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Böker A, Paul W. Thermodynamics and Conformations of Single Polyalanine, Polyserine, and Polyglutamine Chains within the PRIME20 Model. J Phys Chem B 2022; 126:7286-7297. [DOI: 10.1021/acs.jpcb.2c04360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Arne Böker
- Institut für Physik, Martin Luther-Universität Halle-Wittenberg, von Seckendorff Platz 1, 06120 Halle, Germany
| | - Wolfgang Paul
- Institut für Physik, Martin Luther-Universität Halle-Wittenberg, von Seckendorff Platz 1, 06120 Halle, Germany
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2
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Bovine hemoglobin thermal stability in the presence of naringenin: Calorimetric, spectroscopic and molecular modeling studies. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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3
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Ozgur B, Sayar M. Representation of the conformational ensemble of peptides in coarse grained simulations. J Chem Phys 2020; 153:054108. [DOI: 10.1063/5.0012391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Mehmet Sayar
- Chemical and Biological Engineering and Mechanical Engineering Departments, College of Engineering, Koç University, 34450 Istanbul, Turkey
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4
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Wang C, Piroozan N, Javidpour L, Sahimi M. Effect of the geometry of confining media on the stability and folding rate of α -helix proteins. J Chem Phys 2018; 148:194305. [PMID: 30307193 DOI: 10.1063/1.5020841] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Protein folding in confined media has attracted wide attention over the past 15 years due to its importance to both in vivo and in vitro applications. It is generally believed that protein stability increases by decreasing the size of the confining medium, if the medium's walls are repulsive, and that the maximum folding temperature in confinement is in a pore whose size D 0 is only slightly larger than the smallest dimension of a protein's folded state. Until recently, the stability of proteins in pores with a size very close to that of the folded state has not received the attention it deserves. In a previous paper [L. Javidpour and M. Sahimi, J. Chem. Phys. 135, 125101 (2011)], we showed that, contrary to the current theoretical predictions, the maximum folding temperature occurs in larger pores for smaller α-helices. Moreover, in very tight pores, the free energy surface becomes rough, giving rise to a new barrier for protein folding close to the unfolded state. In contrast to unbounded domains, in small nanopores proteins with an α-helical native state that contain the β structures are entropically stabilized implying that folding rates decrease notably and that the free energy surface becomes rougher. In view of the potential significance of such results to interpretation of many sets of experimental data that could not be explained by the current theories, particularly the reported anomalously low rates of folding and the importance of entropic effects on proteins' misfolded states in highly confined environments, we address the following question in the present paper: To what extent the geometry of a confined medium affects the stability and folding rates of proteins? Using millisecond-long molecular dynamics simulations, we study the problem in three types of confining media, namely, cylindrical and slit pores and spherical cavities. Most importantly, we find that the prediction of the previous theories that the dependence of the maximum folding temperature T f on the size D of a confined medium occurs in larger media for larger proteins is correct only in spherical geometry, whereas the opposite is true in the two other geometries that we study. Also studied is the effect of the strength of the interaction between the confined media's walls and the proteins. If the walls are only weakly or moderately attractive, a complex behavior emerges that depends on the size of the confining medium.
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Affiliation(s)
- Congyue Wang
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
| | - Nariman Piroozan
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
| | - Leili Javidpour
- Departments of Energy Engineering and Physics, Amirkabir University of Technology, Tehran 15875-4413, Iran
| | - Muhammad Sahimi
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
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5
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Zheng S, Shing KS, Sahimi M. Dynamics of proteins aggregation. II. Dynamic scaling in confined media. J Chem Phys 2018; 148:104305. [PMID: 29544316 DOI: 10.1063/1.5008543] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In this paper, the second in a series devoted to molecular modeling of protein aggregation, a mesoscale model of proteins together with extensive discontinuous molecular dynamics simulation is used to study the phenomenon in a confined medium. The medium, as a model of a crowded cellular environment, is represented by a spherical cavity, as well as cylindrical tubes with two aspect ratios. The aggregation process leads to the formation of β sheets and eventually fibrils, whose deposition on biological tissues is believed to be a major factor contributing to many neuro-degenerative diseases, such as Alzheimer's, Parkinson's, and amyotrophic lateral sclerosis diseases. Several important properties of the aggregation process, including dynamic evolution of the total number of the aggregates, the mean aggregate size, and the number of peptides that contribute to the formation of the β sheets, have been computed. We show, similar to the unconfined media studied in Paper I [S. Zheng et al., J. Chem. Phys. 145, 134306 (2016)], that the computed properties follow dynamic scaling, characterized by power laws. The existence of such dynamic scaling in unconfined media was recently confirmed by experiments. The exponents that characterize the power-law dependence on time of the properties of the aggregation process in spherical cavities are shown to agree with those in unbounded fluids at the same protein density, while the exponents for aggregation in the cylindrical tubes exhibit sensitivity to the geometry of the system. The effects of the number of amino acids in the protein, as well as the size of the confined media, have also been studied. Similarities and differences between aggregation in confined and unconfined media are described, including the possibility of no fibril formation, if confinement is severe.
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Affiliation(s)
- Size Zheng
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
| | - Katherine S Shing
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
| | - Muhammad Sahimi
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
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6
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Zheng S, Javidpour L, Shing KS, Sahimi M. Dynamics of proteins aggregation. I. Universal scaling in unbounded media. J Chem Phys 2017; 145:134306. [PMID: 27782447 DOI: 10.1063/1.4962837] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
It is well understood that in some cases proteins do not fold correctly and, depending on their environment, even properly-folded proteins change their conformation spontaneously, taking on a misfolded state that leads to protein aggregation and formation of large aggregates. An important factor that contributes to the aggregation is the interactions between the misfolded proteins. Depending on the aggregation environment, the aggregates may take on various shapes forming larger structures, such as protein plaques that are often toxic. Their deposition in tissues is a major contributing factor to many neuro-degenerative diseases, such as Alzheimer's, Parkinson's, amyotrophic lateral sclerosis, and prion. This paper represents the first part in a series devoted to molecular simulation of protein aggregation. We use the PRIME, a meso-scale model of proteins, together with extensive discontinuous molecular dynamics simulation to study the aggregation process in an unbounded fluid system, as the first step toward MD simulation of the same phenomenon in crowded cellular environments. Various properties of the aggregates have been computed, including dynamic evolution of aggregate-size distribution, mean aggregate size, number of peptides that contribute to the formation of β sheets, number of various types of hydrogen bonds formed in the system, radius of gyration of the aggregates, and the aggregates' diffusivity. We show that many of such quantities follow dynamic scaling, similar to those for aggregation of colloidal clusters. In particular, at long times the mean aggregate size S(t) grows with time as, S(t) ∼ tz, where z is the dynamic exponent. To our knowledge, this is the first time that the qualitative similarity between aggregation of proteins and colloidal aggregates has been pointed out.
