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Ivanov YD, Shumov ID, Kozlov AF, Valueva AA, Ershova MO, Ivanova IA, Ableev AN, Tatur VY, Lukyanitsa AA, Ivanova ND, Ziborov VS. Atomic Force Microscopy Study of the Long-Term Effect of the Glycerol Flow, Stopped in a Coiled Heat Exchanger, on Horseradish Peroxidase. MICROMACHINES 2024; 15:499. [PMID: 38675310 PMCID: PMC11052087 DOI: 10.3390/mi15040499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
Glycerol is employed as a functional component of heat-transfer fluids, which are of use in both bioreactors and various biosensor devices. At the same time, flowing glycerol was reported to cause considerable triboelectric effects. Herein, by using atomic force microscopy (AFM), we have revealed the long-term effect of glycerol flow, stopped in a ground-shielded coiled heat exchanger, on horseradish peroxidase (HRP) adsorption on mica. Namely, the solution of HRP was incubated in the vicinity of the side of the cylindrical coil with stopped glycerol flow, and then HRP was adsorbed from this solution onto a mica substrate. This incubation has been found to markedly increase the content of aggregated enzyme on mica-as compared with the control enzyme sample. We explain the phenomenon observed by the influence of triboelectrically induced electromagnetic fields of non-trivial topology. The results reported should be further considered in the development of flow-based heat exchangers of biosensors and bioreactors intended for operation with enzymes.
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Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
| | - Ivan D. Shumov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Andrey F. Kozlov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Anastasia A. Valueva
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Maria O. Ershova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Irina A. Ivanova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Alexander N. Ableev
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Vadim Y. Tatur
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia; (V.Y.T.); (A.A.L.); (N.D.I.)
| | - Andrei A. Lukyanitsa
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia; (V.Y.T.); (A.A.L.); (N.D.I.)
- Faculty of Computational Mathematics and Cybernetics, Moscow State University, 119991 Moscow, Russia
| | - Nina D. Ivanova
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia; (V.Y.T.); (A.A.L.); (N.D.I.)
- Moscow State Academy of Veterinary Medicine and Biotechnology Named after Skryabin, 109472 Moscow, Russia
| | - Vadim S. Ziborov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
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Fusco G, Biancaniello C, Vrettas MD, De Simone A. Thermal tuning of protein hydration in a hyperthermophilic enzyme. Front Mol Biosci 2022; 9:1037445. [PMID: 36518847 PMCID: PMC9742426 DOI: 10.3389/fmolb.2022.1037445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/14/2022] [Indexed: 10/24/2023] Open
Abstract
Water at the protein surface is an active biological molecule that plays a critical role in many functional processes. Using NMR-restrained MD simulations, we here addressed how protein hydration is tuned at high biological temperatures by analysing homologous acylphosphatase enzymes (AcP) possessing similar structure and dynamics under very different thermal conditions. We found that the hyperthermophilic Sso AcP at 80°C interacts with a lower number of structured waters in the first hydration shell than its human homologous mt AcP at 37°C. Overall, the structural and dynamical properties of waters at the surface of the two enzymes resulted similar in the first hydration shell, including solvent molecules residing in the active site. By contrast the dynamical content of water molecules in the second hydration shell was found to diverge, with higher mobility observed in Sso AcP at 80°C. Taken together the results delineate the subtle differences in the hydration properties of mt AcP and Sso AcP, and indicate that the concept of corresponding states with equivalent dynamics in homologous mesophilic and hyperthermophylic proteins should be extended to the first hydration shell.
