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Basu S, Kurgan L. Taxonomy-specific assessment of intrinsic disorder predictions at residue and region levels in higher eukaryotes, protists, archaea, bacteria and viruses. Comput Struct Biotechnol J 2024; 23:1968-1977. [PMID: 38765610 PMCID: PMC11098722 DOI: 10.1016/j.csbj.2024.04.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/22/2024] Open
Abstract
Intrinsic disorder predictors were evaluated in several studies including the two large CAID experiments. However, these studies are biased towards eukaryotic proteins and focus primarily on the residue-level predictions. We provide first-of-its-kind assessment that comprehensively covers the taxonomy and evaluates predictions at the residue and disordered region levels. We curate a benchmark dataset that uniformly covers eukaryotic, archaeal, bacterial, and viral proteins. We find that predictive performance differs substantially across taxonomy, where viruses are predicted most accurately, followed by protists and higher eukaryotes, while bacterial and archaeal proteins suffer lower levels of accuracy. These trends are consistent across predictors. We also find that current tools, except for flDPnn, struggle with reproducing native distributions of the numbers and sizes of the disordered regions. Moreover, analysis of two variants of disorder predictions derived from the AlphaFold2 predicted structures reveals that they produce accurate residue-level propensities for archaea, bacteria and protists. However, they underperform for higher eukaryotes and generally struggle to accurately identify disordered regions. Our results motivate development of new predictors that target bacteria and archaea and which produce accurate results at both residue and region levels. We also stress the need to include the region-level assessments in future assessments.
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Affiliation(s)
- Sushmita Basu
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
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2
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Nayak SS, Krishna R. Phosphorylation at the D56 residue of MtrA in Mycobacterium tuberculosis enhances its DNA binding affinity by modulating inter-domain interaction. Comput Biol Chem 2024; 113:108222. [PMID: 39366081 DOI: 10.1016/j.compbiolchem.2024.108222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 09/15/2024] [Accepted: 09/20/2024] [Indexed: 10/06/2024]
Abstract
The response regulator, MtrA, plays a major role in adaptation to the host environment, cell division, replication, and dormancy activation of Mycobacterium tuberculosis (Mtb). The phosphorylation of the response regulator MtrA alters the downstream activity, typically involving changes in DNA binding activity. However, there is a substantial knowledge gap in understanding the phosphorylation-mediated structural changes in MtrA. Additionally, the active conformation of the protein has yet to be determined. Therefore, in this study, we have investigated the phosphorylation-induced conformational changes of MtrA using all-atom molecular dynamics simulations under various phosphorylation conditions. The results from this study demonstrate that the phosphorylation at D56 (pD56-MtrA) increases the compactness of the MtrA protein by stabilizing the inter-domain interaction between the regulatory domain and DNA binding domain. Notably, the higher occupancy H-bond (over 95 %) between Arg200-Asn100 in case of the pD56-MtrA condition, which is otherwise absent in the non-phosphorylated (uMtrA) condition, suggests the importance of this interaction in the active conformation of the protein. The dynamic cross-correlation analysis reveals that phosphorylation (especially pD56-MtrA) reduces the anti-correlated motions and increases correlated motions between different domains. Moreover, the higher DNA binding affinity of pD56-MtrA compared to uMtrA supported by molecular docking and MD simulation followed by MMPBSA analysis suggests that pD56-MtrA is the possible active conformation of the MtrA protein. Overall, this investigation elucidates the key structural changes in MtrA under different phosphorylated conditions, which might help in designing novel therapeutics against tuberculosis.
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Affiliation(s)
| | - Ramadas Krishna
- Department of Bioinformatics, Pondicherry University, Pondicherry 605014, India.
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3
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Zhang H, Lu C, Yao Q, Jiao Q. In silico study to identify novel NEK7 inhibitors from natural sources by a combination strategy. Mol Divers 2024:10.1007/s11030-024-10838-4. [PMID: 38598164 DOI: 10.1007/s11030-024-10838-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 03/06/2024] [Indexed: 04/11/2024]
Abstract
Cancer poses a significant global health challenge and significantly contributes to mortality. NEK7, related to the NIMA protein kinase family, plays a crucial role in spindle assembly and cell division. The dysregulation of NEK7 is closely linked to the onset and progression of various cancers, especially colon and breast cancer, making it a promising target for cancer therapy. Nevertheless, the shortage of high-quality NEK7 inhibitors highlights the need for new therapeutic strategies. In this study, we utilized a multidisciplinary approach, including virtual screening, molecular docking, pharmacokinetics, molecular dynamics simulations (MDs), and MM/PBSA calculations, to evaluate natural compounds as NEK7 inhibitors comprehensively. Through various docking strategies, we identified three natural compounds: (-)-balanol, digallic acid, and scutellarin. Molecular docking revealed significant interactions at residues such as GLU112 and ALA114, with docking scores of -15.054, -13.059, and -11.547 kcal/mol, respectively, highlighting their potential as NEK7 inhibitors. MDs confirmed the stability of these compounds at the NEK7-binding site. Hydrogen bond analysis during simulations revealed consistent interactions, supporting their strong binding capacity. MM/PBSA analysis identified other crucial amino acids contributing to binding affinity, including ILE20, VAL28, ILE75, LEU93, ALA94, LYS143, PHE148, LEU160, and THR161, crucial for stabilizing the complex. This research demonstrated that these compounds exceeded dabrafenib in binding energy, according to MM/PBSA calculations, underscoring their effectiveness as NEK7 inhibitors. ADME/T predictions showed lower oral toxicity for these compounds, suggesting their potential for further development. This study highlights the promise of these natural compounds as bases for creating more potent derivatives with significant biological activities, paving the way for future experimental validation.
