101
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Pandey P, Meena NK, Prakash A, Kumar V, Lynn AM, Ahmad F. Characterization of heterogeneous intermediate ensembles on the guanidinium chloride-induced unfolding pathway of β-lactoglobulin. J Biomol Struct Dyn 2019; 38:1042-1053. [PMID: 30880641 DOI: 10.1080/07391102.2019.1593245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Folding pathway of β-LgA (β-lactoglobulin) evolves through the conformational α→β transition. The α→β transition is a molecular hallmark of various neurodegenerative diseases. Thus, β-LgA may serve as a good model for understanding molecular mechanism of protein aggregation involved in neurodegenerative diseases. Here, we studied the conformational dynamics of β-LgA in 6 M GdmCl at different temperatures using MD simulations. Structural order parameters such as RMSD, Rg, SASA, native contacts (Q), hydrophobic distal-matrix and free-energy landscape (FEL) were used to investigate the conformational transitions. Our results show that GdmCl destabilizes secondary and tertiary structure of β-LgA by weakening the hydrophobic interactions and hydrogen bond network. Multidimensional FEL shows the presence of different unfolding intermediates at 400 K. I1 is long-lived intermediate which has mostly intact native secondary structure, but loose tertiary structure. I2 is structurally compact intermediate formed after the partial loss of secondary structure. The transiently and infrequently buried evolution of W19 shows that intermediate conformational ensembles are structurally heterogeneous. We observed that the intermediate conformations are largely stabilized by non-native H-bonds. The outcome of this work provides the molecular details of intermediates trapped due to non-native interactions that may be regarded as pathogenic conformations involved in neurodegenerative diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Preeti Pandey
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Naveen Kumar Meena
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Amresh Prakash
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, India
| | - Andrew M Lynn
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Faizan Ahmad
- Jamia Millia Islamia, Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
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102
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Collective Transformation of Water between Hyperactive Antifreeze Proteins: RiAFPs. CRYSTALS 2019. [DOI: 10.3390/cryst9040188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We demonstrate, by molecular dynamics simulations, that water confined between a pair of insect hyperactive antifreeze proteins from the longhorn beetle Rhagium inquisitor is discontinuously expelled as the two proteins approach each other at a certain distance. The extensive striped hydrophobic–hydrophilic pattern on the surface, comprising arrays of threonine residues, enables water to form three independent ice channels through the assistance of hydroxyl groups, even at 300 K. The transformation is reminiscent of a freezing–melting transition rather than a drying transition and governs the stable protein–protein separation in the evaluation of the potential of mean force. The collectivity of water penetration or expulsion and the hysteresis in the time scale of ten nanoseconds predict a potential first-order phase transition at the limit of infinite size and provide a new framework for the water-mediated interaction between solutes.
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103
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Sriroopreddy R, Raghuraman P, Sudandiradoss C. Structural debilitation of mutation G322D associated with MSH2 and their role in triple negative breast cancer. J Biomol Struct Dyn 2019; 38:771-780. [DOI: 10.1080/07391102.2019.1587512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ramireddy Sriroopreddy
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - P. Raghuraman
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - C. Sudandiradoss
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
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104
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Preparation of ropivacaine loaded PLGA microspheres as controlled-release system with narrow size distribution and high loading efficiency. Colloids Surf A Physicochem Eng Asp 2019. [DOI: 10.1016/j.colsurfa.2018.11.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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105
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Narita M, Narita M, Itsuno Y, Itsuno S. Autonomous Sequences in Myoglobin Emerging from X-ray Structure of Holomyoglobin. ACS OMEGA 2019; 4:992-999. [PMID: 31459374 PMCID: PMC6648082 DOI: 10.1021/acsomega.8b03218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 12/28/2018] [Indexed: 06/10/2023]
Abstract
The proposed continuous folding structure units are fundamental to analyze protein structure. Here, we could elucidate for the first time two types of hydrophobic core networks in apomyoglobin using continuous folding structure units. In myoglobin, two autonomous sequences emerged clearly. We could thus characterize the autonomous sequences using well-defined hydrophobic core networks within respective semifolds. A hydrophobic core is defined as a pair of topology-local hydrophobic amino acids in different folding structures. Hydrophobic core formation is indispensable to stabilize the different folding structures via an efficient hydrophobic interaction. Autonomous sequences in myoglobin encode tertiary structure information for semifolds. These sequences fold autonomously into small sets of continuous folding structure units to grow separate semifolds on each separate framework. The autonomous sequence can be defined as the local sequence assigned to the small set of continuous folding structure units. They create the discrete hydrophobic region in a semifold by assembly of their hydrophobic regions. Semifolds were characterized by discrete hydrophobic regions stabilized by respective type I hydrophobic core networks, which were present within each semifold. The discrete hydrophobic region of a semifold propagated itself with that of a different semifold by hydrophobic interactions in type II hydrophobic core network, which was present between different semifolds, as observed by the X-ray structures of semifolds. The most significant feature of semifolds in apomyoglobin was that they could be verified by the X-ray structure of holomyoglobin regardless of the instability of folds characteristic to autonomous sequence fragments. This work presents the first description of autonomous sequences.
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Affiliation(s)
- Mitsuaki Narita
- Department
of Biotechnology & Life Science, Tokyo
University of Agriculture and Technology, Naka-machi 2-24-16, Koganei, Tokyo 183-8588, Japan
| | - Masakuni Narita
- Research
Laboratory, Nihon Pharmaceutical Co., Ltd., Shinizumi 34, Narita 286-0825, Japan
| | - Yasuko Itsuno
- Department
of Environmental and Life Sciences, Toyohashi
University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
| | - Shinichi Itsuno
- Department
of Environmental and Life Sciences, Toyohashi
University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
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106
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Structure of the lipoprotein lipase-GPIHBP1 complex that mediates plasma triglyceride hydrolysis. Proc Natl Acad Sci U S A 2018; 116:1723-1732. [PMID: 30559189 PMCID: PMC6358717 DOI: 10.1073/pnas.1817984116] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Lipoprotein lipase (LPL) is responsible for the intravascular processing of triglyceride-rich lipoproteins. The LPL within capillaries is bound to GPIHBP1, an endothelial cell protein with a three-fingered LU domain and an N-terminal intrinsically disordered acidic domain. Loss-of-function mutations in LPL or GPIHBP1 cause severe hypertriglyceridemia (chylomicronemia), but structures for LPL and GPIHBP1 have remained elusive. Inspired by our recent discovery that GPIHBP1's acidic domain preserves LPL structure and activity, we crystallized an LPL-GPIHBP1 complex and solved its structure. GPIHBP1's LU domain binds to LPL's C-terminal domain, largely by hydrophobic interactions. Analysis of electrostatic surfaces revealed that LPL contains a large basic patch spanning its N- and C-terminal domains. GPIHBP1's acidic domain was not defined in the electron density map but was positioned to interact with LPL's large basic patch, providing a likely explanation for how GPIHBP1 stabilizes LPL. The LPL-GPIHBP1 structure provides insights into mutations causing chylomicronemia.
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107
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König G, Pickard FC, Huang J, Thiel W, MacKerell AD, Brooks BR, York DM. A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes. Molecules 2018; 23:E2695. [PMID: 30347691 PMCID: PMC6222909 DOI: 10.3390/molecules23102695] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 12/01/2022] Open
Abstract
Maintaining a proper balance between specific intermolecular interactions and non-specific solvent interactions is of critical importance in molecular simulations, especially when predicting binding affinities or reaction rates in the condensed phase. The most rigorous metric for characterizing solvent affinity are solvation free energies, which correspond to a transfer from the gas phase into solution. Due to the drastic change of the electrostatic environment during this process, it is also a stringent test of polarization response in the model. Here, we employ both the CHARMM fixed charge and polarizable force fields to predict hydration free energies of twelve simple solutes. The resulting classical ensembles are then reweighted to obtain QM/MM hydration free energies using a variety of QM methods, including MP2, Hartree⁻Fock, density functional methods (BLYP, B3LYP, M06-2X) and semi-empirical methods (OM2 and AM1 ). Our simulations test the compatibility of quantum-mechanical methods with molecular-mechanical water models and solute Lennard⁻Jones parameters. In all cases, the resulting QM/MM hydration free energies were inferior to purely classical results, with the QM/MM Drude force field predictions being only marginally better than the QM/MM fixed charge results. In addition, the QM/MM results for different quantum methods are highly divergent, with almost inverted trends for polarizable and fixed charge water models. While this does not necessarily imply deficiencies in the QM models themselves, it underscores the need to develop consistent and balanced QM/MM interactions. Both the QM and the MM component of a QM/MM simulation have to match, in order to avoid artifacts due to biased solute⁻solvent interactions. Finally, we discuss strategies to improve the convergence and efficiency of multi-scale free energy simulations by automatically adapting the molecular-mechanics force field to the target quantum method.