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Affiliation(s)
- Size Zheng
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
| | - Leili Javidpour
- School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran
| | - Katherine S Shing
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
| | - Muhammad Sahimi
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
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7
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Cheon M, Kang M, Chang I. Polymorphism of fibrillar structures depending on the size of assembled Aβ 17-42 peptides. Sci Rep 2016; 6:38196. [PMID: 27901087 PMCID: PMC5128875 DOI: 10.1038/srep38196] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/04/2016] [Indexed: 01/16/2023] Open
Abstract
The size of assembled Aβ17-42 peptides can determine polymorphism during oligomerization and fibrillization, but the mechanism of this effect is unknown. Starting from separate random monomers, various fibrillar oligomers with distinct structural characteristics were identified using discontinuous molecular dynamics simulations based on a coarse-grained protein model. From the structures observed in the simulations, two characteristic oligomer sizes emerged, trimer and paranuclei, which generated distinct structural patterns during fibrillization. A majority of the simulations for trimers and tetramers formed non-fibrillar oligomers, which primarily progress to off-pathway oligomers. Pentamers and hexamers were significantly converted into U-shape fibrillar structures, meaning that these oligomers, called paranuclei, might be potent on-pathway intermediates in fibril formation. Fibrillar oligomers larger than hexamers generated substantial polymorphism in which hybrid structures were readily formed and homogeneous fibrillar structures appeared infrequently.
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Affiliation(s)
- Mookyung Cheon
- Center for Proteome Biophysics, Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea.,Department of Neural Development and Disease, Korea Brain Research Institute, Daegu 41068, Korea
| | - Mooseok Kang
- Center for Proteome Biophysics, Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Iksoo Chang
- Center for Proteome Biophysics, Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
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8
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Fu IW, Nguyen HD. Sequence-Dependent Structural Stability of Self-Assembled Cylindrical Nanofibers by Peptide Amphiphiles. Biomacromolecules 2015; 16:2209-19. [DOI: 10.1021/acs.biomac.5b00595] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Iris W. Fu
- Department
of Chemical Engineering
and Materials Science, University of California, Irvine, Irvine, California 92697, United States
| | - Hung D. Nguyen
- Department
of Chemical Engineering
and Materials Science, University of California, Irvine, Irvine, California 92697, United States
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9
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Cheon M, Hall CK, Chang I. Structural Conversion of Aβ17-42 Peptides from Disordered Oligomers to U-Shape Protofilaments via Multiple Kinetic Pathways. PLoS Comput Biol 2015; 11:e1004258. [PMID: 25955249 PMCID: PMC4425657 DOI: 10.1371/journal.pcbi.1004258] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/29/2015] [Indexed: 11/18/2022] Open
Abstract
Discovering the mechanisms by which proteins aggregate into fibrils is an essential first step in understanding the molecular level processes underlying neurodegenerative diseases such as Alzheimer's and Parkinson's. The goal of this work is to provide insights into the structural changes that characterize the kinetic pathways by which amyloid-β peptides convert from monomers to oligomers to fibrils. By applying discontinuous molecular dynamics simulations to PRIME20, a force field designed to capture the chemical and physical aspects of protein aggregation, we have been able to trace out the entire aggregation process for a system containing 8 Aβ17-42 peptides. We uncovered two fibrillization mechanisms that govern the structural conversion of Aβ17-42 peptides from disordered oligomers into protofilaments. The first mechanism is monomeric conversion templated by a U-shape oligomeric nucleus into U-shape protofilament. The second mechanism involves a long-lived and on-pathway metastable oligomer with S-shape chains, having a C-terminal turn, en route to the final U-shape protofilament. Oligomers with this C-terminal turn have been regarded in recent experiments as a major contributing element to cell toxicity in Alzheimer's disease. The internal structures of the U-shape protofilaments from our PRIME20/DMD simulation agree well with those from solid state NMR experiments. The approach presented here offers a simple molecular-level framework to describe protein aggregation in general and to visualize the kinetic evolution of a putative toxic element in Alzheimer's disease in particular.
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Affiliation(s)
- Mookyung Cheon
- Center for Proteome Biophysics, Department of Brain & Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
| | - Carol K. Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail: (CKH); (IC)
| | - Iksoo Chang
- Center for Proteome Biophysics, Department of Brain & Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
- * E-mail: (CKH); (IC)
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10
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Conformational behavior of polyalanine peptides with and without protecting groups of varying chain lengths: population of PP-II structure! J Mol Model 2015; 21:123. [PMID: 25903302 DOI: 10.1007/s00894-015-2671-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/31/2015] [Indexed: 10/23/2022]
Abstract
Oculopharyngeal muscular dystrophy (OPMD), a polyalanine myopathy, occurs due to expansion of homo-polyalanine stretch in normal polyadenylating binding protein nuclear 1 (PABPN1) protein from Ala10 to Ala11-17. Therefore, the conformational behavior of polyalanine peptides with n = 10-17, with and without terminal protecting groups, have been investigated with different starting geometries in water by molecular dynamics simulation studies. Alanine peptides are shown to give rise to unordered structure irrespective of starting geometry and not more than two residues at a stretch have the same/similar set of φ, ψ values. However, the final structure with terminal protecting groups look like β-strand. Unprotected poly-Ala peptides adopt twisted β-hairpin/multi hairpin like structure with increasing chain length. The number of residues having φ, ψ values in collagen region is found to be less in peptides with unprotected termini as compared to peptides with protected termini of same chain length. The results have been supported by recent synchrotron radiation circular dichroism spectroscopy of polyproline II and unordered secondary structures. Opening of the helical structure in poly-Ala peptides with protecting groups has been shown to take place from C-terminal and in peptides without protecting groups opening of helix starts from both terminals. Further, opening of helix takes more time in poly-Ala peptides without terminal protecting groups. The deviations in amide bond planarity have been discussed and compared with available experimental and computational results.
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11
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Honarparvar B, Skelton AA. Molecular dynamics simulation and conformational analysis of some catalytically active peptides. J Mol Model 2015; 21:100. [DOI: 10.1007/s00894-015-2645-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 03/09/2015] [Indexed: 01/10/2023]
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12
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Mahmoudinobar F, Dias CL, Zangi R. Role of side-chain interactions on the formation of α-helices in model peptides. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:032710. [PMID: 25871147 DOI: 10.1103/physreve.91.032710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Indexed: 06/04/2023]
Abstract
The role played by side-chain interactions on the formation of α-helices is studied using extensive all-atom molecular dynamics simulations of polyalanine-like peptides in explicit TIP4P water. The peptide is described by the OPLS-AA force field except for the Lennard-Jones interaction between Cβ-Cβ atoms, which is modified systematically. We identify values of the Lennard-Jones parameter that promote α-helix formation. To rationalize these results, potentials of mean force (PMF) between methane-like molecules that mimic side chains in our polyalanine-like peptides are computed. These PMF exhibit a complex distance dependence where global and local minima are separated by an energy barrier. We show that α-helix propensity correlates with values of these PMF at distances corresponding to Cβ-Cβ of i-i+3 and other nearest neighbors in the α-helix. In particular, the set of Lennard-Jones parameters that promote α-helices is characterized by PMF that exhibit a global minimum at distances corresponding to i-i+3 neighbors in α-helices. Implications of these results are discussed.