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Affiliation(s)
- Giuliana Fusco
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Michail D. Vrettas
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
| | - Alfonso De Simone
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
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Balasco N, Diaferia C, Morelli G, Vitagliano L, Accardo A. Amyloid-Like Aggregation in Diseases and Biomaterials: Osmosis of Structural Information. Front Bioeng Biotechnol 2021; 9:641372. [PMID: 33748087 PMCID: PMC7966729 DOI: 10.3389/fbioe.2021.641372] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/05/2021] [Indexed: 11/13/2022] Open
Abstract
The discovery that the polypeptide chain has a remarkable and intrinsic propensity to form amyloid-like aggregates endowed with an extraordinary stability is one of the most relevant breakthroughs of the last decades in both protein/peptide chemistry and structural biology. This observation has fundamental implications, as the formation of these assemblies is systematically associated with the insurgence of severe neurodegenerative diseases. Although the ability of proteins to form aggregates rich in cross-β structure has been highlighted by recent studies of structural biology, the determination of the underlying atomic models has required immense efforts and inventiveness. Interestingly, the progressive molecular and structural characterization of these assemblies has opened new perspectives in apparently unrelated fields. Indeed, the self-assembling through the cross-β structure has been exploited to generate innovative biomaterials endowed with promising mechanical and spectroscopic properties. Therefore, this structural motif has become the fil rouge connecting these diversified research areas. In the present review, we report a chronological recapitulation, also performing a survey of the structural content of the Protein Data Bank, of the milestones achieved over the years in the characterization of cross-β assemblies involved in the insurgence of neurodegenerative diseases. A particular emphasis is given to the very recent successful elucidation of amyloid-like aggregates characterized by remarkable molecular and structural complexities. We also review the state of the art of the structural characterization of cross-β based biomaterials by highlighting the benefits of the osmosis of information between these two research areas. Finally, we underline the new promising perspectives that recent successful characterizations of disease-related amyloid-like assemblies can open in the biomaterial field.
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Affiliation(s)
- Nicole Balasco
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Carlo Diaferia
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples “Federico II”, Naples, Italy
| | - Giancarlo Morelli
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples “Federico II”, Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging (IBB), CNR, Naples, Italy
| | - Antonella Accardo
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples “Federico II”, Naples, Italy
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Mora AK, Murudkar S, Singh PK, Nath S. Effect of fibrillation on the excited state dynamics of tryptophan in serum protein – A time-resolved fluorescence study. J Photochem Photobiol A Chem 2015. [DOI: 10.1016/j.jphotochem.2014.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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5
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Srivastava A, Balaji PV. Interplay of sequence, topology and termini charge in determining the stability of the aggregates of GNNQQNY mutants: a molecular dynamics study. PLoS One 2014; 9:e96660. [PMID: 24817093 PMCID: PMC4015988 DOI: 10.1371/journal.pone.0096660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 04/11/2014] [Indexed: 01/16/2023] Open
Abstract
This study explores the stabilities of single sheet parallel systems of three sequence variants of 1GNNQQNY7, N2D, N2S and N6D, with variations in aggregate size (5–8) and termini charge (charged or neutral). The aggregates were simulated at 300 and 330 K. These mutations decrease amyloid formation in the yeast prion protein Sup35. The present study finds that these mutations cause instability even in the peptide context. The protonation status of termini is found to be a key determinant of stabilities; other determinants are sequence, position of mutation and aggregate size. All systems with charged termini are unstable, whereas both stable and unstable systems are found when the termini are neutral. When termini are charged, the largest stable aggregate for the N2S and N6D systems has 3 to 4 peptides whereas N2D mutation supports oligomers of larger size (5-and 6-mers) as well. Mutation at 2nd position (N2S and N2D) results in fewer H-bonds at the mutated as well as neighboring (Gly1/Gln4) positions. However, no such effect is found if mutation is at 6th position (N6D). The effect of Asn→Asp mutation depends on the position and termini charge: it is more destabilizing at the 2nd position than at the 6th in case of neutral termini, however, the opposite is true in case of charged termini. Appearance of twist in stable systems and in smaller aggregates formed in unstable systems suggests that twist is integral to amyloid arrangement. Disorder, dissociation or rearrangement of peptides, disintegration or collapse of aggregates and formation of amorphous aggregates observed in these simulations are likely to occur during the early stages of aggregation also. The smaller aggregates formed due to such events have a variety of arrangements of peptides. This suggests polymorphic nature of oligomers and presence of a heterogeneous mixture of oligomers during early stages of aggregation.