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Affiliation(s)
- Heng Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Chenhong Lu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Qilong Yao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Qingcai Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
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4
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Faraji N, Daly NL, Arab SS, Khosroushahi AY. In silico design of potential Mcl-1 peptide-based inhibitors. J Mol Model 2024; 30:108. [PMID: 38499818 DOI: 10.1007/s00894-024-05901-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 03/10/2024] [Indexed: 03/20/2024]
Abstract
CONTEXT BIM (Bcl-2 interacting mediator of apoptosis)-derived peptides that specifically target over-expressed Mcl-1 (myeloid cell leukemia-1) protein and induce apoptosis are potentially anti-cancer agents. Since the helicity of BIM-derived peptides has a crucial role in their functionality, a range of strategies have been used to increase the helicity including the introduction of unnatural residues and stapling methods that have some drawbacks such as the accumulation in the liver. To avoid these drawbacks, this study aimed to design a more helical peptide by utilizing bioinformatics algorithms and molecular dynamics simulations without exploiting unnatural residues and stapling methods. MM-PBSA results showed that the mutations of A4fE and A2eE in analogue 5 demonstrate a preference towards binding with Mcl-1. As evidenced by Circular dichroism results, the helicity increases from 18 to 34%, these findings could enhance the potential of analogue 5 as an anti-cancer agent targeting Mcl-1. The applied strategies in this research could shed light on the in silico peptide design. Moreover, analogue 5 as a drug candidate can be evaluated in vitro and in vivo studies. METHODS The sequence of the lead peptide was determined using the ApInAPDB database and PRALINE program. Contact finder and PDBsum web server softwares were used to determine the contact involved amino acids in complex with Mcl-1. All identified salt bridge contributing residues were unaltered to preserve the binding affinity. After proposing novel analogues, their secondary structures were predicted by Cham finder web server software and GOR, Neural Network, and Chou-Fasman algorithms. Finally, molecular dynamics simulations run for 100 ns were done using the GROMACS, version 5.0.7, with the CHARMM36 force field. MM-PBSA was used to assess binding affinity specificity in targeting Mcl-1 and Bcl-xL (B-cell lymphoma extra-large).
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Affiliation(s)
- Naser Faraji
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Daneshgah Street, Tabriz, Iran
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Norelle L Daly
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, 4870, Australia
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Ahmad Yari Khosroushahi
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Daneshgah Street, Tabriz, Iran.
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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5
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Amith W, Dutagaci B. Complex Conformational Space of the RNA Polymerase II C-Terminal Domain upon Phosphorylation. J Phys Chem B 2023; 127:9223-9235. [PMID: 37870995 PMCID: PMC10626582 DOI: 10.1021/acs.jpcb.3c02655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 10/03/2023] [Indexed: 10/25/2023]
Abstract
Intrinsically disordered proteins (IDPs) have been closely studied during the past decade due to their importance in many biological processes. The disordered nature of this group of proteins makes it difficult to observe its full span of the conformational space using either experimental or computational studies. In this article, we explored the conformational space of the C-terminal domain (CTD) of RNA polymerase II (Pol II), which is also an intrinsically disordered low complexity domain, using enhanced sampling methods. We provided a detailed conformational analysis of model systems of CTD with different lengths; first with the last 44 residues of the human CTD sequence and finally the CTD model with 2-heptapeptide repeating units. We then investigated the effects of phosphorylation on CTD conformations by performing simulations at different phosphorylated states. We obtained broad conformational spaces in nonphosphorylated CTD models, and phosphorylation has complex effects on the conformations of the CTD. These complex effects depend on the length of the CTD, spacing between the multiple phosphorylation sites, ion coordination, and interactions with the nearby residues.
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Affiliation(s)
- Weththasinghage
D. Amith
- Department of Molecular and
Cell Biology, University of California,
Merced, Merced, California 95343, United States
| | - Bercem Dutagaci
- Department of Molecular and
Cell Biology, University of California,
Merced, Merced, California 95343, United States
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6
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Nikolsky KS, Kulikova LI, Petrovskiy DV, Rudnev VR, Malsagova KA, Kaysheva AL. Analysis of Structural Changes in the Protein near the Phosphorylation Site. Biomolecules 2023; 13:1564. [PMID: 38002246 PMCID: PMC10668964 DOI: 10.3390/biom13111564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/13/2023] [Accepted: 10/14/2023] [Indexed: 11/26/2023] Open
Abstract
Modification of the protein after synthesis (PTM) often affects protein function as supported by numerous studies. However, there is no consensus about the degree of structural protein changes after modification. For phosphorylation of serine, threonine, and tyrosine, which is a common PTM in the biology of living organisms, we consider topical issues related to changes in the geometric parameters of a protein (Rg, RMSD, Cα displacement, SASA). The effect of phosphorylation on protein geometry was studied both for the whole protein and at the local level (i.e., in different neighborhoods of the modification site). Heterogeneity in the degree of protein structural changes after phosphorylation was revealed, which allowed for us to isolate a group of proteins having pronounced local structural changes in the neighborhoods of up to 15 amino acid residues from the modification site. This is a comparative study of protein structural changes in neighborhoods of 3-15 amino acid residues from the modified site. Amino acid phosphorylation in proteins with pronounced local changes caused switching from the inactive functional state to the active one.
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Affiliation(s)
| | | | | | | | - Kristina A. Malsagova
- Institute of Biomedical Chemistry, Biobanking Group, Pogodinskaya, 10, 119121 Moscow, Russia; (K.S.N.); (L.I.K.); (D.V.P.); (V.R.R.); (A.L.K.)
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7
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Sun B, Kekenes-Huskey PM. Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling. Q Rev Biophys 2023; 56:e2. [PMID: 36628457 PMCID: PMC11070111 DOI: 10.1017/s003358352300001x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The cardiac sarcomere is a cellular structure in the heart that enables muscle cells to contract. Dozens of proteins belong to the cardiac sarcomere, which work in tandem to generate force and adapt to demands on cardiac output. Intriguingly, the majority of these proteins have significant intrinsic disorder that contributes to their functions, yet the biophysics of these intrinsically disordered regions (IDRs) have been characterized in limited detail. In this review, we first enumerate these myofilament-associated proteins with intrinsic disorder (MAPIDs) and recent biophysical studies to characterize their IDRs. We secondly summarize the biophysics governing IDR properties and the state-of-the-art in computational tools toward MAPID identification and characterization of their conformation ensembles. We conclude with an overview of future computational approaches toward broadening the understanding of intrinsic disorder in the cardiac sarcomere.