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Affiliation(s)
- Farbod Mahmoudinobar
- New Jersey Institute of Technology, Physics Department, University Heights, Newark, New Jersey, 07102-1982, USA
| | - Cristiano L Dias
- New Jersey Institute of Technology, Physics Department, University Heights, Newark, New Jersey, 07102-1982, USA
| | - Ronen Zangi
- Department of Organic Chemistry I and POLYMAT, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018, San Sebastian, Spain IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain
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13
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Markegard CB, Fu IW, Reddy KA, Nguyen HD. Coarse-grained simulation study of sequence effects on DNA hybridization in a concentrated environment. J Phys Chem B 2015; 119:1823-34. [PMID: 25581253 DOI: 10.1021/jp509857k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A novel coarse-grained model is developed to elucidate thermodynamics and kinetic mechanisms of DNA self-assembly. It accounts for sequence and solvent conditions to capture key experimental results such as sequence-dependent thermal property and salt-dependent persistence length of ssDNA and dsDNA. Moreover, constant-temperature simulations on two single strands of a homogeneous sequence show two main mechanisms of hybridization: a slow slithering mechanism and a one-order faster zippering mechanism. Furthermore, large-scale simulations at a high DNA strand concentration demonstrate that DNA self-assembly is a robust and enthalpically driven process in which the formation of double helices is deciphered to occur via multiple self-assembly pathways including the strand displacement mechanism. However, sequence plays an important role in shifting the majority of one pathway over the others and controlling size distribution of self-assembled aggregates. This study yields a complex picture on the role of sequence on programmable self-assembly and demonstrates a promising simulation tool that is suitable for studies in DNA nanotechnology.
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Affiliation(s)
- Cade B Markegard
- Department of Chemical Engineering and Materials Science, University of California-Irvine , Irvine, California 92697-2575, United States
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14
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Fu IW, Markegard CB, Nguyen HD. Solvent effects on kinetic mechanisms of self-assembly by peptide amphiphiles via molecular dynamics simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:315-24. [PMID: 25488898 DOI: 10.1021/la503399x] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Peptide amphiphiles are known to form a variety of distinctive self-assembled nanostructures (including cylindrical nanofibers in hydrogels) dependent upon the solvent conditions. Using a novel coarse-grained model, large-scale molecular dynamics simulations are performed on a system of 800 peptide amphiphiles (sequence, palmitoyl-Val3Ala3Glu3) to elucidate kinetic mechanisms of molecular assembly as a function of the solvent conditions. The assembly process is found to occur via a multistep process with transient intermediates that ultimately leads to the stabilized nanostructures including open networks of β-sheets, cylindrical nanofibers, and elongated micelles. Different kinetic mechanisms are compared in terms of peptide secondary structures, solvent-accessible surface area, radius of gyration, relative shape anisotropy, intra/intermolecular interactions, and aggregate size dynamics to provide insightful information for the design of functional biomaterials.
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Affiliation(s)
- Iris W Fu
- Department of Chemical Engineering and Materials Science, University of California, Irvine , Irvine, California 92697, United States
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15
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Cote Y, Fu IW, Dobson ET, Goldberger JE, Nguyen HD, Shen JK. Mechanism of the pH-Controlled Self-Assembly of Nanofibers from Peptide Amphiphiles. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2014; 118:16272-16278. [PMID: 25089166 PMCID: PMC4111372 DOI: 10.1021/jp5048024] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 06/27/2014] [Indexed: 05/23/2023]
Abstract
Stimuli-responsive, self-assembling nanomaterials hold a great promise to revolutionize medicine and technology. However, current discovery is slow and often serendipitous. Here we report a multiscale modeling study to elucidate the pH-controlled self-assembly of nanofibers from the peptide amphiphiles, palmitoyl-I-A3E4-NH2. The coarse-grained simulations revealed the formation of random-coil based spherical micelles at strong electrostatic repulsion. However, at weak or no electrostatic repulsion, the micelles merge into a nanofiber driven by the β-sheet formation between the peptide segments. The all-atom constant pH molecular dynamics revealed a cooperative transition between random coil and β-sheet in the pH range 6-7, matching the CD data. Interestingly, although the bulk pKa is more than one unit below the transition pH, consistent with the titration data, the highest pKa's coincide with the transition pH, suggesting that the latter may be tuned by modulating the pKa's of a few solvent-buried Glu side chains. Together, these data offer, to our best knowledge, the first multiresolution and quantitative view of the pH-dependent self-assembly of nanofibers. The novel protocols and insights gained are expected to advance the computer-aided design and discovery of pH-responsive nanomaterials.
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Affiliation(s)
- Yoann Cote
- The Institute of Genetics and Molecular and Cellular
Biology, 67404 Illkirch Cedex, France
| | - Iris W. Fu
- Department
of Chemical Engineering and Materials Science, The Henry Samueli School
of Engineering, University of California, Irvine, California 92697, United States
| | - Eric T. Dobson
- Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Joshua E. Goldberger
- Department of Chemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Hung D. Nguyen
- Department
of Chemical Engineering and Materials Science, The Henry Samueli School
of Engineering, University of California, Irvine, California 92697, United States
| | - Jana K. Shen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
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16
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Fu IW, Markegard CB, Chu BK, Nguyen HD. Role of hydrophobicity on self-assembly by peptide amphiphiles via molecular dynamics simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:7745-7754. [PMID: 24915982 DOI: 10.1021/la5012988] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Using a novel coarse-grained model, large-scale molecular dynamics simulations were performed to examine self-assembly of 800 peptide amphiphiles (sequence palmitoyl-V3A3E3). Under suitable physiological conditions, these molecules readily assemble into nanofibers leading to hydrogel construction as observed in experiments. Our simulations capture this spontaneous self-assembly process, including formation of secondary structure, to identify morphological transitions of distinctive nanostructures. As the hydrophobic interaction is increased, progression from open networks of secondary structures toward closed cylindrical nanostructures containing either β-sheets or random coils are observed. Moreover, temperature effects are also determined to play an important role in regulating formation of secondary structures within those nanostructures. These understandings of the molecular interactions involved and the role of environmental factors on hydrogel formation provide useful insight for development of innovative smart biomaterials for biomedical applications.
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Affiliation(s)
- Iris W Fu
- Department of Chemical Engineering and Materials Science, University of California-Irvine , Irvine, California 92697, United States
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17
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Wagoner VA, Cheon M, Chang I, Hall CK. Impact of sequence on the molecular assembly of short amyloid peptides. Proteins 2014; 82:1469-83. [PMID: 24449257 DOI: 10.1002/prot.24515] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 12/17/2013] [Accepted: 12/27/2013] [Indexed: 11/08/2022]
Abstract
The goal of this work is to understand how the sequence of a protein affects the likelihood that it will form an amyloid fibril and the kinetics along the fibrillization pathway. The focus is on very short fragments of amyloid proteins since these play a role in the fibrillization of the parent protein and can form fibrils themselves. Discontinuous molecular dynamics simulations using the PRIME20 force field were performed of the aggregation of 48-peptide systems containing SNQNNF (PrP (170-175)), SSTSAA (RNaseA(15-20)), MVGGVV (Aβ(35-40)), GGVVIA (Aβ(37-42)), and MVGGVVIA (Aβ(35-42)). In our simulations SNQQNF, SSTTSAA, and MVGGVV form large numbers of fibrillar structures spontaneously (as in experiment). GGVVIA forms β-sheets that do not stack into fibrils (unlike experiment). The combination sequence MVGGVVIA forms less fibrils than MVGGVV, hindered by the presence of the hydrophobic residues at the C-terminal. Analysis of the simulation kinetics and energetics reveals why MVGGVV forms fibrils and GGVVIA does not, and why adding I and A to MVGGVVIA reduces fibrillization and enhances amorphous aggregation into oligomeric structures. The latter helps explain why Aβ(1-42) assembles into more complex oligomers than Aβ(1-40), a consequence of which is that it is more strongly associated with Alzheimer's disease.