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Affiliation(s)
- Gerhard König
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany.
| | - Frank C Pickard
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Jing Huang
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
- Department of Pharmaceutical Science, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, USA.
- School of Life Sciences, Westlake University, 18 Shilongshan Street, Hangzhou 310024, China.
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany.
| | - Alexander D MacKerell
- Department of Pharmaceutical Science, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, USA.
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
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108
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Tikhomirova TS, Galzitskaya OV. Functionally Significant Amino Acid Motifs of Heat Shock Proteins: Structural and Bioinformatics Analyses of Hsp60/Hsp10 in Five Classes of Chordata. Mol Biol 2018. [DOI: 10.1134/s0026893318050138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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109
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Role of solvent accessibility for aggregation-prone patches in protein folding. Sci Rep 2018; 8:12896. [PMID: 30150761 PMCID: PMC6110721 DOI: 10.1038/s41598-018-31289-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 08/15/2018] [Indexed: 11/21/2022] Open
Abstract
The arrangement of amino acids in a protein sequence encodes its native folding. However, the same arrangement in aggregation-prone regions may cause misfolding as a result of local environmental stress. Under normal physiological conditions, such regions congregate in the protein’s interior to avoid aggregation and attain the native fold. We have used solvent accessibility of aggregation patches (SAAPp) to determine the packing of aggregation-prone residues. Our results showed that SAAPp has low values for native crystal structures, consistent with protein folding as a mechanism to minimize the solvent accessibility of aggregation-prone residues. SAAPp also shows an average correlation of 0.76 with the global distance test (GDT) score on CASP12 template-based protein models. Using SAAPp scores and five structural features, a random forest machine learning quality assessment tool, SAAP-QA, showed 2.32 average GDT loss between best model predicted and actual best based on GDT score on independent CASP test data, with the ability to discriminate native-like folds having an AUC of 0.94. Overall, the Pearson correlation coefficient (PCC) between true and predicted GDT scores on independent CASP data was 0.86 while on the external CAMEO dataset, comprising high quality protein structures, PCC and average GDT loss were 0.71 and 4.46 respectively. SAAP-QA can be used to detect the quality of models and iteratively improve them to native or near-native structures.
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110
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Jong K, Hassanali AA. A Data Science Approach to Understanding Water Networks Around Biomolecules: The Case of Tri-Alanine in Liquid Water. J Phys Chem B 2018; 122:7895-7906. [DOI: 10.1021/acs.jpcb.8b03644] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- KwangHyok Jong
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
- SISSA—Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy
- Department of Physics, Kim Il Sung University, Ryongnam Dong, Taesong District, Pyongyang, D. P. R. Korea
| | - Ali A. Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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111
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Halder R, Jana B. Unravelling the Composition-Dependent Anomalies of Pair Hydrophobicity in Water–Ethanol Binary Mixtures. J Phys Chem B 2018; 122:6801-6809. [DOI: 10.1021/acs.jpcb.8b02528] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ritaban Halder
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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112
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Semerdzhiev SA, Lindhoud S, Stefanovic A, Subramaniam V, van der Schoot P, Claessens MMAE. Hydrophobic-Interaction-Induced Stiffening of α-Synuclein Fibril Networks. PHYSICAL REVIEW LETTERS 2018; 120:208102. [PMID: 29864360 DOI: 10.1103/physrevlett.120.208102] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/14/2018] [Indexed: 05/28/2023]
Abstract
In water, networks of semiflexible fibrils of the protein α-synuclein stiffen significantly with increasing temperature. We make plausible that this reversible stiffening is a result of hydrophobic contacts between the fibrils that become more prominent with increasing temperature. The good agreement of our experimentally observed temperature dependence of the storage modulus of the network with a scaling theory linking network elasticity with reversible cross-linking enables us to quantify the endothermic binding enthalpy and estimate the effective size of hydrophobic patches on the fibril surface. Our findings may not only shed light on the role of amyloid deposits in disease conditions, but can also inspire new approaches for the design of thermoresponsive materials.
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Affiliation(s)
- Slav A Semerdzhiev
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Saskia Lindhoud
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Anja Stefanovic
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Vinod Subramaniam
- Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
| | - Paul van der Schoot
- Theory of Polymers and Soft Matter, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Mireille M A E Claessens
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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113
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Maury CPJ. Amyloid and the origin of life: self-replicating catalytic amyloids as prebiotic informational and protometabolic entities. Cell Mol Life Sci 2018; 75:1499-1507. [PMID: 29550973 PMCID: PMC5897472 DOI: 10.1007/s00018-018-2797-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/19/2018] [Accepted: 03/13/2018] [Indexed: 01/29/2023]
Abstract
A crucial stage in the origin of life was the emergence of the first molecular entity that was able to replicate, transmit information, and evolve on the early Earth. The amyloid world hypothesis posits that in the pre-RNA era, information processing was based on catalytic amyloids. The self-assembly of short peptides into β-sheet amyloid conformers leads to extraordinary structural stability and novel multifunctionality that cannot be achieved by the corresponding nonaggregated peptides. The new functions include self-replication, catalytic activities, and information transfer. The environmentally sensitive template-assisted replication cycles generate a variety of amyloid polymorphs on which evolutive forces can act, and the fibrillar assemblies can serve as scaffolds for the amyloids themselves and for ribonucleotides proteins and lipids. The role of amyloid in the putative transition process from an amyloid world to an amyloid-RNA-protein world is not limited to scaffolding and protection: the interactions between amyloid, RNA, and protein are both complex and cooperative, and the amyloid assemblages can function as protometabolic entities catalyzing the formation of simple metabolite precursors. The emergence of a pristine amyloid-based in-put sensitive, chiroselective, and error correcting information-processing system, and the evolvement of mutualistic networks were, arguably, of essential importance in the dynamic processes that led to increased complexity, organization, compartmentalization, and, eventually, the origin of life.
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114
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Raghuraman P, Sudandiradoss C. R516Q mutation in Melanoma differentiation-associated protein 5 (MDA5) and its pathogenic role towards rare Singleton-Merten syndrome; a signature associated molecular dynamics study. J Biomol Struct Dyn 2018; 37:750-765. [DOI: 10.1080/07391102.2018.1439770] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- P. Raghuraman
- Department of Biotechnology, School of Bioscience and Technology, VIT University, Vellore 632014, India
| | - C. Sudandiradoss
- Department of Biotechnology, School of Bioscience and Technology, VIT University, Vellore 632014, India
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115
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Wang C, Ma CKD, Yeon H, Wang X, Gellman SH, Abbott NL. Nonadditive Interactions Mediated by Water at Chemically Heterogeneous Surfaces: Nonionic Polar Groups and Hydrophobic Interactions. J Am Chem Soc 2017; 139:18536-18544. [DOI: 10.1021/jacs.7b08367] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Chenxuan Wang
- Department
of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
- Department
of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Chi-Kuen Derek Ma
- Department
of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Hongseung Yeon
- Department
of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Xiaoguang Wang
- Department
of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department
of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Nicholas L. Abbott
- Department
of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
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116
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Grajda M, Lewińska MJ, Szumna A. The templation effect as a driving force for the self-assembly of hydrogen-bonded peptidic capsules in competitive media. Org Biomol Chem 2017; 15:8513-8517. [PMID: 28862280 DOI: 10.1039/c7ob01925d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Peptide-based cavitands (resorcin[4]arenes substituted with histidine and glutamine hydrazides) exist as monomeric species in polar solvents (DMSO and methanol). Upon complexation of fullerenes, the cavitands wrap around the hydrophobic guests forming dimeric capsular shells (as evidenced by DOSY). The self-assembly of the cavitands is based on the formation of beta-sheet-like binding motifs around the hydrophobic core. In a polar environment, these hydrogen bonded structures are kinetically stable and highly ordered as manifested by a 100-fold increase of intensity of circular dichroism bands, as well as a separate set of signals and substantial differences in chemical shifts in NMR spectra. This behavior resembles a protein folding process at the molten globule stage with non-specific hydrophobic interactions creating a protective and favourable local environment for the formation of secondary structures of proteins.
