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The role of glycine residues at the C-terminal peptide segment in antinociceptive activity: a molecular dynamics simulation. J Mol Model 2012. [PMID: 23179767 DOI: 10.1007/s00894-012-1666-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Elucidating structural determinants in the functional regions of toxins can provide useful knowledge for designing novel analgesic peptides. Glycine residues at the C-terminal region of the neurotoxin BmK AGP-SYPU2 from the scorpion Buthus martensii Karsch (BmK) have been shown to be crucial to its analgesic activity. However, there has been no research on the structure-function relationship between the C-terminal segment of this toxin and its analgesic activity. To address this issue, we performed three MD simulations: one on the native structure and the other two on mutants of that structure. Results of these calculations suggest that the existence of glycine residues at the C-terminal segment stabilizes the protruding topology of the NC domain, which is considered an important determinant of the analgesic activity of BmK AGP-SYPU2.
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2
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Rajasekaran M, Chen C. Structural effect of the L16Q, K50E, and R53P mutations on homeodomain of pituitary homeobox protein 2. Int J Biol Macromol 2012; 51:305-13. [PMID: 22584078 DOI: 10.1016/j.ijbiomac.2012.05.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 05/03/2012] [Accepted: 05/05/2012] [Indexed: 10/28/2022]
Abstract
The transcription factor pituitary homeobox protein 2 (PITX2) is involved in genetic control of development. Mutations in PITX2, most in the homeodomain, cause the autosomal-dominant disorder Rieger syndrome. The mutants L16Q, K50E and R53P destabilize the structure and disrupt DNA-binding activity. The biological functions of these mutants have been characterized but not the structural basis behind the loss of DNA-binding activity. We performed multiple molecular dynamics simulations at 37°C to investigate the structural and dynamic effects of the 3 PITX2 homeodomain mutants. Compared with the wild type (WT), the L16Q mutant induces a kink in the α3 helix, which is stabilized by the hydrogen bond of Q21-R59. The disruption in backbone hydrogen bonds of V47-N51 and W48-R52 leads to a kink formation in the α3 helix of K50E. The R53P mutant alters the relative orientation of helices, which is apparently stabilized by the formation of new hydrogen bonds of T38-Q11, T38-Q12, T38-R2, N39-R2, L40-Q1, L40-R2, and T41-Q4. The hydrophobic core residues F8, L13, L40 and V45 change their positions in all mutants to break the hydrophobic core. Thus, changes in helical orientations and hydrophobic core cause rearrangement of the DNA-binding surface and disrupt DNA-binding activity in the mutants. The structural and molecular dynamics properties of 3 PITX2 homeodomain mutants differ from those of the WT, especially in formation of a kink in the recognition helix, change in the packing of helices and disruption of the hydrophobic core. This structural basis for the loss of DNA-binding activity for these polymorphisms may help in understanding the effect of mutations on other homeodomains with other diseases.
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Affiliation(s)
- M Rajasekaran
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
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3
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Telke AA, Ghatge SS, Kang SH, Thangapandian S, Lee KW, Shin HD, Um Y, Kim SW. Construction and characterization of chimeric cellulases with enhanced catalytic activity towards insoluble cellulosic substrates. BIORESOURCE TECHNOLOGY 2012; 112:10-7. [PMID: 22409983 DOI: 10.1016/j.biortech.2012.02.066] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 02/13/2012] [Accepted: 02/15/2012] [Indexed: 05/11/2023]
Abstract
The chimeric proteins viz. CBM3-Cel9A, CBM4-Cel9A and CBM30-Cel9A, are constructed by fusion of family 3, 4, and 30 cellulose binding modules (CBMs) to N-terminus of family 9 endoglucanase (Cel9A) from Alicyclobacillus acidocaldrious. The chimeric enzymes were successfully expressed in Escherichia coli and purified to homogeneity. The chimeric enzymes showed significant increase in Avicel (8-12 folds) and filter paper (7-10 folds) degradation activities compared to Cel9A endoglucanase. Computational protein modeling and simulation on the chimeric enzymes were applied to analyze the fused CBMs effect on the increased insoluble cellulosic substrates degradation activity. Thin layer chromatography analysis of the enzymatic hydrolysis products and distribution of reducing sugars between soluble and insoluble fractions indicated processive cleavage of insoluble cellulosic substrates by the chimeras. The fused CBMs played a critical accessory role for the Cel9A catalytic domain and changed its character to facilitate the processive cleavage of insoluble cellulosic substrates.