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Affiliation(s)
- Victoria A Wagoner
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27695-7905
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18
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Fu IW, Markegard CB, Chu BK, Nguyen HD. The role of electrostatics and temperature on morphological transitions of hydrogel nanostructures self-assembled by peptide amphiphiles via molecular dynamics simulations. Adv Healthc Mater 2013; 2:1388-400. [PMID: 23554376 DOI: 10.1002/adhm.201200400] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Revised: 01/30/2013] [Indexed: 02/02/2023]
Abstract
Smart biomaterials that are self-assembled from peptide amphiphiles (PA) are known to undergo morphological transitions in response to specific physiological stimuli. The design of such customizable hydrogels is of significant interest due to their potential applications in tissue engineering, biomedical imaging, and drug delivery. Using a novel coarse-grained peptide/polymer model, which has been validated by comparison of equilibrium conformations from atomistic simulations, large-scale molecular dynamics simulations are performed to examine the spontaneous self-assembly process. Starting from initial random configurations, these simulations result in the formation of nanostructures of various sizes and shapes as a function of the electrostatics and temperature. At optimal conditions, the self-assembly mechanism for the formation of cylindrical nanofibers is deciphered involving a series of steps: (1) PA molecules quickly undergo micellization whose driving force is the hydrophobic interactions between alkyl tails; (2) neighboring peptide residues within a micelle engage in a slow ordering process that leads to the formation of β-sheets exposing the hydrophobic core; (3) spherical micelles merge together through an end-to-end mechanism to form cylindrical nanofibers that exhibit high structural fidelity to the proposed structure based on experimental data. As the temperature and electrostatics vary, PA molecules undergo alternative kinetic mechanisms, resulting in the formation of a wide spectrum of nanostructures. A phase diagram in the electrostatics-temperature plane is constructed delineating regions of morphological transitions in response to external stimuli.
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Affiliation(s)
- Iris W Fu
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, California 92697-2575, United States
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19
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Francis BR. Evolution of the genetic code by incorporation of amino acids that improved or changed protein function. J Mol Evol 2013; 77:134-58. [PMID: 23743924 DOI: 10.1007/s00239-013-9567-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 05/25/2013] [Indexed: 12/31/2022]
Abstract
Fifty years have passed since the genetic code was deciphered, but how the genetic code came into being has not been satisfactorily addressed. It is now widely accepted that the earliest genetic code did not encode all 20 amino acids found in the universal genetic code as some amino acids have complex biosynthetic pathways and likely were not available from the environment. Therefore, the genetic code evolved as pathways for synthesis of new amino acids became available. One hypothesis proposes that early in the evolution of the genetic code four amino acids-valine, alanine, aspartic acid, and glycine-were coded by GNC codons (N = any base) with the remaining codons being nonsense codons. The other sixteen amino acids were subsequently added to the genetic code by changing nonsense codons into sense codons for these amino acids. Improvement in protein function is presumed to be the driving force behind the evolution of the code, but how improved function was achieved by adding amino acids has not been examined. Based on an analysis of amino acid function in proteins, an evolutionary mechanism for expansion of the genetic code is described in which individual coded amino acids were replaced by new amino acids that used nonsense codons differing by one base change from the sense codons previously used. The improved or altered protein function afforded by the changes in amino acid function provided the selective advantage underlying the expansion of the genetic code. Analysis of amino acid properties and functions explains why amino acids are found in their respective positions in the genetic code.
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Affiliation(s)
- Brian R Francis
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071-3944, USA,
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20
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Lee J, Kim S, Chang R, Jayanthi L, Gebremichael Y. Effects of molecular model, ionic strength, divalent ions, and hydrophobic interaction on human neurofilament conformation. J Chem Phys 2013; 138:015103. [DOI: 10.1063/1.4773297] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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21
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Cheon M, Chang I, Hall CK. Influence of temperature on formation of perfect tau fragment fibrils using PRIME20/DMD simulations. Protein Sci 2012; 21:1514-27. [PMID: 22887126 PMCID: PMC3526993 DOI: 10.1002/pro.2141] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 08/06/2012] [Indexed: 02/06/2023]
Abstract
We investigate the fibrillization process for amyloid tau fragment peptides (VQIVYK) by applying the discontinuous molecular dynamics method to a system of 48 VQIVYK peptides modeled using a new protein model/force field, PRIME20. The aim of the article is to ascertain which factors are most important in determining whether or not a peptide system forms perfect coherent fibrillar structures. Two different directional criteria are used to determine when a hydrogen bond occurs: the original H-bond constraints and a parallel preference H-bond constraint that imparts a slight bias towards the formation of parallel versus antiparallel strands in a β-sheet. Under the original H-bond constraints, the resulting fibrillar structures contain a mixture of parallel and antiparallel pairs of strands within each β-sheet over the whole fibrillization temperature range. Under the parallel preference H-bond constraints, the β-sheets within the fibrillar structures are more likely to be parallel and indeed become perfectly parallel, consistent with X-ray crystallography, at a high temperature slightly below the fibrillization temperature. The high temperature environment encourages the formation of perfect fibril structures by providing enough time and space for peptides to rearrange during the aggregation process. There are two different kinetic mechanisms, template assembly with monomer addition at high temperature and merging/rearrangement without monomer addition at low temperature, which lead to significant differences in the final fibrillar structure. This suggests that the diverse fibril morphologies generally observed in vitro depend more on environmental conditions than has heretofore been appreciated.
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Affiliation(s)
- Mookyung Cheon
- Center for Proteome Biophysics, Department of Physics, Pusan National UniversityBusan 609-735, Korea
| | - Iksoo Chang
- Center for Proteome Biophysics, Department of Physics, Pusan National UniversityBusan 609-735, Korea
| | - Carol K Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State UniversityRaleigh, North Carolina 27695-7905
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22
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Phelps EM, Hall CK. Structural transitions and oligomerization along polyalanine fibril formation pathways from computer simulations. Proteins 2012; 80:1582-97. [PMID: 22411226 PMCID: PMC3348993 DOI: 10.1002/prot.24052] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 12/09/2011] [Accepted: 12/16/2011] [Indexed: 11/10/2022]
Abstract
The results of a computer simulation study of the aggregation kinetics of a large system of model peptides with particular focus on the formation of intermediates are presented. Discontinuous molecular dynamic simulations were used in combination with our intermediate-resolution protein model, PRIME, to simulate the aggregation of a system of 192 polyalanine (KA(14) K) peptides at a concentration of 5 mM and a reduced temperature of T* = 0.13 starting from a random configuration and ending in the assembly of a fibrillar structure. The population of various structures, including free monomers, beta sheets, amorphous aggregates, hybrid aggregates, and fibrils, and the transitions between the structures were tracked over the course of 30 independent simulations and averaged together. The aggregation pathway for this system starts with the association of free monomers into small amorphous aggregates that then grow to moderate size by incorporating other free monomers or merging with other small amorphous aggregates. These then rearrange into either small beta sheets or hybrid aggregates formed by association between unstructured chains and beta sheets, both of which grow in size by adding free monomer chains or other small aggregates, one at a time. Fibrillar structures are formed initially either by the stacking of beta sheets, rearrangement of hybrid aggregates or association between beta sheets and hybrid aggregates. They grow by the addition of beta sheets, hybrid aggregates, and other small fibrillar structures. The rearrangement of amorphous aggregates into beta sheets is a critical and necessary step in the fibril formation pathway.