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Affiliation(s)
- M Grajda
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-22 Warsaw, Poland.
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117
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Acar H, Samaeekia R, Schnorenberg MR, Sasmal DK, Huang J, Tirrell MV, LaBelle JL. Cathepsin-Mediated Cleavage of Peptides from Peptide Amphiphiles Leads to Enhanced Intracellular Peptide Accumulation. Bioconjug Chem 2017; 28:2316-2326. [PMID: 28771332 DOI: 10.1021/acs.bioconjchem.7b00364] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Peptides synthesized in the likeness of their native interaction domain(s) are natural choices to target protein-protein interactions (PPIs) due to their fidelity of orthostatic contact points between binding partners. Despite therapeutic promise, intracellular delivery of biofunctional peptides at concentrations necessary for efficacy remains a formidable challenge. Peptide amphiphiles (PAs) provide a facile method of intracellular delivery and stabilization of bioactive peptides. PAs consisting of biofunctional peptide headgroups linked to hydrophobic alkyl lipid-like tails prevent peptide hydrolysis and proteolysis in circulation, and PA monomers are internalized via endocytosis. However, endocytotic sequestration and steric hindrance from the lipid tail are two major mechanisms that limit PA efficacy to target intracellular PPIs. To address these problems, we have constructed a PA platform consisting of cathepsin-B cleavable PAs in which a selective p53-based inhibitory peptide is cleaved from its lipid tail within endosomes, allowing for intracellular peptide accumulation and extracellular recycling of the lipid moiety. We monitor for cleavage and follow individual PA components in real time using a Förster resonance energy transfer (FRET)-based tracking system. Using this platform, we provide a better understanding and quantification of cellular internalization, trafficking, and endosomal cleavage of PAs and of the ultimate fates of each component.
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Affiliation(s)
- Handan Acar
- Institute for Molecular Engineering, University of Chicago, Eckardt Research Center , 5640 South Ellis Avenue, Chicago, Illinois 60637, United States.,Department of Pediatrics, Section of Hematology/Oncology, University of Chicago , 900 East 57th Street, KCBD 5122, Chicago, Illinois 60637, United States
| | - Ravand Samaeekia
- Institute for Molecular Engineering, University of Chicago, Eckardt Research Center , 5640 South Ellis Avenue, Chicago, Illinois 60637, United States.,Department of Pediatrics, Section of Hematology/Oncology, University of Chicago , 900 East 57th Street, KCBD 5122, Chicago, Illinois 60637, United States
| | - Mathew R Schnorenberg
- Institute for Molecular Engineering, University of Chicago, Eckardt Research Center , 5640 South Ellis Avenue, Chicago, Illinois 60637, United States.,Department of Pediatrics, Section of Hematology/Oncology, University of Chicago , 900 East 57th Street, KCBD 5122, Chicago, Illinois 60637, United States.,Medical Scientist Training Program, University of Chicago , 924 East 57th Street, Suite 104, Chicago, Illinois 60637, United States
| | - Dibyendu K Sasmal
- Institute for Molecular Engineering, University of Chicago, Eckardt Research Center , 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Jun Huang
- Institute for Molecular Engineering, University of Chicago, Eckardt Research Center , 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Matthew V Tirrell
- Institute for Molecular Engineering, University of Chicago, Eckardt Research Center , 5640 South Ellis Avenue, Chicago, Illinois 60637, United States.,Institute for Molecular Engineering, Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60639, United States
| | - James L LaBelle
- Department of Pediatrics, Section of Hematology/Oncology, University of Chicago , 900 East 57th Street, KCBD 5122, Chicago, Illinois 60637, United States
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118
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Prakash A, Dixit G, Meena NK, Singh R, Vishwakarma P, Mishra S, Lynn AM. Elucidation of stable intermediates in urea-induced unfolding pathway of human carbonic anhydrase IX. J Biomol Struct Dyn 2017; 36:2391-2406. [DOI: 10.1080/07391102.2017.1355847] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Amresh Prakash
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Gunjan Dixit
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Naveen Kumar Meena
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ruhar Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Poonam Vishwakarma
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Smriti Mishra
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Andrew M. Lynn
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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Effects of NaCl, NaOH, and HCl concentration on the cloud point of poly(vinyl methyl ether) in water—electrostatic interactions are inevitably involved in the hydrophobic interaction. Colloid Polym Sci 2017. [DOI: 10.1007/s00396-017-4130-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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120
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Smolentsev N, Smit WJ, Bakker HJ, Roke S. The interfacial structure of water droplets in a hydrophobic liquid. Nat Commun 2017; 8:15548. [PMID: 28537259 PMCID: PMC5458086 DOI: 10.1038/ncomms15548] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 04/05/2017] [Indexed: 12/21/2022] Open
Abstract
Nanoscopic and microscopic water droplets and ice crystals embedded in liquid hydrophobic surroundings are key components of aerosols, rocks, oil fields and the human body. The chemical properties of such droplets critically depend on the interfacial structure of the water droplet. Here we report the surface structure of 200 nm-sized water droplets in mixtures of hydrophobic oils and surfactants as obtained from vibrational sum frequency scattering measurements. The interface of a water droplet shows significantly stronger hydrogen bonds than the air/water or hexane/water interface and previously reported planar liquid hydrophobic/water interfaces at room temperature. The observed spectral difference is similar to that of a planar air/water surface at a temperature that is ∼50 K lower. Supercooling the droplets to 263 K does not change the surface structure. Below the homogeneous ice nucleation temperature, a single vibrational mode is present with a similar mean hydrogen-bond strength as for a planar ice/air interface.
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Affiliation(s)
- Nikolay Smolentsev
- Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), and Institute of Materials Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | | | - Huib J. Bakker
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Sylvie Roke
- Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), and Institute of Materials Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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van Ravensteijn BGP, Vilanova N, de Feijter I, Kegel WK, Voets IK. Temperature-Induced, Selective Assembly of Supramolecular Colloids in Water. ACS OMEGA 2017; 2:1720-1730. [PMID: 31457536 PMCID: PMC6640978 DOI: 10.1021/acsomega.7b00111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/05/2017] [Indexed: 06/10/2023]
Abstract
In this article, we report the synthesis and physical characterization of colloidal polystyrene particles that carry water-soluble supramolecular N,N',N″,-trialkyl-benzene-1,3,5-tricarboxamides (BTAs) on their surface. These molecules are known to assemble into one-dimensional supramolecular polymers via noncovalent interactions. By tethering the BTAs to charge-stabilized particles, the clustering behavior of the resulting colloids was dictated by a balance between interparticle electrostatic repulsion and the BTA-mediated attractions. Through careful tuning of the dispersing medium's ionic strength, a regime was found in which particle aggregation could be reversibly induced upon heating the dispersion. These findings clearly indicate that hydrophobic interactions, which become stronger upon heating, play an important role during the clustering process. Besides the thermoreversible nature of the generated hydrophobic interparticle attractions, we found the clustering to be selective, that is, the BTA-functionalized colloids do not interact with nonfunctionalized hydrophobic polystyrene particles. This selectivity in the association process can be rationalized by the preferred stacking of the surface-tethered BTAs. These selective intermolecular/particle bonds are likely stabilized by the formation of hydrogen bonds, as previously observed for analogous molecular BTA assemblies. The resulting driving force responsible for particle clustering is therefore dual in nature and depends on both hydrophobic attractions and hydrogen bonding.