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Affiliation(s)
- Bin Sun
- Research Center for Pharmacoinformatics (The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, China
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8
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Wang B, Guo C. Concentration-Dependent Effects of Cholesterol on the Dimerization of Amyloid-β Peptides in Lipid Bilayers. ACS Chem Neurosci 2022; 13:2709-2718. [PMID: 36082607 DOI: 10.1021/acschemneuro.2c00349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Membrane disruption mediated by the accumulation of amyloid-β (Aβ) on cell membranes is central to the pathogenesis of Alzheimer's disease (AD). Cholesterol, an important component of membranes, is well-recognized as a risk factor in AD. It can affect the aggregation and pore formation of Aβ on membranes whereas the specific effects are rather complex, particularly regarding the non-linear response to cholesterol concentrations. Yet, the mechanistic understanding of the role of cholesterol in Aβ-membrane interactions remains incomplete. Herein, we employed microsecond-scale molecular dynamics simulations to investigate the effects of cholesterol on Aβ dimerization in a lipid bilayer containing different molar ratios of cholesterol (0, 20, and 40 mol %). Cholesterol reduces the time required for the formation of stable dimers and exerts dual effects on Aβ-membrane interactions. First, cholesterol promotes the extraction of the C-terminal region from the membrane to water. Consequently, at the ratios of 0 and 20 mol %, peptides are anchored at the membrane-water interface, but they are repelled to water at a ratio of 40 mol % with high structural flexibility. Second, cholesterol weakens Aβ-membrane interactions, thereby enhancing inter-peptide interactions. The former is favorable for dimerization while the latter is not. The balance between two factors eventually leads to a non-monotonic effect on the degree of dimerization, whereby the number of inter-peptide contacts is the largest at a cholesterol ratio of 20 mol %. These results provide atomistic insights into the regulation mechanism of Aβ42 aggregation by cholesterol and help to understand the pathological link between cholesterol and AD.
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Affiliation(s)
- Bin Wang
- Department of Physics and International Centre for Quantum and Molecular Structures, College of Sciences, Shanghai University, Shanghai 200444, China
| | - Cong Guo
- Department of Physics and International Centre for Quantum and Molecular Structures, College of Sciences, Shanghai University, Shanghai 200444, China
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9
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Mosallanejad S, Mahmoodi M, Tavakkoli H, Khosravi A, Salarkia E, Keyhani A, Dabiri S, Gozashti MH, Pardakhty A, Khodabandehloo H, Pourghadamyari H. Empagliflozin induces apoptotic-signaling pathway in embryonic vasculature: In vivo and in silico approaches via chick’s yolk sac membrane model. Front Pharmacol 2022; 13:970402. [PMID: 36120349 PMCID: PMC9474685 DOI: 10.3389/fphar.2022.970402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/12/2022] [Indexed: 11/18/2022] Open
Abstract
The present investigation was conducted to evaluate the vascular-toxicity of empagliflozin (EMP) in embryonic vasculature. Firstly, the vascular-toxicity of the drug as well as its interaction with apoptotic regulator proteins was predicted via in silico approach. In the next step, the apoptotic-signaling pathway in embryonic vasculature was evaluated using a chick’s YSM model. In silico simulation confirmed vascular-toxicity of EMP. There was also an accurate affinity between EMP, Bax and Bcl-2 (−7.9 kcal/mol). Molecular dynamics assay revealed complex stability in the human body conditions. Furthermore, EMP is suggested to alter Bcl-2 more than BAX. Morphometric quantification of the vessels showed that the apoptotic activity of EMP in embryonic vasculature was related to a marked reduction in vessel area, vessel diameter and mean capillary area. Based on the qPCR and immunohistochemistry assays, enhanced expression level of BAX and reduced expression level of Bcl-2 confirmed apoptotic responses in the vessels of the YSM. We observed that induction of an apoptotic signal can cause the embryonic defect of the vascular system following EMP treatment. The acquired data also raised suspicions that alteration in apoptotic genes and proteins in the vasculature are two critical pathways in vascular-toxicity of EMP.
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Affiliation(s)
- Saeedeh Mosallanejad
- Department of Clinical Biochemistry, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehdi Mahmoodi
- Department of Clinical Biochemistry, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
- *Correspondence: Mehdi Mahmoodi, ; Hossein Pourghadamyari,
| | - Hadi Tavakkoli
- Department of Clinical Sciences, School of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Ahmad Khosravi
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Ehsan Salarkia
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Alireza Keyhani
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Shahriar Dabiri
- Afzalipour School of Medicine, Pathology and Stem Cell Research Center, Kerman University of Medical Science, Kerman, Iran
| | - Mohammad Hossein Gozashti
- Endocrinology and Metabolism Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Abbas Pardakhty
- Pharmaceutics Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Hadi Khodabandehloo
- Department of Clinical Biochemistry, School of Medicine Zanjan University of Medical Sciences, Zanjan, Iran
| | - Hossein Pourghadamyari
- Department of Clinical Biochemistry, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
- Gastroenterology and Hepatology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
- *Correspondence: Mehdi Mahmoodi, ; Hossein Pourghadamyari,
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Al Adem K, Shanti A, Srivastava A, Homouz D, Thomas SA, Khair M, Stefanini C, Chan V, Kim TY, Lee S. Linking Alzheimer’s Disease and Type 2 Diabetes: Characterization and Inhibition of Cytotoxic Aβ and IAPP Hetero-Aggregates. Front Mol Biosci 2022; 9:842582. [PMID: 35372522 PMCID: PMC8968156 DOI: 10.3389/fmolb.2022.842582] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/07/2022] [Indexed: 12/18/2022] Open
Abstract
The cytotoxic self-aggregation of β-amyloid (Aβ) peptide and islet amyloid polypeptide (IAPP) is implicated in the pathogenesis of Alzheimer’s disease (AD) and Type 2 diabetes (T2D), respectively. Increasing evidence, particularly the co-deposition of Aβ and IAPP in both brain and pancreatic tissues, suggests that Aβ and IAPP cross-interaction may be responsible for a pathological link between AD and T2D. Here, we examined the nature of IAPP-Aβ40 co-aggregation and its inhibition by small molecules. In specific, we characterized the kinetic profiles, morphologies, secondary structures and toxicities of IAPP-Aβ40 hetero-assemblies and compared them to those formed by their homo-assemblies. We demonstrated that monomeric IAPP and Aβ40 form stable hetero-dimers and hetero-assemblies that further aggregate into β-sheet-rich hetero-aggregates that are toxic (cell viability <50%) to both PC-12 cells, a neuronal cell model, and RIN-m5F cells, a pancreatic cell model for β-cells. We then selected polyphenolic candidates to inhibit IAPP or Aβ40 self-aggregation and examined the inhibitory effect of the most potent candidate on IAPP-Aβ40 co-aggregation. We demonstrated that epigallocatechin gallate (EGCG) form inter-molecular hydrogen bonds with each of IAPP and Aβ40. We also showed that EGCG reduced hetero-aggregate formation and resulted in lower β-sheets content and higher unordered structures in IAPP-Aβ40-EGCG samples. Importantly, we showed that EGCG is highly effective in reducing the toxicity of IAPP-Aβ40 hetero-aggregates on both cell models, specifically at concentrations that are equivalent to or are 2.5-fold higher than the mixed peptide concentrations. To the best of our knowledge, this is the first study to report the inhibition of IAPP-Aβ40 co-aggregation by small molecules. We conclude that EGCG is a promising candidate to prevent co-aggregation and cytotoxicity of IAPP-Aβ40, which in turn, contribute to the pathological link between AD and T2D.