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Affiliation(s)
- Erin M. Phelps
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Carol K. Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
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23
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Baker PJ, Numata K. Chemoenzymatic Synthesis of Poly(l-alanine) in Aqueous Environment. Biomacromolecules 2012; 13:947-51. [PMID: 22380731 DOI: 10.1021/bm201862z] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Peter James Baker
- Enzyme Research Team, RIKEN Biomass Engineering Program, RIKEN, 2-1 Hirosawa, Wako-shi, 351-0198 Saitama,
Japan
| | - Keiji Numata
- Enzyme Research Team, RIKEN Biomass Engineering Program, RIKEN, 2-1 Hirosawa, Wako-shi, 351-0198 Saitama,
Japan
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24
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Carmichael SP, Shell MS. A New Multiscale Algorithm and Its Application to Coarse-Grained Peptide Models for Self-Assembly. J Phys Chem B 2012; 116:8383-93. [DOI: 10.1021/jp2114994] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Scott P. Carmichael
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California
| | - M. Scott Shell
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California
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25
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Javidpour L, Sahimi M. Confinement in nanopores can destabilize α-helix folding proteins and stabilize the β structures. J Chem Phys 2012; 135:125101. [PMID: 21974560 DOI: 10.1063/1.3641482] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Protein folding in confined media has attracted wide attention over the past decade due to its importance in both in vivo and in vitro applications. Currently, it is generally believed that protein stability increases by decreasing the size of the confining medium, if its interaction with the confining walls is repulsive, and that the maximum folding temperature in confinement occurs for a pore size only slightly larger than the smallest dimension of the folded state of a protein. Protein stability in pore sizes, very close to the size of the folded state, has not however received the attention that it deserves. Using detailed, 0.3-ms-long molecular dynamics simulations, we show that proteins with an α-helix native state can have an optimal folding temperature in pore sizes that do not affect the folded-state structure. In contradiction to the current theoretical explanations, we find that the maximum folding temperature occurs in larger pores for smaller α-helices. In highly confined pores the free energy surface becomes rough, and a new barrier for protein folding may appear close to the unfolded state. In addition, in small nanopores the protein states that contain the β structures are entropically stabilized, in contrast to the bulk. As a consequence, folding rates decrease notably and the free energy surface becomes rougher. The results shed light on many recent experimental observations that cannot be explained by the current theories, and demonstrate the importance of entropic effects on proteins' misfolded states in highly confined environments. They also support the concept of passive effect of chaperonin GroEL on protein folding by preventing it from aggregation in crowded environment of biological cells, and provide deeper clues to the α → β conformational transition, believed to contribute to Alzheimer's and Parkinson's diseases. The strategy of protein and enzyme stabilization in confined media may also have to be revisited in the case of tight confinement. For in silico studies of protein folding in confined media, use of non-Go potentials may be more appropriate.
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Affiliation(s)
- Leili Javidpour
- School of Physics, Institute for Research in Fundamental Sciences, IPM, Tehran 19395-5531, Iran
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26
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Wu J, Zhen X, Shen H, Li G, Ren P. Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent. J Chem Phys 2012; 135:155104. [PMID: 22029338 DOI: 10.1063/1.3651626] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is described by the Generalized Kirkwood theory. The CG model is calibrated using the results of all-atom simulations of model compounds in solution. Instead of matching the overall effective forces produced by atomic models, the fundamental intermolecular forces such as electrostatic, repulsion-dispersion, and solvation are represented explicitly at a CG level. We demonstrate that the CG alanine dipeptide model is able to reproduce quantitatively the conformational energy of all-atom force fields in both gas and solution phases, including the electrostatic and solvation components. Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanine of 5 and 12 residues reveal that the CG polyalanines fold into "alpha helix" and "beta sheet" structures. The 5-residue polyalanine displays a substantial increase in the "beta strand" fraction relative to the 12-residue polyalanine. The detailed conformational distribution is compared with those reported from recent all-atom simulations and experiments. The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling.
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Affiliation(s)
- Johnny Wu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712-1062, USA
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27
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López GE, Colón-Díaz I, Cruz A, Ghosh S, Nicholls SB, Viswanathan U, Hardy JA, Auerbach SM. Modeling Nonaqueous Proton Wires Built from Helical Peptides: Biased Proton Transfer Driven by Helical Dipoles. J Phys Chem A 2012; 116:1283-8. [DOI: 10.1021/jp210208m] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gustavo E. López
- Department of Chemistry, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico 00681
- Department of Chemistry, Lehman College-CUNY, Bronx, New York 10034, United States
| | - Inara Colón-Díaz
- Department of Chemistry, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico 00681
| | - Anthony Cruz
- Department of Chemistry, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico 00681
- Department of Chemistry, Lehman College-CUNY, Bronx, New York 10034, United States
| | - Sumana Ghosh
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, United States
| | - Samantha B. Nicholls
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, United States
| | - Usha Viswanathan
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, United States
| | - Jeanne A. Hardy
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, United States
| | - Scott M. Auerbach
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, United States
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28
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Fibrillization propensity for short designed hexapeptides predicted by computer simulation. J Mol Biol 2011; 416:598-609. [PMID: 22227390 DOI: 10.1016/j.jmb.2011.12.038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 11/30/2011] [Accepted: 12/17/2011] [Indexed: 12/16/2022]
Abstract
Assembly of normally soluble proteins into ordered aggregates, known as amyloid fibrils, is a cause or associated symptom of numerous human disorders, including Alzheimer's and the prion diseases. Here, we test the ability of discontinuous molecular dynamics (DMD) simulations based on PRIME20, a new intermediate-resolution protein force field, to predict which designed hexapeptide sequences will form fibrils, which will not, and how this depends on temperature and concentration. Simulations were performed on 48-peptide systems containing STVIIE, STVIFE, STVIVE, STAIIE, STVIAE, STVIGE, and STVIEE starting from random-coil configurations. By the end of the simulations, STVIIE and STVIFE (which form fibrils in vitro) form fibrils over a range of temperatures, STVIEE (which does not form fibrils in vitro) does not form fibrils, and STVIVE, STAIIE, STVIAE, and STVIGE (which do not form fibrils in vitro) form fibrils at lower temperatures but stop forming fibrils at higher temperatures. At the highest temperatures simulated, the results on the fibrillization propensity of the seven short de novo designed peptides all agree with the experiments of López de la Paz and Serrano. Our results suggest that the fibrillization temperature (temperature above which fibrils cease to form) is a measure of fibril stability and that by rank ordering the fibrillization temperatures of various sequences, PRIME20/DMD simulations could be used to ascertain their relative fibrillization propensities. A phase diagram showing regions in the temperature-concentration plane where fibrils are formed in our simulations is presented.
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29
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Dias CL, Karttunen M, Chan HS. Hydrophobic interactions in the formation of secondary structures in small peptides. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:041931. [PMID: 22181199 DOI: 10.1103/physreve.84.041931] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Indexed: 05/31/2023]
Abstract
Effects of the attractive and repulsive parts of hydrophobic interactions on α helices and β sheets in small peptides are investigated using a simple atomic potential. Typically, a physical spatial range of attraction tends to favor β sheets, but α helices would be favored if the attractive range were more extended. We also found that desolvation barriers favor β sheets in collapsed conformations of polyalanine, polyvaline, polyleucine, and three fragments of amyloid peptides tested in this study. Our results provide insight into the multifaceted role of hydrophobicity in secondary structure formation, including the α to β transitions in certain amyloid peptides.