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Affiliation(s)
- Bas G. P. van Ravensteijn
- Van
’t Hoff Laboratory for Physical and Colloid Chemistry, Debye
Institute for NanoMaterials Science, Utrecht
University, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Neus Vilanova
- Institute for Complex
Molecular Systems, Laboratory of Macromolecular Organic
Chemistry, and Laboratory of Physical Chemistry, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Isja de Feijter
- Institute for Complex
Molecular Systems, Laboratory of Macromolecular Organic
Chemistry, and Laboratory of Physical Chemistry, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Willem K. Kegel
- Van
’t Hoff Laboratory for Physical and Colloid Chemistry, Debye
Institute for NanoMaterials Science, Utrecht
University, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Ilja K. Voets
- Institute for Complex
Molecular Systems, Laboratory of Macromolecular Organic
Chemistry, and Laboratory of Physical Chemistry, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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122
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Chanphai P, Tajmir-Riahi H. Trypsin and trypsin inhibitor bind milk beta-lactoglobulin: Protein–protein interactions and morphology. Int J Biol Macromol 2017; 96:754-758. [DOI: 10.1016/j.ijbiomac.2016.12.075] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 12/21/2016] [Accepted: 12/29/2016] [Indexed: 11/16/2022]
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Abstract
Although each type of protein fold and in some cases individual proteins within a fold classification can have very different mechanisms of folding, the underlying biophysical and biochemical principles that operate to cause a linear polypeptide chain to fold into a globular structure must be the same. In an aqueous solution, the protein takes up the thermodynamically most stable structure, but the pathway along which the polypeptide proceeds in order to reach that structure is a function of the amino acid sequence, which must be the final determining factor, not only in shaping the final folded structure, but in dictating the folding pathway. A number of groups have focused on a single protein or group of proteins, to determine in detail the factors that influence the rate and mechanism of folding in a defined system, with the hope that hypothesis-driven experiments can elucidate the underlying principles governing the folding process. Our research group has focused on the folding of the globin family of proteins, and in particular on the monomeric protein apomyoglobin. Apomyoglobin (apoMb) folds relatively slowly (∼2 s) via an ensemble of obligatory intermediates that form rapidly after the initiation of folding. The folding pathway can be dissected using rapid-mixing techniques, which can probe processes in the millisecond time range. Stopped-flow measurements detected by circular dichroism (CD) or fluorescence spectroscopy give information on the rates of folding events. Quench-flow experiments utilize the differential rates of hydrogen-deuterium exchange of amide protons protected in parts of the structure that are folded early; protection of amides can be detected by mass spectrometry or proton nuclear magnetic resonance spectroscopy (NMR). In addition, apoMb forms an intermediate at equilibrium at pH ∼ 4, which is sufficiently stable for it to be structurally characterized by solution methods such as CD, fluorescence and NMR spectroscopies, and the conformational ensembles formed in the presence of denaturing agents and low pH can be characterized as models for the unfolded states of the protein. Newer NMR techniques such as measurement of residual dipolar couplings in the various partly folded states, and relaxation dispersion measurements to probe invisible states present at low concentrations, have contributed to providing a detailed picture of the apomyoglobin folding pathway. The research summarized in this Account was aimed at characterizing and comparing the equilibrium and kinetic intermediates both structurally and dynamically, as well as delineating the complete folding pathway at a residue-specific level, in order to answer the question: "What is it about the amino acid sequence that causes each molecule in the unfolded protein ensemble to start folding, and, once started, to proceed towards the formation of the correctly folded three-dimensional structure?"
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Affiliation(s)
- H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla California 92037, United States
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla California 92037, United States
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NISHIMURA C. Folding of apomyoglobin: Analysis of transient intermediate structure during refolding using quick hydrogen deuterium exchange and NMR. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2017; 93:10-27. [PMID: 28077807 PMCID: PMC5406622 DOI: 10.2183/pjab.93.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/31/2016] [Indexed: 05/27/2023]
Abstract
The structures of apomyoglobin folding intermediates have been widely analyzed using physical chemistry methods including fluorescence, circular dichroism, small angle X-ray scattering, NMR, mass spectrometry, and rapid mixing. So far, at least two intermediates (on sub-millisecond- and millisecond-scales) have been demonstrated for apomyoglobin folding. The combination of pH-pulse labeling and NMR is a useful tool for analyzing the kinetic intermediates at the atomic level. Its use has revealed that the latter-phase kinetic intermediate of apomyoglobin (6 ms) was composed of helices A, B, G and H, whereas the equilibrium intermediate, called the pH 4 molten-globule intermediate, was composed mainly of helices A, G and H. The improved strategy for the analysis of the kinetic intermediate was developed to include (1) the dimethyl sulfoxide method, (2) data processing with the various labeling times, and (3) a new in-house mixer. Particularly, the rapid mixing revealed that helices A and G were significantly more protected at the earlier stage (400 µs) of the intermediate (former-phase intermediate) than the other helices. Mutation studies, where each hydrophobic residue was replaced with an alanine in helices A, B, E, F, G and H, indicated that both non-native and native-like structures exist in the latter-phase folding intermediate. The N-terminal part of helix B is a weak point in the intermediate, and the docking of helix E residues to the core of the A, B, G and H helices was interrupted by a premature helix B, resulting in the accumulation of the intermediate composed of helices A, B, G and H. The prediction-based protein engineering produced important mutants: Helix F in a P88K/A90L/S92K/A94L mutant folded in the latter-phase intermediate, although helix F in the wild type does not fold even at the native state. Furthermore, in the L11G/W14G/A70L/G73W mutant, helix A did not fold but helix E did, which is similar to what was observed in the kinetic intermediate of apoleghemoglobin. Thus, this protein engineering resulted in a changed structure for the apomyoglobin folding intermediate.
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Affiliation(s)
- Chiaki NISHIMURA
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano-ku, Tokyo, Japan
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125
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High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop. PLoS Genet 2016; 12:e1006321. [PMID: 27898685 PMCID: PMC5127505 DOI: 10.1371/journal.pgen.1006321] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/24/2016] [Indexed: 11/30/2022] Open
Abstract
The active sites of multisubunit RNA polymerases have a “trigger loop” (TL) that multitasks in substrate selection, catalysis, and translocation. To dissect the Saccharomyces cerevisiae RNA polymerase II TL at individual-residue resolution, we quantitatively phenotyped nearly all TL single variants en masse. Three mutant classes, revealed by phenotypes linked to transcription defects or various stresses, have distinct distributions among TL residues. We find that mutations disrupting an intra-TL hydrophobic pocket, proposed to provide a mechanism for substrate-triggered TL folding through destabilization of a catalytically inactive TL state, confer phenotypes consistent with pocket disruption and increased catalysis. Furthermore, allele-specific genetic interactions among TL and TL-proximal domain residues support the contribution of the funnel and bridge helices (BH) to TL dynamics. Our structural genetics approach incorporates structural and phenotypic data for high-resolution dissection of transcription mechanisms and their evolution, and is readily applicable to other essential yeast proteins. Proper regulation of Pol II transcription, the first step of gene expression, is essential for life. Extensive evidence has revealed a widely conserved and dynamic polymerase active site component, termed the Trigger Loop (TL), in balancing transcription rate and fidelity while possibly allowing control of transcription elongation. Coupling high-throughput sequencing with our previously established genetic system, we are able to assess the in vivo phenotypes for almost all possible single substitution Pol II TL mutants in the budding yeast Saccharomyces cerevisiae. We show that mutants in the TL nucleotide interacting and linker regions widely confer dominant and severe growth defects. Clustering of TL mutants’ transcription-related and general stress phenotypes reveals three main classes of TL mutants, including previously identified fast and slow elongating mutants. Comprehensive analyses of the distribution of fast and slow elongation mutants in light of existing Pol II crystal structures reveal critical regions contributing to proper TL dynamics and function. Evidence is presented linking a previously observed hydrophobic pocket to NTP substrate-induced TL closing, the mechanism critical for correct substrates selection and transcription fidelity. Finally, we assess the functional interplay between TL and its proximal domains, and their presumptive roles in the function and evolution of the TL. Utilizing the Pol II TL as a case study, we present a structural genetics approach that reveals insights into a complex, multi-functional, and essential domain in yeast.