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Affiliation(s)
- Kenana Al Adem
- Department of Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Aya Shanti
- Department of Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Amit Srivastava
- Department of Physics, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Dirar Homouz
- Department of Physics, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Physics, University of Houston, Houston, TX, United States
- Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
| | - Sneha Ann Thomas
- Core Technology Platforms, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Mostafa Khair
- Core Technology Platforms, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Cesare Stefanini
- Department of Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Vincent Chan
- Department of Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Tae-Yeon Kim
- Department of Civil Infrastructure and Environmental Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Sungmun Lee
- Department of Biomedical Engineering and Healthcare Engineering Innovation Center, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Khalifa University’s Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- *Correspondence: Sungmun Lee,
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11
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Rafaee A, Kashani-Amin E, Meybodi AM, Ebrahim-Habibi A, Sabbaghian M. Structural modeling of human AKAP3 protein and in silico analysis of single nucleotide polymorphisms associated with sperm motility. Sci Rep 2022; 12:3656. [PMID: 35256641 PMCID: PMC8901789 DOI: 10.1038/s41598-022-07513-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 01/28/2022] [Indexed: 11/20/2022] Open
Abstract
AKAP3 is a member of the A-kinase anchoring proteins and it is a constituent of the sperm fibrous sheath. AKAP3 is needed for the formation of sperm flagellum structure, sperm motility, and male fertility. This study aims to model the AKAP3 tertiary structure and identify the probable impact of four mutations characterized in infertile men on the AKAP3 structure. The T464S, I500T, E525K, and I661T substitutions were analyzed using in silico methods. The secondary structure and three-dimensional model of AKAP3 were determined using PSI-BLAST based secondary structure prediction and Robetta servers. The TM-score was used to quantitatively measure the structural similarities between native and mutated models. All of the desired substitutions were classified as benign. I-Mutant results showed all of the substitutions decreased AKAP3 stability; however, the I500T and I661T were more effective. Superposition and secondary structure comparisons between native and mutants showed no dramatic deviations. Our study provided an appropriate model for AKAP3. Destabilization of AKAP3 caused by these substitutions did not appear to induce structural disturbances. As AKAP3 is involved in male infertility, providing more structural insights and the impact of mutations that cause protein functional diversity could elucidate the etiology of male fertility problems at molecular level.
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Affiliation(s)
- Alemeh Rafaee
- Department of Andrology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.,Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Elaheh Kashani-Amin
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Anahita Mohseni Meybodi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.,Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Azadeh Ebrahim-Habibi
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Marjan Sabbaghian
- Department of Andrology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.
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12
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Müller WA, Sarkis JR, Marczak LDF, Muniz AR. Molecular dynamics study of the effects of static and oscillating electric fields in ovalbumin. INNOV FOOD SCI EMERG 2022. [DOI: 10.1016/j.ifset.2021.102911] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Real-time in-situ quantification of protein secondary structures in aqueous solution based on ATR-FTIR subtraction spectrum. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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14
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Fatafta H, Khaled M, Owen MC, Sayyed-Ahmad A, Strodel B. Amyloid-β peptide dimers undergo a random coil to β-sheet transition in the aqueous phase but not at the neuronal membrane. Proc Natl Acad Sci U S A 2021; 118:e2106210118. [PMID: 34544868 PMCID: PMC8488611 DOI: 10.1073/pnas.2106210118] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2021] [Indexed: 11/21/2022] Open
Abstract
Mounting evidence suggests that the neuronal cell membrane is the main site of oligomer-mediated neuronal toxicity of amyloid-β peptides in Alzheimer's disease. To gain a detailed understanding of the mutual interference of amyloid-β oligomers and the neuronal membrane, we carried out microseconds of all-atom molecular dynamics (MD) simulations on the dimerization of amyloid-β (Aβ)42 in the aqueous phase and in the presence of a lipid bilayer mimicking the in vivo composition of neuronal membranes. The dimerization in solution is characterized by a random coil to β-sheet transition that seems on pathway to amyloid aggregation, while the interactions with the neuronal membrane decrease the order of the Aβ42 dimer by attenuating its propensity to form a β-sheet structure. The main lipid interaction partners of Aβ42 are the surface-exposed sugar groups of the gangliosides GM1. As the neurotoxic activity of amyloid oligomers increases with oligomer order, these results suggest that GM1 is neuroprotective against Aβ-mediated toxicity.