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Affiliation(s)
- Cristiano L Dias
- Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8.
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30
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Mu Y. Effects of surface hydrophobicity on the conformational changes of polypeptides of different length. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:031906. [PMID: 22060402 DOI: 10.1103/physreve.84.031906] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Indexed: 05/31/2023]
Abstract
We studied the effects of surface hydrophobicity on the conformational changes of different length polypeptides by calculating the free energy difference between peptide structures using the bias-potential Monte Carlo technique and the probability ratio method. It was found that the hydrophobic surface plays an important role in the stability of secondary structures of the polypeptides with hydrophobic side chains. For short GAAAAG peptides, the hydrophobic surface destabilizes the α helix but stabilizes the β hairpin in the entire temperature region considered in our study. Interestingly, when the surface hydrophobic strength ε(hpsf)≥ε(hp), the most stable structure in the low temperature region changes from α helix to β hairpin, and the corresponding phase transition temperature increases slightly. For longer GAAAAAAAAAAG peptides, the effects of the relatively weak hydrophobic surface (ε(hpsf) < ε(hp)) on α-helical structures may be neglected, while the relatively strongly hydrophobic surface (ε(hpsf)≥ε(hp)) leads to the obvious partial helicity loss. In contrast, the stability of β structures can be enhanced significantly by the hydrophobic surface, especially by the strongly hydrophobic surface, at low and intermediate temperatures. At high temperatures, in addition to thermal fluctuations, the strongly hydrophobic surface (ε(hpsf)>ε(hp)) may further disturb the formation of both α-helical and β structures. Moreover, the phase transition temperature between α-helical structures and random coils significantly decreases due to the helicity loss when ε(hpsf)>ε(hp). Our findings provide a basic and quantitative picture for understanding the effects of a hydrophobic surface on the conformational changes of the polypeptides with hydrophobic side chains. From an application viewpoint, the present study is helpful in developing alternative strategies of producing high-quality biological fibrillar materials and functional nanoscale devices by the self-assembly of the polypeptides on hydrophobic surfaces.
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Affiliation(s)
- Yan Mu
- College of Materials Science and Engineering, South China University of Technology, Guangzhou, Guangdong, 510641, China
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31
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Engin O, Villa A, Peter C, Sayar M. A Challenge for Peptide Coarse Graining: Transferability of Fragment-Based Models. MACROMOL THEOR SIMUL 2011. [DOI: 10.1002/mats.201100005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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32
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Wagoner VA, Cheon M, Chang I, Hall CK. Computer simulation study of amyloid fibril formation by palindromic sequences in prion peptides. Proteins 2011; 79:2132-45. [PMID: 21557317 DOI: 10.1002/prot.23034] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 01/26/2011] [Accepted: 02/11/2011] [Indexed: 11/11/2022]
Abstract
We simulate the aggregation of large systems containing palindromic peptides from the Syrian hamster prion protein SHaPrP 113-120 (AGAAAAGA) and the mouse prion protein MoPrP 111-120 (VAGAAAAGAV) and eight sequence variations: GAAAAAAG, (AG)(4) , A8, GAAAGAAA, A10, V10, GAVAAAAVAG, and VAVAAAAVAV The first two peptides are thought to act as the Velcro that holds the parent prion proteins together in amyloid structures and can form fibrils themselves. Kinetic events along the fibrillization pathway influence the types of structures that occur and variations in the sequence affect aggregation kinetics and fibrillar structure. Discontinuous molecular dynamics simulations using the PRIME20 force field are performed on systems containing 48 peptides starting from a random coil configuration. Depending on the sequence, fibrillar structures form spontaneously over a range of temperatures, below which amorphous aggregates form and above which no aggregation occurs. AGAAAAGA forms well organized fibrillar structures whereas VAGAAAAGAV forms less well organized structures that are partially fibrillar and partially amorphous. The degree of order in the fibrillar structure stems in part from the types of kinetic events leading up to its formation, with AGAAAAGA forming less amorphous structures early in the simulation than VAGAAAAGAV. The ability to form fibrils increases as the chain length and the length of the stretch of hydrophobic residues increase. However as the hydrophobicity of the sequence increases, the ability to form well-ordered structures decreases. Thus, longer hydrophobic sequences form slightly disordered aggregates that are partially fibrillar and partially amorphous. Subtle changes in sequence result in slightly different fibril structures.
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Affiliation(s)
- Victoria A Wagoner
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
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33
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Mao X, Wang C, Ma X, Zhang M, Liu L, Zhang L, Niu L, Zeng Q, Yang Y, Wang C. Molecular level studies on binding modes of labeling molecules with polyalanine peptides. NANOSCALE 2011; 3:1592-1599. [PMID: 21283870 DOI: 10.1039/c0nr00782j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In this work, the binding modes of typical labeling molecules (thioflavin T (ThT), Congo red (CR) and copper(II) phthalocyanine tetrasulfonic acid tetrasodium salt (PcCu(SO(3)Na)(4))) on pentaalanine, which is a model peptide segment of amyloid peptides, have been resolved at the molecular level by using scanning tunneling microscopy (STM). In the STM images, ThT molecules are predominantly adsorbed parallel to the peptide strands and two binding modes could be identified. It was found that ThT molecules are preferentially binding on top of the peptide strand, and the mode of intercalated between neighboring peptides also exists. The parallel binding mode of CR molecules can be observed with pentaalanine peptides. Besides the binding modes of labeling molecules, the CR and PcCu(SO(3)Na)(4) display different adsorption affinity with the pentaalanine peptides. The results could be beneficial for obtaining molecular level insight of the interactions between labeling molecules and peptides.
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Affiliation(s)
- Xiaobo Mao
- National Center for Nanoscience and Technology, Beijing, 100190, China
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34
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Proctor EA, Ding F, Dokholyan NV. Discrete molecular dynamics. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.4] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Elizabeth A. Proctor
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Feng Ding
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nikolay V. Dokholyan
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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35
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Czapiewski D, Zielkiewicz J. Structural Properties of Hydration Shell Around Various Conformations of Simple Polypeptides. J Phys Chem B 2010; 114:4536-50. [DOI: 10.1021/jp9086199] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Dariusz Czapiewski
- Gdańsk University of Technology, Department of Chemistry Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Jan Zielkiewicz
- Gdańsk University of Technology, Department of Chemistry Narutowicza 11/12, 80-952 Gdańsk, Poland
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36
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Mu Y, Gao YQ. Self-assembly of polypeptides into left-handedly twisted fibril-like structures. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:041927. [PMID: 19905362 DOI: 10.1103/physreve.80.041927] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2009] [Indexed: 05/28/2023]
Abstract
In this paper, we investigated the spontaneous formation of aggregation structures of amyloid-forming peptide (GGVVIA) using a coarse-grained model and Monte Carlo simulations. The effects of concentration and temperature on the formation of different aggregation structures were studied. Three types of aggregation structures, single-layer beta sheet, amorphous beta-sheet aggregate, and fibril-like structures, were observed in our simulations. The fibril-like structures obtained in simulations have a common cross-beta spine structure in which beta sheets twist in a left-handed fashion. The averaged twisting angle of the beta sheet in the fibril-like structures is 12 degrees +/-2 degrees. Moreover, it was found that the peptides in the same beta sheets prefer to arrange in a parallel way, which is consistent with the corresponding GGVVIA crystalline structure. On the other hand, it was found that there is a rich family of beta-sheet stacking patterns in the fibril-like structures suggesting that the fibril structures are more complex than the corresponding crystalline structure and there exist many local free-energy minima rather than a distinct global minimum.