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126
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Raghuraman P, Jesu Jaya Sudan R, Lesitha Jeeva Kumari J, Sudandiradoss C. Casting the critical regions in nucleotide binding oligomerization domain 2 protein: a signature mediated structural dynamics approach. J Biomol Struct Dyn 2016; 35:3297-3315. [PMID: 27790943 DOI: 10.1080/07391102.2016.1254116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nucleotide binding oligomerization domain 2 (NOD2), a protein involved in the first line defence mechanism has a pivotal role in innate immunity. Impaired function of this protein is implicated in disorders such as Blau syndrome and Crohn's disease. Since an altered function is linked to protein's structure, we framed a systematic strategy to interpret the structure-function relationship of the protein. Initiated with mutation-based pattern prediction and identified a distant ortholog (DO) of NOD2 from which the intra-residue interaction network was elucidated. The network was used to identify hotspots that serve as critical points to maintain the stable architecture of the protein. Structural comparison of NOD2 domains with a DO revealed the minimal number of intra-protein interactions required by the protein to maintain the structural fold. In addition, the conventional molecular dynamics simulation emphasized the conformational transitions at hot spot residues between native NOD2 domains and its respective mutants (G116R, R42W and R54A) structures. The analysis of intra-protein interactions globally and the displacement of residues locally around the mutational site revealed loss of several critical bonds and residues vital for the protein's function. Conclusively we report, about 10 residues in leucine-rich repeat, 13 residues in NOD and 6 residues in CARD domain are required by the NOD2 to maintain its function. This protocol will help the researchers to achieve for more prospective studies to attest druggable site utility in discovering novel drug candidates.
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Affiliation(s)
- P Raghuraman
- a Department of Biotechnology , School of Bioscience and Technology, VIT University , Vellore 632301 , India
| | - R Jesu Jaya Sudan
- a Department of Biotechnology , School of Bioscience and Technology, VIT University , Vellore 632301 , India
| | - J Lesitha Jeeva Kumari
- a Department of Biotechnology , School of Bioscience and Technology, VIT University , Vellore 632301 , India
| | - C Sudandiradoss
- a Department of Biotechnology , School of Bioscience and Technology, VIT University , Vellore 632301 , India
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127
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Goluguri RR, Udgaonkar JB. Microsecond Rearrangements of Hydrophobic Clusters in an Initially Collapsed Globule Prime Structure Formation during the Folding of a Small Protein. J Mol Biol 2016; 428:3102-17. [PMID: 27370109 DOI: 10.1016/j.jmb.2016.06.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 06/17/2016] [Accepted: 06/19/2016] [Indexed: 12/14/2022]
Abstract
Determining how polypeptide chain collapse initiates structure formation during protein folding is a long standing goal. It has been challenging to characterize experimentally the dynamics of the polypeptide chain, which lead to the formation of a compact kinetic molten globule (MG) in about a millisecond. In this study, the sub-millisecond events that occur early during the folding of monellin from the guanidine hydrochloride-unfolded state have been characterized using multiple fluorescence and fluorescence resonance energy transfer probes. The kinetic MG is shown to form in a noncooperative manner from the unfolded (U) state as a result of at least three different processes happening during the first millisecond of folding. Initial chain compaction completes within the first 37μs, and further compaction occurs only after structure formation commences at a few milliseconds of folding. The transient nonnative and native-like hydrophobic clusters with side chains of certain residues buried form during the initial chain collapse and the nonnative clusters quickly disassemble. Subsequently, partial chain desolvation occurs, leading to the formation of a kinetic MG. The initial chain compaction and subsequent chain rearrangement appear to be barrierless processes. The two structural rearrangements within the collapsed globule appear to prime the protein for the actual folding transition.
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Affiliation(s)
- Rama Reddy Goluguri
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India.
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128
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Chen W, Shi C, Shen J. Nascent β-Hairpin Formation of a Natively Unfolded Peptide Reveals the Role of Hydrophobic Contacts. Biophys J 2016; 109:630-8. [PMID: 26244744 PMCID: PMC4571001 DOI: 10.1016/j.bpj.2015.06.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 11/21/2022] Open
Abstract
Despite the important role of the unfolded states in protein stability, folding, and aggregation, they remain poorly understood due to the lack of residue-specific experimental data. Here, we explore features of the unfolded state of the NTL9 protein by applying all-atom replica-exchange simulations to the two fragment peptides NTL9(1–22) and NTL9(6–17). We found that while NTL9(6–17) is unstructured, NTL9(1–22) transiently folds as various β-hairpins, a fraction of which contain a native β-sheet. Interestingly, despite a large number of charged residues, the formation of backbone hydrogen bonds is concomitant with hydrophobic but not electrostatic contacts. Although the fragment peptides lack a proposed specific contact between Asp8 and Lys12, the individually weak, nonspecific interactions with lysines together stabilize the charged Asp8, leading to a pKa shift of nearly 0.5 units, in agreement with the NMR data. Taken together, our data suggest that the unfolded state of NTL9 likely contains a β-hairpin in segment 1–22 with sequence-distant hydrophobic contacts, thus lending support to a long-standing hypothesis that the unfolded states of proteins exhibit native-like topology with hydrophobic clusters.
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Affiliation(s)
- Wei Chen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Chuanyin Shi
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Jana Shen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland.
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129
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Zheng X, Wang J. Universal statistical fluctuations in thermodynamics and kinetics of single molecular recognition. Phys Chem Chem Phys 2016; 18:8570-8. [PMID: 26947972 DOI: 10.1039/c5cp06416c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated the main universal statistical distributions of single molecular recognition. The distributions of the single molecule binding free energy spectrum or density of states were characterized in the ligand-receptor binding energy landscape. The analytical results are consistent with the microscopic molecular simulations. The free energy distribution of different binding modes or states for a single molecule ligand receptor pair is approximately Gaussian near the mean and exponential at the tail. The equilibrium constant of single molecule binding is log-normal distributed near the mean and power law distributed near the tail. Additionally, we found that the kinetics distribution of single molecule ligand binding can be characterized by log-normal around the mean and power law distribution near the tail. This distribution is caused by exploration of the underlying inhomogeneous free energy landscape. Different ligand-receptor binding complexes have the same universal form of distribution but differ in parameters.
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Affiliation(s)
- Xiliang Zheng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China and Department of Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, NY 11794-3400, USA.
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130
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Avery AW, Crain J, Thomas DD, Hays TS. A human β-III-spectrin spinocerebellar ataxia type 5 mutation causes high-affinity F-actin binding. Sci Rep 2016; 6:21375. [PMID: 26883385 PMCID: PMC4756369 DOI: 10.1038/srep21375] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/21/2016] [Indexed: 01/06/2023] Open
Abstract
Spinocerebellar ataxia type 5 (SCA5) is a human neurodegenerative disease that stems from mutations in the SPTBN2 gene encoding the protein β-III-spectrin. Here we investigated the molecular consequence of a SCA5 missense mutation that results in a L253P substitution in the actin-binding domain (ABD) of β-III-spectrin. We report that the L253P substitution in the isolated β-III-spectrin ABD causes strikingly high F-actin binding affinity (Kd = 75.5 nM) compared to the weak F-actin binding affinity of the wild-type ABD (Kd = 75.8 μM). The mutation also causes decreased thermal stability (Tm = 44.6 °C vs 59.5 °C). Structural analyses indicate that leucine 253 is in a loop at the interface of the tandem calponin homology (CH) domains comprising the ABD. Leucine 253 is predicted to form hydrophobic contacts that bridge the CH domains. The decreased stability of the mutant indicates that these bridging interactions are probably disrupted, suggesting that the high F-actin binding affinity of the mutant is due to opening of the CH domain interface. These results support a fundamental role for leucine 253 in regulating opening of the CH domain interface and binding of the ABD to F-actin. This study indicates that high-affinity actin binding of L253P β-III-spectrin is a likely driver of neurodegeneration.
