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Rohmer M, Ucak Ö, Fredrick R, Binder WH. Chiral amines as initiators for ROP and their chiral induction on poly(2-aminoisobutyric acid) chains. Polym Chem 2021. [DOI: 10.1039/d1py01021b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chirality induction by chiral amines in poly(amino acid)s by ring opening polymerization.
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Affiliation(s)
- Matthias Rohmer
- Martin-Luther University Halle Wittenberg, Chair of Macromolecular Chemistry, D-06120 Halle, Germany
| | - Özgün Ucak
- Martin-Luther University Halle Wittenberg, Chair of Macromolecular Chemistry, D-06120 Halle, Germany
| | - Rahul Fredrick
- Martin-Luther University Halle Wittenberg, Chair of Polymer Reaction Engineering, D-06099 Halle, Germany
| | - Wolfgang H. Binder
- Martin-Luther University Halle Wittenberg, Chair of Macromolecular Chemistry, D-06120 Halle, Germany
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2
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Conformational dynamics of [Formula: see text]-conotoxin PnIB in complex solvent systems. Mol Divers 2019; 24:1291-1299. [PMID: 31502188 DOI: 10.1007/s11030-019-09993-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/03/2019] [Indexed: 01/13/2023]
Abstract
Cone snails are slow-moving animals that secure survival by injecting to their prey a concoction of highly potent and stable neurotoxic peptides called conotoxins. These small toxins (~ 10-30 AA) interact with ion channels and their diverse structures account for various variables such as the environment and the prey of preference. This study probed the conformational space of α-conotoxin PnIB from Conus pennaceus by performing all-atom molecular dynamics simulations on the conotoxin in complex solvent systems of water and octanol. Secondary structure analyses showed a uniform conformation for the pure (C100Oc, C100W) and minute (C95Oc, C5Oc) systems. In C50Oc, however, structural changes were observed. The original helices were converted to turns and were shown to happen simultaneously with the elongation of the helix and shortening of end-to-end distance. The transitions complement the orientation of the peptide at the interface. The shift to the broken helix conformation is marked by the rearrangement of solvent molecules to a framework that favors the accumulation of water molecules at residues 6-11 of the H2 region. This promotes specific protein-solvent interactions that facilitate secondary structure transitions. As PnIB has shown favorable binding toward neuronal nicotinic acetylcholine receptors, this study may provide insights on this conotoxin's therapeutic potential. Description: Structural changes in PnIB are accompanied by a simultaneous change in solvent density.
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Cheng C, Jiang T, Wu Y, Cui L, Qin S, He B. Elucidation of lid open and orientation of lipase activated in interfacial activation by amphiphilic environment. Int J Biol Macromol 2018; 119:1211-1217. [DOI: 10.1016/j.ijbiomac.2018.07.158] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 11/25/2022]
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4
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Thiruvengadam K, Baskaran SK, Pennathur G. Understanding domain movements and interactions of Pseudomonas aeruginosa lipase with lipid molecule tristearoyl glycerol: A molecular dynamics approach. J Mol Graph Model 2018; 85:190-197. [PMID: 30227364 DOI: 10.1016/j.jmgm.2018.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 06/27/2018] [Accepted: 09/03/2018] [Indexed: 10/28/2022]
Abstract
Lipases are biocatalysts which exhibit optimal activity at the aqueous-lipid interface. Molecular Dynamics (MD) Simulation studies on lipases have revealed the structural changes occurring in the enzyme, at the loop-helix-loop, often designated as the "lid", which is responsible for its interfacial activation. In recent years, MD simulation of lipases at molecular level have been studied in detail, whereas very few studies are carried over on its interaction with lipid molecules. Hence, in the current study we have investigated molecular interaction of bacterial lipase (Pseudomonas aeruginosa lipase, PAL) with a lipid molecule (tristearoyl glycerol, TGL). This provides an insight into the interfacial activation of the enzyme. The lipid molecule was placed near the lids of the enzyme and MD simulations were performed for 100 ns to understand the nature and site of the interaction. The results clearly indicate that, the presence of a lipid molecule near the lids affects the motion of the enzyme through changes in conformation. Lipid molecule near the lids reduces the movements of both lids, and the TGL molecule was observed moving towards the active site. The movement of the lids, surface accessibility and the domain movements of PAL are discussed and the results provide valuable insight in to the role played by the two lids in the interfacial activation of PAL with TGL.
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Affiliation(s)
| | | | - Gautam Pennathur
- Department of Biotechnology, Anna University, Chennai, 600025, India.