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Affiliation(s)
- Yan Mu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
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37
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Sharma N, Top A, Kiick K, Pochan D. One-Dimensional Gold Nanoparticle Arrays by Electrostatically Directed Organization Using Polypeptide Self-Assembly. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200901621] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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38
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Bannerman MN, Magee JE, Lue L. Structure and stability of helices in square-well homopolymers. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:021801. [PMID: 19792144 DOI: 10.1103/physreve.80.021801] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Indexed: 05/28/2023]
Abstract
Recently, it has been demonstrated [Magee, Phys. Rev. Lett. 96, 207802 (2006)] that isolated square-well homopolymers can spontaneously break chiral symmetry and "freeze" into helical structures at sufficiently low temperatures. This behavior is interesting because the square-well homopolymer is itself achiral. In this work, we use event-driven molecular dynamics combined with an optimized parallel tempering scheme to study this polymer model over a wide range of parameters. We examine the conditions where the helix structure is stable and determine how the interaction parameters of the polymer govern the details of the helix structure. The width of the square well (proportional to lambda) is found to control the radius of the helix, which decreases with increasing well width until the polymer forms a coiled sphere for sufficiently large wells. The helices are found to be stable for only a "window" of molecular weights. If the polymer is too short, the helix will not form. If the polymer is too long, the helix is no longer the minimum energy structure, and other folded structures will form. The size of this window is governed by the chain stiffness, which in this model is a function of the ratio of the monomer size to the bond length. Outside this window, the polymer still freezes into a locked structure at low temperature; however, unless the chain is sufficiently stiff, this structure will not be unique and is similar to a glassy state.
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Affiliation(s)
- M N Bannerman
- School of Chemical Engineering and Analytical Science, The University of Manchester, Manchester M60 1QD, United Kingdom
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39
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Javidpour L, Tabar MRR, Sahimi M. Molecular simulation of protein dynamics in nanopores. II. Diffusion. J Chem Phys 2009; 130:085105. [PMID: 19256630 DOI: 10.1063/1.3080770] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model of proteins, is used to carry out long (several microsecond) simulations in order to study transport of proteins in nanopores. We simulated single-domain proteins with the alpha-helical native structure. Both attractive and repulsive interaction potentials between the proteins and the pores' walls are considered. The diffusivity D of the proteins is computed not only under the bulk conditions but also as a function of their "length" (the number of the amino-acid groups), temperature T, pore size, and interaction potentials with the walls. Compared with the experimental data, the computed diffusivities under the bulk conditions are of the correct order of magnitude. The diffusivities both in the bulk and in the pores follow a power law in the length [script-l] of the proteins and are larger in pores with repulsive walls. D(+)/D(-), the ratio of the diffusivities in pores with attractive and repulsive walls, exhibits two local maxima in its dependence on the pore size h, which are attributed to the pore sizes and protein configurations that induce long-lasting simultaneous interactions with both walls of the pores. Far from the folding temperature T(f), D increases about linearly with T, but due to the thermal fluctuations and their effect on the proteins' structure near T(f), the dependence of D on T in this region is nonlinear. We propose a novel and general "phase diagram," consisting of four regions, that describes qualitatively the effect of h, T, and interaction potentials with the walls on the diffusivity D of a protein.
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Affiliation(s)
- Leili Javidpour
- Department of Physics, Sharif University of Technology, Tehran 11155-9161, IranInstitute of Physics, Carl von Ossietzky University, Oldenburg D-26111, Germany
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Kouzayha A, Nasir MN, Buchet R, Wattraint O, Sarazin C, Besson F. Conformational and Interfacial Analyses of K3A18K3 and Alamethicin in Model Membranes. J Phys Chem B 2009; 113:7012-9. [DOI: 10.1021/jp810539b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Achraf Kouzayha
- Université de Lyon, Université Lyon 1, INSA de Lyon, and ICBMS CNRS UMR 5246, Villeurbanne, F-69622, France, CPE Lyon, Villeurbanne, F-69616, France, and Unité de Génie Enzymatique et Cellulaire, UMR 6022 du CNRS—Université de Picardie Jules Verne, Amiens, France
| | - Mehmet N. Nasir
- Université de Lyon, Université Lyon 1, INSA de Lyon, and ICBMS CNRS UMR 5246, Villeurbanne, F-69622, France, CPE Lyon, Villeurbanne, F-69616, France, and Unité de Génie Enzymatique et Cellulaire, UMR 6022 du CNRS—Université de Picardie Jules Verne, Amiens, France
| | - René Buchet
- Université de Lyon, Université Lyon 1, INSA de Lyon, and ICBMS CNRS UMR 5246, Villeurbanne, F-69622, France, CPE Lyon, Villeurbanne, F-69616, France, and Unité de Génie Enzymatique et Cellulaire, UMR 6022 du CNRS—Université de Picardie Jules Verne, Amiens, France
| | - Olivier Wattraint
- Université de Lyon, Université Lyon 1, INSA de Lyon, and ICBMS CNRS UMR 5246, Villeurbanne, F-69622, France, CPE Lyon, Villeurbanne, F-69616, France, and Unité de Génie Enzymatique et Cellulaire, UMR 6022 du CNRS—Université de Picardie Jules Verne, Amiens, France
| | - Catherine Sarazin
- Université de Lyon, Université Lyon 1, INSA de Lyon, and ICBMS CNRS UMR 5246, Villeurbanne, F-69622, France, CPE Lyon, Villeurbanne, F-69616, France, and Unité de Génie Enzymatique et Cellulaire, UMR 6022 du CNRS—Université de Picardie Jules Verne, Amiens, France
| | - Françoise Besson
- Université de Lyon, Université Lyon 1, INSA de Lyon, and ICBMS CNRS UMR 5246, Villeurbanne, F-69622, France, CPE Lyon, Villeurbanne, F-69616, France, and Unité de Génie Enzymatique et Cellulaire, UMR 6022 du CNRS—Université de Picardie Jules Verne, Amiens, France
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Sharma N, Top A, Kiick KL, Pochan DJ. One-dimensional gold nanoparticle arrays by electrostatically directed organization using polypeptide self-assembly. Angew Chem Int Ed Engl 2009; 48:7078-82. [PMID: 19691075 PMCID: PMC2796555 DOI: 10.1002/anie.200901621] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - Kristi L. Kiick
- Department of Materials Science & Engineering, University of Delaware, 201 DuPont Hall, Newark, DE 19716 (USA), Fax: (+1)302-831-4545
| | - Darrin J. Pochan
- Department of Materials Science & Engineering, University of Delaware, 201 DuPont Hall, Newark, DE 19716 (USA), Fax: (+1)302-831-4545
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42
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Kuffel A, Zielkiewicz J. Structural and Dynamic Properties of Water within the Solvation Layer around Various Conformations of the Glycine-based Polypeptide. J Phys Chem B 2008; 112:15503-12. [DOI: 10.1021/jp805440n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anna Kuffel
- Gdańsk University of Technology, Department of Chemistry, Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Jan Zielkiewicz
- Gdańsk University of Technology, Department of Chemistry, Narutowicza 11/12, 80-952 Gdańsk, Poland
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43
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Fenwick MK. A direct multiple histogram reweighting method for optimal computation of the density of states. J Chem Phys 2008; 129:125106. [DOI: 10.1063/1.2981800] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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Schilke KF, Kelly C. Activation of immobilized lipase in non-aqueous systems by hydrophobic poly-DL-tryptophan tethers. Biotechnol Bioeng 2008; 101:9-18. [PMID: 18393315 PMCID: PMC4124937 DOI: 10.1002/bit.21870] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Many industrially important reactions use immobilized enzymes in non-aqueous, organic systems, particularly for the production of chiral compounds such as pharmaceutical precursors. The addition of a spacer molecule ("tether") between a supporting surface and enzyme often substantially improves the activity and stability of enzymes in aqueous solution. Most "long" linkers (e.g., polyethylene oxide derivatives) are relatively hydrophilic, improving the solubility of the linker-enzyme conjugate in polar environments, but this provides little benefit in non-polar environments such as organic solvents. We present a novel method for the covalent immobilization of enzymes on solid surfaces using a long, hydrophobic polytryptophan tether. Candida antarctica lipase B (CALB) was covalently immobilized on non-porous, functionalized 1-microm silica microspheres, with and without an intervening hydrophobic poly-DL-tryptophan tether (n approximately 78). The polytryptophan-tethered enzyme exhibited 35 times greater esterification of n-propanol with lauric acid in the organic phase and five times the hydrolytic activity against p-nitrophenol palmitate, compared to the activity of the same enzyme immobilized without tethers. In addition, the hydrophobic tethers caused the silica microspheres to disperse more readily in the organic phase, while the surface-immobilized control treatment was less lipophilic and quickly settled out of the organic phase when the suspensions were not vigorously mixed.