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Affiliation(s)
- Adam W Avery
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455
| | - Jonathan Crain
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
| | - David D Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
| | - Thomas S Hays
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455
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131
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Ferreira DC, van der Linden MG, de Oliveira LC, Onuchic JN, de Araújo AFP. Information and redundancy in the burial folding code of globular proteins within a wide range of shapes and sizes. Proteins 2016; 84:515-31. [PMID: 26815167 DOI: 10.1002/prot.24998] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/28/2015] [Accepted: 01/19/2016] [Indexed: 11/09/2022]
Abstract
Recent ab initio folding simulations for a limited number of small proteins have corroborated a previous suggestion that atomic burial information obtainable from sequence could be sufficient for tertiary structure determination when combined to sequence-independent geometrical constraints. Here, we use simulations parameterized by native burials to investigate the required amount of information in a diverse set of globular proteins comprising different structural classes and a wide size range. Burial information is provided by a potential term pushing each atom towards one among a small number L of equiprobable concentric layers. An upper bound for the required information is provided by the minimal number of layers L(min) still compatible with correct folding behavior. We obtain L(min) between 3 and 5 for seven small to medium proteins with 50 ≤ Nr ≤ 110 residues while for a larger protein with Nr = 141 we find that L ≥ 6 is required to maintain native stability. We additionally estimate the usable redundancy for a given L ≥ L(min) from the burial entropy associated to the largest folding-compatible fraction of "superfluous" atoms, for which the burial term can be turned off or target layers can be chosen randomly. The estimated redundancy for small proteins with L = 4 is close to 0.8. Our results are consistent with the above-average quality of burial predictions used in previous simulations and indicate that the fraction of approachable proteins could increase significantly with even a mild, plausible, improvement on sequence-dependent burial prediction or on sequence-independent constraints that augment the detectable redundancy during simulations.
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Affiliation(s)
- Diogo C Ferreira
- Laboratório de Biofísica Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Marx G van der Linden
- Laboratório de Biofísica Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Leandro C de Oliveira
- Departamento de Física, IBILCE, Universidade Estadual Paulista - UNESP, São José do Rio Preto, SP, 15054-000, Brazil
| | - José N Onuchic
- Center for Theoretical Biological Physics and Departments of Physics and Astronomy, Chemistry and Biosciences Rice University, 6100 Main Street, Houston, Texas, 77005
| | - Antônio F Pereira de Araújo
- Laboratório de Biofísica Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
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132
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Maury CPJ. Origin of life. Primordial genetics: Information transfer in a pre-RNA world based on self-replicating beta-sheet amyloid conformers. J Theor Biol 2015. [DOI: 10.1016/j.jtbi.2015.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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133
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Ahn S, Lee SJ. Dehydration-mediated cluster formation of nanoparticles. Sci Rep 2015; 5:11383. [PMID: 26077841 PMCID: PMC4468418 DOI: 10.1038/srep11383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 05/21/2015] [Indexed: 11/09/2022] Open
Abstract
Drying procedure is a powerful method to modulate the bottom-up assembly of basic building component. The initially weak attraction between the components screened in a solution strengthens as the solvent evaporates, organizing the components into structures. Drying is process-dependent, irreversible, and nonequilibrated, thus the mechanism and the dynamics are influenced by many factors. Therefore, the interaction of the solvent and the elements during the drying procedure as well as the resulting pattern formations are strongly related. Nonetheless still many things are open in questions in terms of their dynamics. In this study, nanoscale dehydration procedure is experimentally investigated using a nanoparticle (NP) model system. The role of water is verified in a single NP scale and the patterns of collective NP clusters are determined. Stepwise drying procedures are proposed based on the location from which water is removed. Effective water exodus from a unit NP surface enhances the attractive interaction in nanoscale and induces heterogeneous distribution in microscale. This study provides fundamental proof of systematic relation between the dehydration process and the resultant cluster patterns in hierarchical multiscales.
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Affiliation(s)
- Sungsook Ahn
- 1] Biofluid and Biomimic Research Center [2] Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang, 790-784, Korea
| | - Sang Joon Lee
- 1] Biofluid and Biomimic Research Center [2] Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang, 790-784, Korea
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134
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135
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Abstract
This is a tour of a physical chemist through 65 years of protein chemistry from the time when emphasis was placed on the determination of the size and shape of the protein molecule as a colloidal particle, with an early breakthrough by James Sumner, followed by Linus Pauling and Fred Sanger, that a protein was a real molecule, albeit a macromolecule. It deals with the recognition of the nature and importance of hydrogen bonds and hydrophobic interactions in determining the structure, properties, and biological function of proteins until the present acquisition of an understanding of the structure, thermodynamics, and folding pathways from a linear array of amino acids to a biological entity. Along the way, with a combination of experiment and theoretical interpretation, a mechanism was elucidated for the thrombin-induced conversion of fibrinogen to a fibrin blood clot and for the oxidative-folding pathways of ribonuclease A. Before the atomic structure of a protein molecule was determined by x-ray diffraction or nuclear magnetic resonance spectroscopy, experimental studies of the fundamental interactions underlying protein structure led to several distance constraints which motivated the theoretical approach to determine protein structure, and culminated in the Empirical Conformational Energy Program for Peptides (ECEPP), an all-atom force field, with which the structures of fibrous collagen-like proteins and the 46-residue globular staphylococcal protein A were determined. To undertake the study of larger globular proteins, a physics-based coarse-grained UNited-RESidue (UNRES) force field was developed, and applied to the protein-folding problem in terms of structure, thermodynamics, dynamics, and folding pathways. Initially, single-chain and, ultimately, multiple-chain proteins were examined, and the methodology was extended to protein-protein interactions and to nucleic acids and to protein-nucleic acid interactions. The ultimate results led to an understanding of a variety of biological processes underlying natural and disease phenomena.
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136
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Bignucolo O, Leung HTA, Grzesiek S, Bernèche S. Backbone hydration determines the folding signature of amino acid residues. J Am Chem Soc 2015; 137:4300-3. [PMID: 25794270 DOI: 10.1021/jacs.5b00660] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The relation between the sequence of a protein and its three-dimensional structure remains largely unknown. A lasting dream is to elucidate the side-chain-dependent driving forces that govern the folding process. Different structural data suggest that aromatic amino acids play a particular role in the stabilization of protein structures. To better understand the underlying mechanism, we studied peptides of the sequence EGAAXAASS (X = Gly, Ile, Tyr, Trp) through comparison of molecular dynamics (MD) trajectories and NMR residual dipolar coupling (RDC) measurements. The RDC data for aromatic substitutions provide evidence for a kink in the peptide backbone. Analysis of the MD simulations shows that the formation of internal hydrogen bonds underlying a helical turn is key to reproduce the experimental RDC values. The simulations further reveal that the driving force leading to such helical-turn conformations arises from the lack of hydration of the peptide chain on either side of the bulky aromatic side chain, which can potentially act as a nucleation point initiating the folding process.
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Affiliation(s)
- Olivier Bignucolo
- †SIB Swiss Institute of Bioinformatics and ‡Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Hoi Tik Alvin Leung
- †SIB Swiss Institute of Bioinformatics and ‡Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Stephan Grzesiek
- †SIB Swiss Institute of Bioinformatics and ‡Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Simon Bernèche
- †SIB Swiss Institute of Bioinformatics and ‡Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
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137
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Ma CD, Wang C, Acevedo-Vélez C, Gellman SH, Abbott NL. Modulation of hydrophobic interactions by proximally immobilized ions. Nature 2015; 517:347-50. [DOI: 10.1038/nature14018] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/27/2014] [Indexed: 11/09/2022]
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138
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Shao Q, Jiang S. Molecular understanding and design of zwitterionic materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:15-26. [PMID: 25367090 DOI: 10.1002/adma.201404059] [Citation(s) in RCA: 542] [Impact Index Per Article: 60.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/04/2014] [Indexed: 05/20/2023]
Abstract
Zwitterionic materials have moieties possessing cationic and anionic groups. This molecular structure leads to unique properties that can be the solutions of various application problems. A typical example is that zwitterionic carboxybetaine (CB) and sulfobetaine (SB) materials resist nonspecific protein adsorption in complex media. Considering the vast number of cationic and anionic groups in the current chemical inventory, there are many possible structural variations of zwitterionic materials. The diversified structures provide the possibility to achieve many desired properties and urge a better understanding of zwitterionic materials to provide design principles. Molecular simulations and modeling are a versatile tool to understand the structure-property relationships of materials at the molecular level. This progress report summarizes recent simulation and modeling studies addressing two fundamental questions regarding zwitterionic materials and their applications as biomaterials. First, what are the differences between zwitterionic and nonionic materials? Second, what are the differences among zwitterionic materials? This report also demonstrates a molecular design of new protein-resistant zwitterionic moieties beyond conventional CB and SB based on design principles developed from these simulation studies.