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Affiliation(s)
- Alka Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Petety V. Balaji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- * E-mail:
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Molecular Dynamics Studies on Amyloidogenic Proteins. COMPUTATIONAL METHODS TO STUDY THE STRUCTURE AND DYNAMICS OF BIOMOLECULES AND BIOMOLECULAR PROCESSES 2014. [DOI: 10.1007/978-3-642-28554-7_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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7
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Biedermann F, Uzunova VD, Scherman OA, Nau WM, De Simone A. Release of High-Energy Water as an Essential Driving Force for the High-Affinity Binding of Cucurbit[n]urils. J Am Chem Soc 2012; 134:15318-23. [DOI: 10.1021/ja303309e] [Citation(s) in RCA: 401] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Frank Biedermann
- Melville Laboratory for Polymer
Synthesis and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Vanya D. Uzunova
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen,
Germany
| | - Oren A. Scherman
- Melville Laboratory for Polymer
Synthesis and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Werner M. Nau
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen,
Germany
| | - Alfonso De Simone
- Division of Molecular
Biosciences, Imperial College London, South
Kensington, SW7 2AZ,
U.K
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Srivastava A, Balaji PV. Size, orientation and organization of oligomers that nucleate amyloid fibrils: Clues from MD simulations of pre-formed aggregates. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:963-73. [DOI: 10.1016/j.bbapap.2012.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 04/27/2012] [Accepted: 05/04/2012] [Indexed: 11/30/2022]
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9
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Hu L, Cui W, He Z, Shi X, Feng K, Ma B, Cai YD. Cooperativity among short amyloid stretches in long amyloidogenic sequences. PLoS One 2012; 7:e39369. [PMID: 22761773 PMCID: PMC3382238 DOI: 10.1371/journal.pone.0039369] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Accepted: 05/18/2012] [Indexed: 12/29/2022] Open
Abstract
Amyloid fibrillar aggregates of polypeptides are associated with many neurodegenerative diseases. Short peptide segments in protein sequences may trigger aggregation. Identifying these stretches and examining their behavior in longer protein segments is critical for understanding these diseases and obtaining potential therapies. In this study, we combined machine learning and structure-based energy evaluation to examine and predict amyloidogenic segments. Our feature selection method discovered that windows consisting of long amino acid segments of ~30 residues, instead of the commonly used short hexapeptides, provided the highest accuracy. Weighted contributions of an amino acid at each position in a 27 residue window revealed three cooperative regions of short stretch, resemble the β-strand-turn-β-strand motif in A-βpeptide amyloid and β-solenoid structure of HET-s(218-289) prion (C). Using an in-house energy evaluation algorithm, the interaction energy between two short stretches in long segment is computed and incorporated as an additional feature. The algorithm successfully predicted and classified amyloid segments with an overall accuracy of 75%. Our study revealed that genome-wide amyloid segments are not only dependent on short high propensity stretches, but also on nearby residues.
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Affiliation(s)
- Lele Hu
- Institute of Systems Biology, Shanghai University, Shanghai, People’s Republic of China
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, People’s Republic of China
| | - Weiren Cui
- CAS-MPG Partner Institute of Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Zhisong He
- CAS-MPG Partner Institute of Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Xiaohe Shi
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Kaiyan Feng
- Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Buyong Ma
- Basic Science Program, SAIC – Frederick, Center for Cancer Research Nanobiology Program, National Cancer Institute-Fredeick, National Institute of Health, Frederick, Maryland, United States of America
| | - Yu-Dong Cai
- Institute of Systems Biology, Shanghai University, Shanghai, People’s Republic of China
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10
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Role of hydration in collagen recognition by bacterial adhesins. Biophys J 2011; 100:2253-61. [PMID: 21539794 DOI: 10.1016/j.bpj.2011.03.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 02/22/2011] [Accepted: 03/09/2011] [Indexed: 11/23/2022] Open
Abstract
Protein-protein recognition regulates the vast majority of physiological or pathological processes. We investigated the role of hydration in collagen recognition by bacterial adhesin CNA by means of first principle molecular-dynamics samplings. Our characterization of the hydration properties of the isolated partners highlights dewetting-prone areas on the surface of CNA that closely match the key regions involved in hydrophobic intermolecular interactions upon complex formation, suggesting that the hydration state of the ligand-free CNA predisposes the protein to the collagen recognition. Moreover, hydration maps of the CNA-collagen complex reveal the presence of a number of structured water molecules that mediate intermolecular interactions at the interface between the two proteins. These hydration sites feature long residence times, significant binding free energies, and a geometrical distribution that closely resembles the hydration pattern of the isolated collagen triple helix. These findings are striking evidence that CNA recognizes the collagen triple helix as a hydrated molecule. For this structural motif, the exposure of several unsatisfied backbone carbonyl groups results in a strong interplay with the solvent, which is shown to also play a role in collagen recognition.