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Affiliation(s)
- Hebah Fatafta
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Mohammed Khaled
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Michael C Owen
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
- Institute of Chemistry, University of Miskolc, 3515 Miskolc-Egyetemváros, Hungary
| | | | - Birgit Strodel
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany;
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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15
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Antony JV, Madhu P, Balakrishnan JP, Yadav H. Assigning secondary structure in proteins using AI. J Mol Model 2021; 27:252. [PMID: 34402969 DOI: 10.1007/s00894-021-04825-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 06/16/2021] [Indexed: 12/16/2022]
Abstract
Knowledge about protein structure assignment enriches the structural and functional understanding of proteins. Accurate and reliable structure assignment data is crucial for secondary structure prediction systems. Since the 1980s, various methods based on hydrogen bond analysis and atomic coordinate geometry, followed by machine learning, have been employed in protein structure assignment. However, the assignment process becomes challenging when missing atoms are present in the protein files. Our method proposed a multi-class classifier program named DLFSA for assigning protein secondary structure elements (SSE) using convolutional neural networks (CNNs). A fast and efficient GPU-based parallel procedure extracts fragments from protein files. The model implemented in this work is trained with a subset of the protein fragments and achieves 88.1% and 82.5% train and test accuracy, respectively. The model uses only Cα coordinates for secondary structure assignments. The model has been successfully tested on a few full-length proteins also. Results from the fragment-based studies demonstrate the feasibility of applying deep learning solutions for structure assignment problems.
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Affiliation(s)
- Jisna Vellara Antony
- Department of Computer Science and Engineering, National Institute of Technology Calicut, Kerala, 673601, India.
| | - Prayagh Madhu
- Computer Science and Engineering Dept., Rajiv Gandhi Institute of Technology, Kottayam, India
| | | | - Hemant Yadav
- Department of Computer Science and Engineering, National Institute of Technology Calicut, Kerala, 673601, India
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16
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Alimohammadi E, Nikzad A, Khedri M, Shafiee S, Miri Jahromi A, Maleki R, Rezaei N. Molecular Tuning of the Nano–Bio Interface: Alpha-Synuclein’s Surface Targeting with Doped Carbon Nanostructures. ACS APPLIED BIO MATERIALS 2021; 4:6073-6083. [DOI: 10.1021/acsabm.1c00421] [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)
- Ehsan Alimohammadi
- Department of Neurosurgery, Kermanshah University of Medical Sciences, Imam Reza Hospital, 67158-47141 Kermanshah, Iran
| | - Arash Nikzad
- Department of Mechanical Engineering, University of British Columbia, 2054-6250 Applied
Science Lane, Vancouver, British Columbia V6T1Z4, Canada
| | - Mohammad Khedri
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Sepehr Shafiee
- School of Medicine, Shahid Beheshti University of Medical Sciences, 19839-63113 Tehran, Iran
| | - Ahmad Miri Jahromi
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Reza Maleki
- Computational Biology and Chemistry Group (CBCG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran University of Medical Sciences, 14167-53955 Tehran, Iran
- Network of Immunity in Infection, Malignancy, and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran 1419733141, Iran
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, 14167-53955 Tehran, Iran
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17
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Meirson T, Bomze D, Markel G. Structural basis of SARS-CoV-2 spike protein induced by ACE2. Bioinformatics 2021; 37:929-936. [PMID: 32818261 PMCID: PMC7558967 DOI: 10.1093/bioinformatics/btaa744] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/20/2020] [Accepted: 08/14/2020] [Indexed: 12/24/2022] Open
Abstract
Motivation The recent emergence of the novel SARS-coronavirus 2 (SARS-CoV-2) and its international
spread pose a global health emergency. The spike (S) glycoprotein binds ACE2 and
promotes SARS-CoV-2 entry into host cells. The trimeric S protein binds the receptor
using the receptor-binding domain (RBD) causing conformational changes in S protein that
allow priming by host cell proteases. Unraveling the dynamic structural features used by
SARS-CoV-2 for entry might provide insights into viral transmission and reveal novel
therapeutic targets. Using structures determined by X-ray crystallography and cryo-EM,
we performed structural analysis and atomic comparisons of the different conformational
states adopted by the SARS-CoV-2-RBD. Results Here, we determined the key structural components induced by the receptor and
characterized their intramolecular interactions. We show that κ-helix (polyproline-II)
is a predominant structure in the binding interface and in facilitating the conversion
to the active form of the S protein. We demonstrate a series of conversions between
switch-like κ-helix and β-strand, and conformational variations in a set of short
α-helices which affect the hinge region. These conformational changes lead to an
alternating pattern in conserved disulfide bond configurations positioned at the hinge,
indicating a possible disulfide exchange, an important allosteric switch implicated in
viral entry of various viruses, including HIV and murine coronavirus. The structural
information presented herein enables to inspect and understand the important dynamic
features of SARS-CoV-2-RBD and propose a novel potential therapeutic strategy to block
viral entry. Overall, this study provides guidance for the design and optimization of
structure-based intervention strategies that target SARS-CoV-2. Availability We have implemented the proposed methods in an R package freely available at https://github.com/Grantlab/bio3d Supplementary information Supplementary data are
available at Bioinformatics online.
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Affiliation(s)
- Tomer Meirson
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Ramat-Gan 526260, Israel.,The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | | | - Gal Markel
- Ella Lemelbaum Institute for Immuno-oncology, Sheba Medical Center, Ramat-Gan 526260, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel.,Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
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18
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Halat M, Klimek-Chodacka M, Orleanska J, Baranska M, Baranski R. Electronic Circular Dichroism of the Cas9 Protein and gRNA:Cas9 Ribonucleoprotein Complex. Int J Mol Sci 2021; 22:2937. [PMID: 33805827 PMCID: PMC8002190 DOI: 10.3390/ijms22062937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 12/26/2022] Open
Abstract
The Streptococcus pyogenes Cas9 protein (SpCas9), a component of CRISPR-based immune system in microbes, has become commonly utilized for genome editing. This nuclease forms a ribonucleoprotein (RNP) complex with guide RNA (gRNA) which induces Cas9 structural changes and triggers its cleavage activity. Here, electronic circular dichroism (ECD) spectroscopy was used to confirm the RNP formation and to determine its individual components. The ECD spectra had characteristic features differentiating Cas9 and gRNA, the former showed a negative/positive profile with maxima located at 221, 209 and 196 nm, while the latter revealed positive/negative/positive/negative pattern with bands observed at 266, 242, 222 and 209 nm, respectively. For the first time, the experimental ECD spectrum of the gRNA:Cas9 RNP complex is presented. It exhibits a bisignate positive/negative ECD couplet with maxima at 273 and 235 nm, and it differs significantly from individual spectrum of each RNP components. Additionally, the Cas9 protein and RNP complex retained biological activity after ECD measurements and they were able to bind and cleave DNA in vitro. Hence, we conclude that ECD spectroscopy can be considered as a quick and non-destructive method of monitoring conformational changes of the Cas9 protein as a result of Cas9 and gRNA interaction, and identification of the gRNA:Cas9 RNP complex.