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Affiliation(s)
- Qing Shao
- Department of Chemical Engineering, University of Washington, Seattle, Washington, 98195, USA
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139
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Duarte Alaniz V, Rocha-Rinza T, Cuevas G. Assessment of hydrophobic interactions and their contributions through the analysis of the methane dimer. J Comput Chem 2014; 36:361-75. [DOI: 10.1002/jcc.23798] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 10/21/2014] [Accepted: 11/02/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Víctor Duarte Alaniz
- Departamento de Fisicoquímica; Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; México 04510 D. F. México
| | - Tomás Rocha-Rinza
- Departamento de Fisicoquímica; Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; México 04510 D. F. México
| | - Gabriel Cuevas
- Departamento de Fisicoquímica; Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; México 04510 D. F. México
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140
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McDowell GS, Hindley CJ, Lippens G, Landrieu I, Philpott A. Phosphorylation in intrinsically disordered regions regulates the activity of Neurogenin2. BMC BIOCHEMISTRY 2014; 15:24. [PMID: 25374254 PMCID: PMC4422318 DOI: 10.1186/s12858-014-0024-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 10/18/2014] [Indexed: 11/10/2022]
Abstract
Background Neuronal differentiation is largely under the control of basic Helix-Loop-Helix (bHLH) proneural transcription factors that play key roles during development of the embryonic nervous system. In addition to well-characterised regulation of their expression, increasing evidence is emerging for additional post-translational regulation of proneural protein activity. Of particular interest is the bHLH proneural factor Neurogenin2 (Ngn2), which orchestrates progression from neural progenitor to differentiated neuron in several regions of the central nervous system. Previous studies have demonstrated a key role for cell cycle-dependent multi-site phosphorylation of Ngn2 protein at Serine-Proline (SP) sites for regulation of its neuronal differentiation activity, although the potential structural and functional consequences of phosphorylation at different regions of the protein are unclear. Results Here we characterise the role of phosphorylation of specific regions of Ngn2 on the stability of Ngn2 protein and on its neuronal differentiation activity in vivo in the developing embryo, demonstrating clearly that the location of SP sites is less important than the number of SP sites available for control of Ngn2 activity in vivo. We also provide structural evidence that Ngn2 contains large, intrinsically disordered regions that undergo phosphorylation by cyclin-dependent kinases (cdks). Conclusions Phosphorylation of Ngn2 occurs in both the N- and C-terminal regions, either side of the conserved basic Helix-Loop-Helix domain. While these phosphorylation events do not change the intrinsic stability of Ngn2, phosphorylation on multiple sites acts to limit its ability to drive neuronal differentiation in vivo. Phosphorylated regions of Ngn2 are predicted to be intrinsically disordered and cdk-dependent phosphorylation of these intrinsically disordered regions contributes to Ngn2 regulation.
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Affiliation(s)
- Gary S McDowell
- Department of Oncology, MRC/Hutchison Research Centre, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK. .,Current address: Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Medford, MA, 02155, USA.
| | - Christopher J Hindley
- Department of Oncology, MRC/Hutchison Research Centre, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK. .,Current address: The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
| | - Guy Lippens
- CNRS, Université de Lille 1, UMR 8576, Villeneuve d'Ascq, France.
| | | | - Anna Philpott
- Department of Oncology, MRC/Hutchison Research Centre, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK.
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141
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Sant'Anna R, Braga C, Varejão N, Pimenta KM, Graña-Montes R, Alves A, Cortines J, Cordeiro Y, Ventura S, Foguel D. The importance of a gatekeeper residue on the aggregation of transthyretin: implications for transthyretin-related amyloidoses. J Biol Chem 2014; 289:28324-37. [PMID: 25086037 PMCID: PMC4192486 DOI: 10.1074/jbc.m114.563981] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Protein aggregation into β-sheet-enriched amyloid fibrils is associated with an increasing number of human disorders. The adoption of such amyloid conformations seems to constitute a generic property of polypeptide chains. Therefore, during evolution, proteins have adopted negative design strategies to diminish their intrinsic propensity to aggregate, including enrichment of gatekeeper charged residues at the flanks of hydrophobic aggregation-prone segments. Wild type transthyretin (TTR) is responsible for senile systemic amyloidosis, and more than 100 mutations in the TTR gene are involved in familial amyloid polyneuropathy. The TTR 26–57 segment bears many of these aggressive amyloidogenic mutations as well as the binding site for heparin. We demonstrate here that Lys-35 acts as a gatekeeper residue in TTR, strongly decreasing its amyloidogenic potential. This protective effect is sequence-specific because Lys-48 does not affect TTR aggregation. Lys-35 is part of the TTR basic heparin-binding motif. This glycosaminoglycan blocks the protective effect of Lys-35, probably by neutralization of its side chain positive charge. A K35L mutation emulates this effect and results in the rapid self-assembly of the TTR 26–57 region into amyloid fibrils. This mutation does not affect the tetrameric protein stability, but it strongly increases its aggregation propensity. Overall, we illustrate how TTR is yet another amyloidogenic protein exploiting negative design to prevent its massive aggregation, and we show how blockage of conserved protective features by endogenous factors or mutations might result in increased disease susceptibility.
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Affiliation(s)
- Ricardo Sant'Anna
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Carolina Braga
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Nathalia Varejão
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Karinne M Pimenta
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Ricardo Graña-Montes
- the Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Aline Alves
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Juliana Cortines
- the Instituto de Microbiologia Professor Paulo de Goés, Universidade Federal do Rio de Janeiro, Rio de Janeiro CEP 21941-590, Brazil and
| | | | - Salvador Ventura
- the Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Debora Foguel
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural,
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142
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Jennaro TS, Beaty MR, Kurt-Yilmaz N, Luskin BL, Cavagnero S. Burial of nonpolar surface area and thermodynamic stabilization of globins as a function of chain elongation. Proteins 2014; 82:2318-31. [DOI: 10.1002/prot.24590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/11/2014] [Accepted: 04/12/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Theodore S. Jennaro
- Department of Chemistry; University of Wisconsin-Madison; Madison Wisconsin 53706
| | - Matthew R. Beaty
- Department of Chemistry; University of Wisconsin-Madison; Madison Wisconsin 53706
| | - Neşe Kurt-Yilmaz
- Department of Chemistry; University of Wisconsin-Madison; Madison Wisconsin 53706
| | - Benjamin L. Luskin
- Department of Chemistry; University of Wisconsin-Madison; Madison Wisconsin 53706
| | - Silvia Cavagnero
- Department of Chemistry; University of Wisconsin-Madison; Madison Wisconsin 53706
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143
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Lipinski B. Iron-induced parafibrin formation in tumors fosters immune evasion. Oncoimmunology 2014; 3:e28539. [PMID: 25050219 PMCID: PMC4063136 DOI: 10.4161/onci.28539] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 03/12/2014] [Accepted: 03/14/2014] [Indexed: 01/29/2023] Open
Abstract
Although efficacious in vitro, it is well known that adoptive immunotherapeutic modalities lose their potency when applied in vivo. Furthermore, malignant cell exposure to blood platelets attenuates the anticancer activity of natural killer (NK) cells. We argue that upon contact with redox iron, fibrinogen is converted to a hydrophobic fibrin-like polymer that coats tumor cells and provides protection from immune-mediated destruction.