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Ge R, Sun X. The in vivo functions of a histidine-rich protein Hpn in Helicobacter pylori: linking gastric and Alzheimer's diseases together? Med Hypotheses 2011; 77:788-90. [PMID: 21852052 DOI: 10.1016/j.mehy.2011.07.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 07/18/2011] [Indexed: 12/17/2022]
Abstract
Helicobacter pylori causes such gastric diseases as gastritis, peptic ulcerations, gastric cancer and MALT lymphoma. Hpn is a histidine-rich protein abundant in this bacterium and forms amyloid-like oligomers in physiologically relevant conditions. Here we proposed the in vivo functions of this protein with relevance to its physical locations. The collective evidence presented here shed some light on the pathologic mechanisms of H. pylori infections, with emphasis on the bacterial colonization in the gastric environment, pathological effects to the gastric epithelial cells and the possible link to Alzheimer's disease.
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Affiliation(s)
- Ruiguang Ge
- The Laboratory of Integrative Biosciences, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
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12
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Ge R, Sun X, Wang D, Zhou Q, Sun H. Histidine-rich protein Hpn from Helicobacter pylori forms amyloid-like fibrils in vitro and inhibits the proliferation of gastric epithelial AGS cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1813:1422-7. [DOI: 10.1016/j.bbamcr.2011.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 04/06/2011] [Accepted: 04/11/2011] [Indexed: 02/06/2023]
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13
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Vitagliano L, Stanzione F, De Simone A, Esposito L. Dynamics and stability of amyloid-like steric zipper assemblies with hydrophobic dry interfaces. Biopolymers 2010; 91:1161-71. [PMID: 19280623 DOI: 10.1002/bip.21182] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Recent seminal investigations have suggested that the basic structural motif of amyloid fibers may be constituted by a tight association of two facing beta-sheets (steric zipper). Although this model has been derived from crystal structures of small peptide models, several theoretical investigations, essentially focused on steric zipper interface containing large polar and/or aromatic side chains, have confirmed the stability of this motif in a crystal-free context. To analyze the general validity of these findings, we carried out molecular dynamics (MD) simulations on aggregates stabilized by steric zipper interfaces made also of small or hydrophobic residues. In particular, we here characterized assemblies formed by the peptides SSTSAA and VQIVYK, whose structures have been recently solved at high resolution. In contrast to previous results obtained for polar/aromatic aggregates of the same size and with similar interface area, steric zipper assemblies composed of a pair of 10-stranded beta-sheets show high fluctuations and significant distortions in the simulation timescales (40-60 ns). Taking into account the crystal packing, the effect of the addition of an extra sheet to the assemblies was also evaluated. The MD results indicate that this addition does not provide extra-stabilization to the pair of sheet models. Although present data do not preclude the possibility that the steric zipper association identified in the crystal structure is the basic motif of SSTSAA and VQIVYK fibers, our findings highlight the importance of the nature of residues directly involved in the motif. Indeed, polar and aromatic residues that may form intrasheet and intersheet interactions likely provide a strong contribution to the steric zipper motif stability. Along this line, assemblies endowed with hydrophobic residues presumably require larger interfaces. In line with this suggestion, MD analysis of the HET-s(218-289) prion models composed of a similar number of strands shows that the assembly is endowed with a remarkable stability.
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Affiliation(s)
- Luigi Vitagliano
- Istituto di Biostrutture e Bioimmagini, CNR via Mezzocannone 16, I-80134 Napoli, Italy.