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Affiliation(s)
- Monika Halat
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; (M.H.); (J.O.)
| | - Magdalena Klimek-Chodacka
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. 29 Listopada 54, 31-425 Krakow, Poland;
| | - Jagoda Orleanska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; (M.H.); (J.O.)
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; (M.H.); (J.O.)
- Jagiellonian Centre for Experimental Therapeutics (JCET), Bobrzyńskiego 14, 30-348 Krakow, Poland
| | - Rafal Baranski
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. 29 Listopada 54, 31-425 Krakow, Poland;
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19
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Mahmoudi Gomari M, Rostami N, Omidi-Ardali H, Arab SS. Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. J Biomol Struct Dyn 2021; 40:5634-5642. [PMID: 33475020 PMCID: PMC7832383 DOI: 10.1080/07391102.2021.1872418] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Undoubtedly, the SARS-CoV-2 has become a major concern for all societies due to its catastrophic effects on public health. In addition, mutations and changes in the structure of the virus make it difficult to design effective treatment. Moreover, the amino acid sequence of a protein is a major factor in the formation of the second and tertiary structure in a protein. Amino acid replacement can have noticeable effects on the folding of a protein, especially if an asymmetric change (substitution of polar residue with non-polar, charged with an uncharged, positive charge with a negative charge, or large residue with small residue) occurs. D614G as a spike mutant of SARS-CoV-2 previously identified as an associated risk factor with a high mortality rate of this virus. Using structural bioinformatics, our group determined that D614G mutation could cause extensive changes in SARS-CoV-2 behavior including the secondary structure, receptor binding pattern, 3D conformation, and stability of it. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
| | - Neda Rostami
- Department of Chemical Engineering, Faculty of Engineering, Arak University, Iran
| | - Hossein Omidi-Ardali
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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20
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Xiong Y, Zhang Y, Liu X, Yao J, Lu H. A novel method for large-scale confirmation of protein structures and surface accessible modification sites. Talanta 2020; 211:120697. [DOI: 10.1016/j.talanta.2019.120697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/24/2019] [Accepted: 12/27/2019] [Indexed: 11/24/2022]
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21
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Quantitative description and classification of protein structures by a novel robust amino acid network: interaction selective network (ISN). Sci Rep 2019. [PMCID: PMC6853966 DOI: 10.1038/s41598-019-52766-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To quantitatively categorize protein structures, we developed a quantitative coarse-grained model of protein structures with a novel amino acid network, the interaction selective network (ISN), characterized by the links based on interactions in both the main and side chains. We found that the ISN is a novel robust network model to show the higher classification probability in the plots of average vertex degree (k) versus average clustering coefficient (C), both of which are typical network parameters for protein structures, and successfully distinguished between “all-α” and “all-β” proteins. On the other hand, one of the typical conventional networks, the α-carbon network (CAN), was found to be less robust than the ISN, and another typical network, atomic distance network (ADN), failed to distinguish between these two protein structures. Considering that the links in the CAN and ADN are defined by the interactions only between the main chain atoms and by the distance of the closest atom pair between the two amino acid residues, respectively, we can conclude that reflecting structural information from both secondary and tertiary structures in the network parameters improves the quantitative evaluation and robustness in network models, resulting in a quantitative and more robust description of three-dimensional protein structures in the ISN.
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22
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Liu WS, Wang RR, Li WY, Rong M, Liu CL, Ma Y, Wang RL. Investigating the reason for loss-of-function of Src homology 2 domain-containing protein tyrosine phosphatase 2 (SHP2) caused by Y279C mutation through molecular dynamics simulation. J Biomol Struct Dyn 2019; 38:2509-2520. [DOI: 10.1080/07391102.2019.1634641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Wen-Shan Liu
- School of Pharmacy, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), Tianjin Medical University, Tianjin, China
| | - Rui-Rui Wang
- School of Pharmacy, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), Tianjin Medical University, Tianjin, China
| | - Wei-Ya Li
- School of Pharmacy, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), Tianjin Medical University, Tianjin, China
| | - Mei Rong
- School of Pharmacy, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), Tianjin Medical University, Tianjin, China
| | - Chi-Lu Liu
- School of Pharmacy, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), Tianjin Medical University, Tianjin, China
| | - Ying Ma
- School of Pharmacy, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), Tianjin Medical University, Tianjin, China
| | - Run-Ling Wang
- School of Pharmacy, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), Tianjin Medical University, Tianjin, China
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23
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Liu WS, Wang RR, Sun YZ, Li WY, Li HL, Liu CL, Ma Y, Wang RL. Exploring the effect of inhibitor AKB-9778 on VE-PTP by molecular docking and molecular dynamics simulation. J Cell Biochem 2019; 120:17015-17029. [PMID: 31125141 DOI: 10.1002/jcb.28963] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/03/2019] [Accepted: 03/15/2019] [Indexed: 01/02/2023]
Abstract
Diabetic macular edema, also known as diabetic eye disease, is mainly caused by the overexpression of vascular endothelial protein tyrosine phosphatase (VE-PTP) at hypoxia/ischemic. AKB-9778 is a known VE-PTP inhibitor that can effectively interact with the active site of VE-PTP to inhibit the activity of VE-PTP. However, the binding pattern of VE-PTP with AKB-9778 and the dynamic implications of AKB-9778 on VE-PTP system at the molecular level are poorly understood. Through molecular docking, it was found that the AKB-9778 was docked well in the binding pocket of VE-PTP by the interactions of hydrogen bond and Van der Waals. Furthermore, after molecular dynamic simulations on VE-PTP system and VE-PTP AKB-9778 system, a series of postdynamic analyses found that the flexibility and conformation of the active site undergone an obvious transition after VE-PTP binding with AKB-9778. Moreover, by constructing the RIN, it was found that the different interactions in the active site were the detailed reasons for the conformational differences between these two systems. Thus, the finding here might provide a deeper understanding of AKB-9778 as VE-PTP Inhibitor.