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144
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Abstract
There has been a great level of enthusiasm to downregulate overactive N-methyl-D-aspartate (NMDA) receptors to protect neurons from excitotoxicity. NMDA receptors play pivotal roles in basic brain development and functions as well as in neurological disorders and diseases. However, mechanistic understanding of antagonism in NMDA receptors is limited due to complete lack of antagonist-bound structures for the L-glutamate-binding GluN2 subunits. Here, we report the crystal structures of GluN1/GluN2A NMDA receptor ligand-binding domain (LBD) heterodimers in complex with GluN1- and GluN2-targeting antagonists. The crystal structures reveal that the antagonists, D-(-)-2-amino-5-phosphonopentanoic acid (D-AP5) and 1-(phenanthrene-2-carbonyl)piperazine-2,3-dicarboxylic acid (PPDA), have discrete binding modes and mechanisms for opening of the bilobed architecture of GluN2A LBD compared to the agonist-bound form. The current study shows distinct ways by which the conformations of NMDA receptor LBDs may be controlled and coupled to receptor inhibition and provides possible strategies to develop therapeutic compounds with higher subtype-specificity.
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145
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Ghosh S, Vishveshwara S. Ranking the quality of protein structure models using sidechain based network properties. F1000Res 2014; 3:17. [PMID: 25580218 PMCID: PMC4038323 DOI: 10.12688/f1000research.3-17.v1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/20/2014] [Indexed: 01/31/2023] Open
Abstract
Determining the correct structure of a protein given its sequence still remains an arduous task with many researchers working towards this goal. Most structure prediction methodologies result in the generation of a large number of probable candidates with the final challenge being to select the best amongst these. In this work, we have used Protein Structure Networks of native and modeled proteins in combination with Support Vector Machines to estimate the quality of a protein structure model and finally to provide ranks for these models. Model ranking is performed using regression analysis and helps in model selection from a group of many similar and good quality structures. Our results show that structures with a rank greater than 16 exhibit native protein-like properties while those below 10 are non-native like. The tool is also made available as a web-server ( http://vishgraph.mbu.iisc.ernet.in/GraProStr/native_non_native_ranking.html), where, 5 modelled structures can be evaluated at a given time.
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Affiliation(s)
- Soma Ghosh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India ; I.I.Sc. Mathematics Initiative, Indian Institute of Science, Bangalore, 560012, India
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146
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Noé F, Prinz JH. Analysis of Markov Models. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 797:75-90. [DOI: 10.1007/978-94-007-7606-7_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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147
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Shao Q, White AD, Jiang S. Difference of carboxybetaine and oligo(ethylene glycol) moieties in altering hydrophobic interactions: a molecular simulation study. J Phys Chem B 2013; 118:189-94. [PMID: 24328129 DOI: 10.1021/jp410224w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Polycarboxybetaine and poly(ethylene glycol) materials resist nonspecific protein adsorption but differ in influencing biological functions such as enzymatic activity. To investigate this difference, we studied the influence of carboxybetaine and oligo(ethylene glycol) moieties on hydrophobic interactions using molecular simulations. We employed a model system composed of two non-polar plates and studied the potential of mean force of plate-plate association in carboxybetaine, (ethylene glycol)4, and (ethylene glycol)2 solutions using well-tempered metadynamics simulations. Water, trimethylamine N-oxide, and urea solutions were used as reference systems. We analyzed the variation of the potential of mean force in various solutions to study how carboxybetaine and oligo(ethylene glycol) moieties influence the hydrophobic interactions. To study the origin of their influence, we analyzed the normalized distributions of moieties and water molecules using molecular dynamics simulations. The simulation results showed that oligo(ethylene glycol) moieties repel water molecules away from the non-polar plates and weaken the hydrophobic interactions. Carboxybetaine moieties do not repel water molecules away from the plates and therefore do not influence the hydrophobic interactions.
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Affiliation(s)
- Qing Shao
- Department of Chemical Engineering, University of Washington , Seattle, Washington 98195, United States
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148
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Tabor RF, Wu C, Grieser F, Dagastine RR, Chan DYC. Measurement of the Hydrophobic Force in a Soft Matter System. J Phys Chem Lett 2013; 4:3872-3877. [PMID: 27045729 DOI: 10.1021/jz402068k] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The hydrophobic attraction describes the well-known tendency for nonpolar molecules and surfaces to agglomerate in water, controlled by the reorganization of intervening water molecules to minimize disruption to their hydrogen bonding network. Measurements of the attraction between chemically hydrophobised solid surfaces have reported ranges varying from tens to hundreds of nanometers, all attributed to hydrophobic forces. Here, by studying the interaction between two hydrophobic oil drops in water under well-controlled conditions where all known surface forces are suppressed, we observe only a strong, short-ranged attraction with an exponential decay length of 0.30 ± 0.03 nm-comparable to molecular correlations of water molecules. This attraction is implicated in a range of fundamental phenomena from self-assembled monolayer formation to the action of membrane proteins and nonstick surface coatings.
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Affiliation(s)
- Rico F Tabor
- School of Chemistry, Monash University , Clayton 3800, Australia
| | - Chu Wu
- Particulate Fluids Processing Centre, University of Melbourne , Parkville 3010, Australia
- Department of Mathematics and Statistics, University of Melbourne , Parkville 3010, Australia
| | - Franz Grieser
- Particulate Fluids Processing Centre, University of Melbourne , Parkville 3010, Australia
- School of Chemistry, University of Melbourne , Parkville 3010, Australia
| | - Raymond R Dagastine
- Particulate Fluids Processing Centre, University of Melbourne , Parkville 3010, Australia
- Department of Chemical and Biomolecular Engineering, University of Melbourne , Parkville 3010, Australia
- Melbourne Centre for Nanofabrication , 151 Wellington Road, Clayton, Victoria, 3168, Australia
| | - Derek Y C Chan
- Particulate Fluids Processing Centre, University of Melbourne , Parkville 3010, Australia
- Department of Mathematics and Statistics, University of Melbourne , Parkville 3010, Australia
- Faculty of Life and Social Sciences, Swinburne University of Technology , Hawthorn 3122, Australia
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149
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150
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Melamed D, Young DL, Gamble CE, Miller CR, Fields S. Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein. RNA (NEW YORK, N.Y.) 2013; 19:1537-51. [PMID: 24064791 PMCID: PMC3851721 DOI: 10.1261/rna.040709.113] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The RNA recognition motif (RRM) is the most common RNA-binding domain in eukaryotes. Differences in RRM sequences dictate, in part, both RNA and protein-binding specificities and affinities. We used a deep mutational scanning approach to study the sequence-function relationship of the RRM2 domain of the Saccharomyces cerevisiae poly(A)-binding protein (Pab1). By scoring the activity of more than 100,000 unique Pab1 variants, including 1246 with single amino acid substitutions, we delineated the mutational constraints on each residue. Clustering of residues with similar mutational patterns reveals three major classes, composed principally of RNA-binding residues, of hydrophobic core residues, and of the remaining residues. The first class also includes a highly conserved residue not involved in RNA binding, G150, which can be mutated to destabilize Pab1. A comparison of the mutational sensitivity of yeast Pab1 residues to their evolutionary conservation reveals that most residues tolerate more substitutions than are present in the natural sequences, although other residues that tolerate fewer substitutions may point to specialized functions in yeast. An analysis of ∼40,000 double mutants indicates a preference for a short distance between two mutations that display an epistatic interaction. As examples of interactions, the mutations N139T, N139S, and I157L suppress other mutations that interfere with RNA binding and protein stability. Overall, this study demonstrates that living cells can be subjected to a single assay to analyze hundreds of thousands of protein variants in parallel.
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Affiliation(s)
- Daniel Melamed
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - David L. Young
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Caitlin E. Gamble
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Christina R. Miller
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Stanley Fields
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
- Department of Medicine, University of Washington, Seattle, Washington 98195, USA
- Corresponding authorE-mail
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