamics simulations are aimed to characterize the structural and dynamical features to understand the effect of backbone modification on the structure and dynamics along with the stability of the resulting 10mer complexes of PNA with DNA/RNA. Twelve Molecular Dynamics (MD) simulations of duplexes and triplexes with and without cyclohexyl modification were carried out for 10ns each. The simulations indicate that the cyclohexyl modification with different stereoisomers has influenced all the PNA-DNA/RNA complexes. Modification has added rigidity to backbone by restricting beta to +60 in case of (1R,2S) cyclohexyl PNA and to -60 in case of (1S,2R) cyclohexyl PNA. The results of MD simulations were able to show the backbone rigidification and preference for RNA complexes over DNA due to presence of cyclohexyl ring in the PNA backbone.
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Affiliation(s)
- Smriti Sharma
- Bioinformatics Team, Centre for Development of Advanced Computing, Ganesh Khind, Pune University Campus, Pune - 411007
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