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Affiliation(s)
- Karl F Schilke
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, Oregon 97331, USA
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Hall CK. Thermodynamic and kinetic origins of Alzheimer's and related diseases: A chemical engineer's perspective. AIChE J 2008. [DOI: 10.1002/aic.11589] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Mukherjee S, Chowdhury P, Bunagan MR, Gai F. Folding Kinetics of a Naturally Occurring Helical Peptide: Implication of the Folding Speed Limit of Helical Proteins. J Phys Chem B 2008; 112:9146-50. [DOI: 10.1021/jp801721p] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Smita Mukherjee
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Pramit Chowdhury
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Michelle R. Bunagan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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Calvo F, Dugourd P. Folding of gas-phase polyalanines in a static electric field: alignment, deformations, and polarization effects. Biophys J 2008; 95:18-32. [PMID: 18223004 PMCID: PMC2426642 DOI: 10.1529/biophysj.107.124685] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Accepted: 12/28/2007] [Indexed: 11/18/2022] Open
Abstract
Monte Carlo simulations of the temperature-induced unfolding of small gas-phase polyalanines in a static, homogeneous electric field are reported, based on the AMBER ff96 force field. The peptides exhibit a structural transition from the native alpha-helix state to entropically favored beta-sheet conformations, before eventually turning to extended coil at higher temperatures. Upon switching the electric field, the molecules undergo preferential alignment of their dipole moment vector toward the field axis and a shift of the alpha-beta transition to higher temperatures. At higher field strengths (>10(8) V/m) the molecules stretch and the alpha-beta and beta-coil transitions merge. A simple three-state model is shown to account for the observed behavior. Under even higher fields, density functional theory calculations and a polarizable force field both show that electronic rearrangements tend to further increase the dipole moment, polarization effects being approximately half in magnitude with respect to stretching effect. Finally a tentative (temperature, field-strength) phase diagram is sketched.
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Affiliation(s)
- F Calvo
- Centre National de la Recherche Scientifique, Laboratoire de Spectrometrie Ionique et Moleculaire, Université de Lyon, Université Lyon 1, Villeurbanne, France.
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48
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Zielkiewicz J. Two-Particle Entropy and Structural Ordering in Liquid Water. J Phys Chem B 2008; 112:7810-5. [DOI: 10.1021/jp7103837] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jan Zielkiewicz
- Department of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-952 Gdańsk, Poland
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Javidpour L, Tabar MRR, Sahimi M. Molecular simulation of protein dynamics in nanopores. I. Stability and folding. J Chem Phys 2008; 128:115105. [PMID: 18361620 DOI: 10.1063/1.2894299] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Discontinuous molecular dynamics simulations, together with the protein intermediate resolution model, an intermediate-resolution model of proteins, are used to carry out several microsecond-long simulations and study folding transition and stability of alpha-de novo-designed proteins in slit nanopores. Both attractive and repulsive interaction potentials between the proteins and the pore walls are considered. Near the folding temperature T(f) and in the presence of the attractive potential, the proteins undergo a repeating sequence of folding/partially folding/unfolding transitions, with T(f) decreasing with decreasing pore sizes. The unfolded states may even be completely adsorbed on the pore's walls with a negative potential energy. In such pores the energetic effects dominate the entropic effects. As a result, the unfolded state is stabilized, with a folding temperature T(f) which is lower than its value in the bulk and that, compared with the bulk, the folding rate decreases. The opposite is true in the presence of a repulsive interaction potential between the proteins and the walls. Moreover, for short proteins in very tight pores with attractive walls, there exists an unfolded state with only one alpha-helical hydrogen bond and an energy nearly equal to that of the folded state. The proteins have, however, high entropies, implying that they cannot fold onto their native structure, whereas in the presence of repulsive walls the proteins do attain their native structure. There is a pronounced asymmetry between the two termini of the protein with respect to their interaction with the pore walls. The effect of a variety of factors, including the pore size and the proteins' length, as well as the temperature, is studied in detail.
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Affiliation(s)
- Leili Javidpour
- Department of Physics, Sharif University of Technology, Tehran, Iran
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Top A, Kiick KL, Roberts CJ. Modulation of self-association and subsequent fibril formation in an alanine-rich helical polypeptide. Biomacromolecules 2008; 9:1595-603. [PMID: 18452331 DOI: 10.1021/bm800056r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thermal unfolding, reversible self-association, and irreversible aggregation were investigated for an alanine-rich helical polypeptide, 17-H-6, with sequence [AAAQEAAAAQAAAQAEAAQAAQ] 6. Dynamic light scattering, transmission electron microscopy, and thermal unfolding measurements indicate that 17-H-6 spontaneously and reversibly self-associates at acidic pH and low temperature. The resulting multimers have a compact, globular morphology with an average hydrodynamic radius approximately 10-20 nm and reversibly dissociate to monomers upon an increase to pH 7.4. Both free monomer and 17-H-6 chains within the multimers are alpha-helical and folded at low temperature. Reversible unfolding of the monomer occurs upon heating of solutions at pH 7.4. At pH 2.3, heating first causes incomplete dissociation and unfolding of the constituent chains. Further incubation at elevated temperature induces additional structural and morphological changes and results in fibrils with a beta-sheet 2 degrees structure and a characteristic diameter of 5-10 nm (7 nm mean). The ability to modulate association and aggregation suggests opportunities for this class of polypeptides in nanotechnology and biomedical applications.
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Affiliation(s)
- Ayben Top
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA
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