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14
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Vitagliano L, Esposito L, Pedone C, De Simone A. Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: antiparallel versus parallel association. Biochem Biophys Res Commun 2008; 377:1036-41. [PMID: 18938138 DOI: 10.1016/j.bbrc.2008.10.039] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Accepted: 10/03/2008] [Indexed: 11/28/2022]
Abstract
Protein and peptide aggregation into amyloid plaques is associated with a large variety of neurodegenerative diseases. The definition of the molecular bases of these pathologies is hampered by the transient nature of pre-fibrillar small-oligomers that are considered the toxic species. The ability of the peptide GNNQQNY to form amyloid-like structures makes it a good model to investigate the complex processes involved into amyloid fiber formation. By employing full atomistic replica exchange molecular dynamics simulations, we constructed the free energy surface of small assemblies of GNNQQNY to gain novel insights into the fiber formation process. The calculations suggest that the peptide exhibits a remarkable tendency to form both parallel and antiparallel beta-sheets. The data show that GNNQQNY preference for parallel or antiparallel beta-sheets is governed by a subtle balance of factors including assemblies' size, sidechain-sidechain interactions and pH. The samplings analysis provides a rationale to the observed trends.
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Affiliation(s)
- Luigi Vitagliano
- Istituto di Biostrutture e Bioimmagini, CNR via Mezzocannone 16, I-80134 Napoli, Italy
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15
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De Simone A, Vitagliano L, Berisio R. Role of hydration in collagen triple helix stabilization. Biochem Biophys Res Commun 2008; 372:121-5. [PMID: 18485893 DOI: 10.1016/j.bbrc.2008.04.190] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Accepted: 04/30/2008] [Indexed: 11/30/2022]
Abstract
Collagen is the most abundant protein in higher vertebrates. Despite collagen repetitive sequence, several aspects of its structure and stability are controversial. Here we performed molecular dynamics simulations to analyze triple helix hydration in regions characterized by different imino/aminoacid contents. Data emerged from MD simulations show that (a) MD simulations can reliably reproduce the hydration sites identified experimentally, (b) water molecules bound to regions with a different amino/iminoacid content exhibit diversified residence times, and (c) in the aminoacid-rich region the binding of water molecules is strongly influenced by the local sequence of the peptide. MD results also suggest that, in aminoacid-rich regions, the stabilizing effects of Arg and Hyp residues on collagen triple helix also depend on water-mediated interactions. On this basis, we propose that the mechanism of triple helix stabilization is sequence-dependent.
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Affiliation(s)
- Alfonso De Simone
- Istituto di Biostrutture e Bioimmagini, C.N.R., via Mezzocannone 16, I-80134 Napoli, Italy.
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16
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Insights into stability and toxicity of amyloid-like oligomers by replica exchange molecular dynamics analyses. Biophys J 2008; 95:1965-73. [PMID: 18469082 DOI: 10.1529/biophysj.108.129213] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Deposition of insoluble amyloid plaques is frequently associated with a large variety of neurodegenerative diseases. However, data collected in the last decade have suggested that the neurotoxic action is exerted by prefibrillar, soluble assemblies of amyloid-forming proteins and peptides. The scarcity of structural data available for both amyloid-like fibrils and soluble oligomers is a major limitation for the definition of the molecular mechanisms linked to the onset of these diseases. Recently, the structural characterization of GNNQQNY and other peptides has shown a general feature of amyloid-like fibers, the so-called steric zipper motif. However, very little is known still about the prefibrillar oligomeric forms. By using replica exchange molecular dynamics we carried out extensive analyses of the properties of several small and medium GNNQQNY aggregates arranged through the steric zipper motif. Our data show that the assembly formed by two sheets, each made of two strands, arranged as in the crystalline states are highly unstable. Conformational free energy surfaces indicate that the instability of the model can be ascribed to the high reactivity of edge backbone hydrogen bonding donors/acceptors. On the other hand, data on larger models show that steric zipper interactions may keep small oligomeric forms in a stable state. These models simultaneously display two peculiar structural motifs: a tightly packed steric zipper interface and a large number of potentially reactive exposed strands. The presence of highly reactive groups on these assemblies likely generates two distinct evolutions. On one side the reactive groups quickly lead, through self-association, to the formation of ordered fibrils, on the other they may interfere with several cellular components thereby generating toxic effects. In this scenario, fiber formation propensity and toxicity of oligomeric states are two different manifestations of the same property: the hyper-reactivity of the exposed strands.
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