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Affiliation(s)
- Amar A Telke
- Division of Applied Life Sciences (BK21), PMBBRC, Gyeongsang National University, 900 Gajwa-dong, Jinju, Gyeongnam 660-701, Republic of Korea
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4
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Molecular modeling of the M3 acetylcholine muscarinic receptor and its binding site. J Biomed Biotechnol 2012; 2012:789741. [PMID: 22500107 PMCID: PMC3303834 DOI: 10.1155/2012/789741] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 11/08/2011] [Indexed: 11/21/2022] Open
Abstract
The present study reports the results of a combined computational and site mutagenesis study designed to provide new insights into the orthosteric binding site of the human M3 muscarinic acetylcholine receptor. For this purpose a three-dimensional structure of the receptor at atomic resolution was built by homology modeling, using the crystallographic structure of bovine rhodopsin as a template. Then, the antagonist N-methylscopolamine was docked in the model and subsequently embedded in a lipid bilayer for its refinement using molecular dynamics simulations. Two different lipid bilayer compositions were studied: one component palmitoyl-oleyl phosphatidylcholine (POPC) and two-component palmitoyl-oleyl phosphatidylcholine/palmitoyl-oleyl phosphatidylserine (POPC-POPS). Analysis of the results suggested that residues F222 and T235 may contribute to the ligand-receptor recognition. Accordingly, alanine mutants at positions 222 and 235 were constructed, expressed, and their binding properties determined. The results confirmed the role of these residues in modulating the binding affinity of the ligand.
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5
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Fanelli F, De Benedetti PG. Update 1 of: computational modeling approaches to structure-function analysis of G protein-coupled receptors. Chem Rev 2011; 111:PR438-535. [PMID: 22165845 DOI: 10.1021/cr100437t] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Francesca Fanelli
- Dulbecco Telethon Institute, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena, Italy.
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6
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Kim TY, Schlieter T, Haase S, Alexiev U. Activation and molecular recognition of the GPCR rhodopsin--insights from time-resolved fluorescence depolarisation and single molecule experiments. Eur J Cell Biol 2011; 91:300-10. [PMID: 21803442 DOI: 10.1016/j.ejcb.2011.03.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 03/29/2011] [Accepted: 03/29/2011] [Indexed: 10/18/2022] Open
Abstract
The cytoplasmic surface of the G-protein coupled receptor (GPCR) rhodopsin is a key element in membrane receptor activation, molecular recognition by signalling molecules, and receptor deactivation. Understanding of the coupling between conformational changes in the intramembrane domain and the membrane-exposed surface of the photoreceptor rhodopsin is crucial for the elucidation of the molecular mechanism in GPCR activation. As little is known about protein dynamics, particularly the conformational dynamics of the cytoplasmic surface elements on the nanoseconds timescale, we utilised time-resolved fluorescence anisotropy experiments and site-directed fluorescence labelling to provide information on both, conformational space and motion. We summarise our recent advances in understanding rhodopsin dynamics and function using time-resolved fluorescence depolarisation and single molecule fluorescence experiments, with particular focus on the amphipathic helix 8, lying parallel to the cytoplasmic membrane surface and connecting transmembrane helix 7 with the long C-terminal tail.
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Affiliation(s)
- Tai-Yang Kim
- Physics Department, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
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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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8
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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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9
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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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11
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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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12
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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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13
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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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14
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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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15
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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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16
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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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17
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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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18
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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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19
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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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Chen CYC. Weighted Equation and Rules—A Novel Concept for Evaluating Protein-Ligand Interaction. J Biomol Struct Dyn 2009; 27:271-82. [DOI: 10.1080/07391102.2009.10507315] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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