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Wang J, Liu K, Xing R, Yan X. Peptide self-assembly: thermodynamics and kinetics. Chem Soc Rev 2016; 45:5589-5604. [PMID: 27487936 DOI: 10.1039/c6cs00176a] [Citation(s) in RCA: 626] [Impact Index Per Article: 78.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Self-assembling systems play a significant role in physiological functions and have therefore attracted tremendous attention due to their great potential for applications in energy, biomedicine and nanotechnology. Peptides, consisting of amino acids, are among the most popular building blocks and programmable molecular motifs. Nanostructures and materials assembled using peptides exhibit important potential for green-life new technology and biomedical applications mostly because of their bio-friendliness and reversibility. The formation of these ordered nanostructures pertains to the synergistic effect of various intermolecular non-covalent interactions, including hydrogen-bonding, π-π stacking, electrostatic, hydrophobic, and van der Waals interactions. Therefore, the self-assembly process is mainly driven by thermodynamics; however, kinetics is also a critical factor in structural modulation and function integration. In this review, we focus on the influence of thermodynamic and kinetic factors on structural assembly and regulation based on different types of peptide building blocks, including aromatic dipeptides, amphiphilic peptides, polypeptides, and amyloid-relevant peptides.
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Affiliation(s)
- Juan Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
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6
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Lindsay RJ, Johnson QR, Evangelista W, Nellas RB, Shen T. DMSO enhanced conformational switch of an interfacial enzyme. Biopolymers 2016; 105:864-72. [PMID: 27463323 DOI: 10.1002/bip.22924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 07/25/2016] [Indexed: 11/05/2022]
Abstract
Interfacial proteins function in unique heterogeneous solvent environments, such as water-oil interfaces. One important example is microbial lipase, which is activated in an oil-water emulsion phase and has many important enzymatic functions. A unique aprotic dipolar organic solvent, dimethyl sulfoxide (DMSO), has been shown to increase the activity of lipases, but the mechanism behind this enhancement is still unknown. Here, all-atom molecular dynamics simulations of lipase in a binary solution were performed to examine the effects of DMSO on the dynamics of the gating mechanism. The amphiphilic α5 region of the lipase was a focal point for the analysis, since the structural ordering of α5 has been shown to be important for gating under other perturbations. Compared to the closed-gorge ensemble in an aqueous environment, the conformational ensemble shifts towards open-gorge structures in the presence of DMSO solvents. Increased width of the access channel is particularly prevalent in 45% and 60% DMSO concentrations (w/w). As the amount of DMSO increases, the α5 region of the lipase becomes more α-helical, as we previously observed in studies that address water-oil interfacial and high pressure activation. We believe that the structural ordering of α5 plays an essential role on gating and lipase activity.
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Affiliation(s)
- Richard J Lindsay
- UT-ORNL Graduate School of Genome Science and Technology, Knoxville, TN, 37996.,Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, TN, 37830
| | - Quentin R Johnson
- Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, TN, 37830.,National Institute for Mathematical and Biological Synthesis, Knoxville, TN, 37996
| | - Wilfredo Evangelista
- Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, TN, 37830.,Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996
| | - Ricky B Nellas
- Institute of Chemistry, University of the Philippines Diliman, Quezon City, Philippines
| | - Tongye Shen
- Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, TN, 37830. .,Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996.