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Affiliation(s)
- Wen-Shan Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Rui-Rui Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ying-Zhan Sun
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Ya Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Hong-Lian Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Chi-Lu Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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24
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Efficient construction of a diverse conformational library for amyloid-β as an intrinsically disordered protein. J Mol Graph Model 2019; 88:183-193. [DOI: 10.1016/j.jmgm.2019.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 01/11/2019] [Accepted: 01/16/2019] [Indexed: 12/16/2022]
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25
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Wang RR, Ma Y, Du S, Li WY, Sun YZ, Zhou H, Wang RL. Exploring the reason for increased activity of SHP2 caused by D61Y mutation through molecular dynamics. Comput Biol Chem 2019; 78:133-143. [DOI: 10.1016/j.compbiolchem.2018.10.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 10/26/2018] [Accepted: 10/26/2018] [Indexed: 01/01/2023]
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26
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Watts CR, Gregory A, Frisbie C, Lovas S. Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations. Proteins 2017; 86:279-300. [PMID: 29235155 DOI: 10.1002/prot.25439] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/10/2017] [Indexed: 12/14/2022]
Abstract
The conformational space and structural ensembles of amyloid beta (Aβ) peptides and their oligomers in solution are inherently disordered and proven to be challenging to study. Optimum force field selection for molecular dynamics (MD) simulations and the biophysical relevance of results are still unknown. We compared the conformational space of the Aβ(1-40) dimers by 300 ns replica exchange MD simulations at physiological temperature (310 K) using: the AMBER-ff99sb-ILDN, AMBER-ff99sb*-ILDN, AMBER-ff99sb-NMR, and CHARMM22* force fields. Statistical comparisons of simulation results to experimental data and previously published simulations utilizing the CHARMM22* and CHARMM36 force fields were performed. All force fields yield sampled ensembles of conformations with collision cross sectional areas for the dimer that are statistically significantly larger than experimental results. All force fields, with the exception of AMBER-ff99sb-ILDN (8.8 ± 6.4%) and CHARMM36 (2.7 ± 4.2%), tend to overestimate the α-helical content compared to experimental CD (5.3 ± 5.2%). Using the AMBER-ff99sb-NMR force field resulted in the greatest degree of variance (41.3 ± 12.9%). Except for the AMBER-ff99sb-NMR force field, the others tended to under estimate the expected amount of β-sheet and over estimate the amount of turn/bend/random coil conformations. All force fields, with the exception AMBER-ff99sb-NMR, reproduce a theoretically expected β-sheet-turn-β-sheet conformational motif, however, only the CHARMM22* and CHARMM36 force fields yield results compatible with collapse of the central and C-terminal hydrophobic cores from residues 17-21 and 30-36. Although analyses of essential subspace sampling showed only minor variations between force fields, secondary structures of lowest energy conformers are different.
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Affiliation(s)
- Charles R Watts
- Department of Neurosurgery, Mayo Clinic, College of Medicine, Rochester, Minnesota.,Department of Neurosurgery, Mayo Clinic Health System, La Crosse, Wisconsin
| | - Andrew Gregory
- Department of Neurosurgery, Mayo Clinic Health System, La Crosse, Wisconsin
| | - Cole Frisbie
- Department of Neurosurgery, Mayo Clinic Health System, La Crosse, Wisconsin.,Department of Biomedical Sciences, Creighton University, Omaha, Nebraska
| | - Sándor Lovas
- Department of Biomedical Sciences, Creighton University, Omaha, Nebraska
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27
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Protein secondary structure prediction: A survey of the state of the art. J Mol Graph Model 2017; 76:379-402. [DOI: 10.1016/j.jmgm.2017.07.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 11/21/2022]
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28
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Pereira J, Lamzin VS. A distance geometry-based description and validation of protein main-chain conformation. IUCRJ 2017; 4:657-670. [PMID: 28989721 PMCID: PMC5619857 DOI: 10.1107/s2052252517008466] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/07/2017] [Indexed: 06/07/2023]
Abstract
Understanding the protein main-chain conformational space forms the basis for the modelling of protein structures and for the validation of models derived from structural biology techniques. Presented here is a novel idea for a three-dimensional distance geometry-based metric to account for the fine details of protein backbone conformations. The metrics are computed for dipeptide units, defined as blocks of Cαi-1-O i-1-Cαi -O i -Cαi+1 atoms, by obtaining the eigenvalues of their Euclidean distance matrices. These were computed for ∼1.3 million dipeptide units collected from nonredundant good-quality structures in the Protein Data Bank and subjected to principal component analysis. The resulting new Euclidean orthogonal three-dimensional space (DipSpace) allows a probabilistic description of protein backbone geometry. The three axes of the DipSpace describe the local extension of the dipeptide unit structure, its twist and its bend. By using a higher-dimensional metric, the method is efficient for the identification of Cα atoms in an unlikely or unusual geometrical environment, and its use for both local and overall validation of protein models is demonstrated. It is also shown, for the example of trypsin proteases, that the detection of unusual conformations that are conserved among the structures of this protein family may indicate geometrically strained residues of potentially functional importance.