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Johnson QR, Lindsay RJ, Nellas RB, Shen T. Pressure-induced conformational switch of an interfacial protein. Proteins 2016; 84:820-7. [DOI: 10.1002/prot.25031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 02/04/2016] [Accepted: 03/01/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Quentin R. Johnson
- UT-ORNL Graduate School of Genome Science and Technology; University of Tennessee; Knoxville Tennessee 37996
- Oak Ridge National Laboratory; Center for Molecular Biophysics; Oak Ridge Tennessee 37830
| | - Richard J. Lindsay
- Oak Ridge National Laboratory; Center for Molecular Biophysics; Oak Ridge Tennessee 37830
- Department of Biochemistry and Cellular & Molecular Biology; University of Tennessee; Knoxville Tennessee 37996
| | - Ricky B. Nellas
- Institute of Chemistry, University of the Philippines Diliman; Quezon City Philippines
| | - Tongye Shen
- Oak Ridge National Laboratory; Center for Molecular Biophysics; Oak Ridge Tennessee 37830
- Department of Biochemistry and Cellular & Molecular Biology; University of Tennessee; Knoxville Tennessee 37996
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Kaur H, Sasidhar YU. Environmental polarity induces conformational transitions in a helical peptide sequence from bacteriophage T4 lysozyme and its tandem duplicate: a molecular dynamics simulation study. J Mol Model 2015; 21:88. [PMID: 25773700 DOI: 10.1007/s00894-015-2621-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 02/15/2015] [Indexed: 11/29/2022]
Abstract
Our recent molecular dynamics (MD) simulation of an insertion/duplication mutant 'L20' of bacteriophage T4 lysozyme demonstrated a solvent induced α→β transition in a loosely held duplicate helical region, while α-helical conformation in the parent region was relatively stabilized by its tertiary interactions with the neighboring residues. The solution NMR of the parent helical sequence, sans its protein context, showed no inherent tendency to adopt a particular secondary structure in pure water but showed α-helical propensity in TFE/water and SDS micelles. In this study we investigate the conformational preference of the 'parent' and 'duplicate' sequences, sans the protein context, in pure water and an apolar TFE/water solution. Apolar TFE/water solution is a model for non-polar protein context. We performed MD simulations of the two peptides, in explicit water and 80% (v/v) TFE/water, using GROMOS 53a6 force field, at 300 K and 1 bar (under NPT conditions). We show that in TFE/water mixture, salt bridges are stabilized by apolar TFE molecules and main chain-main chain hydrogen bonds promote the α-helical conformation, particularly in the duplicate peptide. Solvent exposure, in pure water, resulted in an α→β transition to form a triple stranded β-sheet structure in the 'duplicate' sequence, with a rare psi-loop topology, while a mixture of turn/bend conformations were adopted by the 'parent' sequence. Thus the differences in conformational preference of the parent and duplicate sequence sans protein context, in pure water and TFE/water, implicate the importance of the environment polarity in dictating the peptide conformation. Mechanism of folding of the observed psi-loop in the duplicate sequence gives insights into folding of this rare β-sheet topology.
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Affiliation(s)
- Harpreet Kaur
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
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Johnson QR, Lindsay RJ, Nellas RB, Fernandez EJ, Shen T. Mapping allostery through computational glycine scanning and correlation analysis of residue-residue contacts. Biochemistry 2015; 54:1534-41. [PMID: 25658131 DOI: 10.1021/bi501152d] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Understanding allosteric mechanisms is essential for the physical control of molecular switches and downstream cellular responses. However, it is difficult to decode essential allosteric motions in a high-throughput scheme. A general two-pronged approach to performing automatic data reduction of simulation trajectories is presented here. The first step involves coarse-graining and identifying the most dynamic residue-residue contacts. The second step is performing principal component analysis of these contacts and extracting the large-scale collective motions expressed via these residue-residue contacts. We demonstrated the method using a protein complex of nuclear receptors. Using atomistic modeling and simulation, we examined the protein complex and a set of 18 glycine point mutations of residues that constitute the binding pocket of the ligand effector. The important motions that are responsible for the allostery are reported. In contrast to conventional induced-fit and lock-and-key binding mechanisms, a novel "frustrated-fit" binding mechanism of RXR for allosteric control was revealed.
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Affiliation(s)
- Quentin R Johnson
- UT-ORNL Graduate School of Genome Science and Technology , Knoxville, Tennessee 37996, United States
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Crisma M, De Zotti M, Formaggio F, Peggion C, Moretto A, Toniolo C. Handedness preference and switching of peptide helices. Part II: Helices based on noncodedα-amino acids. J Pept Sci 2015; 21:148-77. [DOI: 10.1002/psc.2743] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 12/19/2014] [Accepted: 12/19/2014] [Indexed: 12/27/2022]
Affiliation(s)
| | - Marta De Zotti
- Department of Chemistry; University of Padova; Padova Italy
| | - Fernando Formaggio
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| | | | - Alessandro Moretto
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| | - Claudio Toniolo
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
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Shen H, Cheng W, Zhang FS. Structural conservation of the short α-helix in modified higher and lower polarity water solutions. RSC Adv 2015. [DOI: 10.1039/c4ra14739a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Which conformation is preferred when the polarity of water molecules is scaled byEP=ELJ+S2EC?
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Affiliation(s)
- Hao Shen
- The Key Laboratory of Beam Technology and Material Modification of the Ministry of Education
- College of Nuclear Science and Technology
- Beijing Normal University
- Beijing 100875
- China
| | - Wei Cheng
- The Key Laboratory of Beam Technology and Material Modification of the Ministry of Education
- College of Nuclear Science and Technology
- Beijing Normal University
- Beijing 100875
- China
| | - Feng-Shou Zhang
- The Key Laboratory of Beam Technology and Material Modification of the Ministry of Education
- College of Nuclear Science and Technology
- Beijing Normal University
- Beijing 100875
- China
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