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Affiliation(s)
- Joana Pereira
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Victor S. Lamzin
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
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29
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30
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Chowdhury SD, Sarkar AK, Lahiri A. Effect of Inactivating Mutations on Peptide Conformational Ensembles: The Plant Polypeptide Hormone Systemin. J Chem Inf Model 2016; 56:1267-81. [PMID: 27341535 DOI: 10.1021/acs.jcim.5b00666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
As part of their basal immune mechanism against insect/herbivore attacks, plants have evolved systemic response mechanisms. Such a systemic wound response in tomato was found to involve an 18 amino acid polypeptide called systemin, the first polypeptide hormone to be discovered in plants. Systematic alanine scanning and deletion studies showed differential modulation in its activity, particularly a major loss of function due to alanine substitution at positions 13 and 17 and less extentive loss of function due to substitution at position 12. We have studied the conformational ensembles of wild-type systemin along with its 17 variants by carrying out a total of 5.76 μs of replica-exchange molecular dynamics simulation in an implicit solvent environment. In our simulations, wild-type systemin showed a lack of α-helical and β-sheet structures, in conformity with earlier circular dichroism and NMR data. On the other hand, two regions containing diproline segments showed a tendency to adopt polyproline II structures. Examination of conformational ensembles of the 17 variants revealed a change in the population distributions, suggesting a less flexible structure for alanine substitutions at positions 12 and 13 but not for position 17. Combined with the experimental observations that positions 1-14 of systemin are important for the formation of the peptide-receptor complex, this leads to the hypothesis that loss of conformational flexibility may play a role in the loss of activity of systemin due to the P12A and P13A substitutions, while T17A deactivation probably occurs for a different reason, most likely the loss of the threonine phosphorylation site. We also indicate possible structural reasons why the substitution of the prolines at positions 12 and 13 leads to a loss of conformational freedom in the peptide.
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Affiliation(s)
- Saikat Dutta Chowdhury
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta , 92 Acharya Prafulla Chandra Road, Kolkata 700009, West Bengal, India
| | - Aditya K Sarkar
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta , 92 Acharya Prafulla Chandra Road, Kolkata 700009, West Bengal, India
| | - Ansuman Lahiri
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta , 92 Acharya Prafulla Chandra Road, Kolkata 700009, West Bengal, India
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Zhang Y, Man VH, Roland C, Sagui C. Amyloid Properties of Asparagine and Glutamine in Prion-like Proteins. ACS Chem Neurosci 2016; 7:576-87. [PMID: 26911543 DOI: 10.1021/acschemneuro.5b00337] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Sequences rich in glutamine (Q) and asparagine (N) are intrinsically disordered in monomeric form, but can aggregate into highly ordered amyloids, as seen in Q/N-rich prion domains (PrDs). Amyloids are fibrillar protein aggregates rich in β-sheet structures that can self-propagate through protein-conformational chain reactions. Here, we present a comprehensive theoretical study of N/Q-rich peptides, including sequences found in the yeast Sup35 PrD, in parallel and antiparallel β-sheet aggregates, and probe via fully atomistic molecular dynamics simulations all their possible steric-zipper interfaces in order to determine their protofibril structure and their relative stability. Our results show that polyglutamine aggregates are more stable than polyasparagine aggregates. Enthalpic contributions to the free energy favor the formation of polyQ protofibrils, while entropic contributions favor the formation of polyN protofibrils. The considerably larger phase space that disordered polyQ must sample on its way to aggregation probably is at the root of the associated slower kinetics observed experimentally. When other amino acids are present, such as in the Sup35 PrD, their shorter side chains favor steric-zipper formation for N but not Q, as they preclude the in-register association of the long Q side chains.
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Affiliation(s)
- Yuan Zhang
- Department of Physics, and
Center for High Performance Simulations (CHiPS), North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Viet Hoang Man
- Department of Physics, and
Center for High Performance Simulations (CHiPS), North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Christopher Roland
- Department of Physics, and
Center for High Performance Simulations (CHiPS), North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Celeste Sagui
- Department of Physics, and
Center for High Performance Simulations (CHiPS), North Carolina State University, Raleigh, North Carolina 27695, United States
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Haghighi H, Higham J, Henchman RH. Parameter-Free Hydrogen-Bond Definition to Classify Protein Secondary Structure. J Phys Chem B 2016; 120:8566-70. [PMID: 27067825 DOI: 10.1021/acs.jpcb.6b02571] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hasti Haghighi
- Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Jonathan Higham
- Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Richard H. Henchman
- Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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Lu X, Murphy RM. Asparagine Repeat Peptides: Aggregation Kinetics and Comparison with Glutamine Repeats. Biochemistry 2015. [PMID: 26204228 DOI: 10.1021/acs.biochem.5b00644] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amino acid repeat runs are common occurrences in eukaryotic proteins, with glutamine (Q) and asparagine (N) as particularly frequent repeats. Abnormal expansion of Q-repeat domains causes at least nine neurodegenerative disorders, most likely because expansion leads to protein misfolding, aggregation, and toxicity. The linkage between Q-repeats and disease has motivated several investigations into the mechanism of aggregation and the role of Q-repeat length in aggregation. Curiously, glutamine repeats are common in vertebrates, whereas N-repeats are virtually absent in vertebrates, but common in invertebrates. One hypothesis for the lack of N-repeats in vertebrates is biophysical; that is, there is strong selective pressure in higher organisms against aggregation-prone proteins. If true, then asparagine and glutamine repeats must differ substantially in their aggregation properties despite their chemical similarities. In this work, aggregation of peptides with asparagine repeats of variable length (12-24) were characterized and compared to that of similar peptides with glutamine repeats. As with glutamine, aggregation of N-repeat peptides was strongly length-dependent. Replacement of glutamine with asparagine caused a subtle shift in the conformation of the monomer, which strongly affected the rate of aggregation. Specifically, N-repeat peptides adopted β-turn structural elements, leading to faster self-assembly into globular oligomers and much more rapid conversion into fibrillar aggregates, compared to Q-repeat peptides. These biophysical differences may account for the differing biological roles of N- versus Q-repeat domains.
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Affiliation(s)
- Xiaomeng Lu
- †Biophysics Program and ‡Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Regina M Murphy
- †Biophysics Program and ‡Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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