1
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He PY, Zhou Y, Chen PG, Zhang MQ, Hu JJ, Lim YJ, Zhang H, Liu K, Li YM. A Hydroxylamine-Mediated Amidination of Lysine Residues That Retains the Protein's Positive Charge. Angew Chem Int Ed Engl 2024; 63:e202402880. [PMID: 38758629 DOI: 10.1002/anie.202402880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 05/12/2024] [Accepted: 05/17/2024] [Indexed: 05/19/2024]
Abstract
Lysine-specific peptide and protein modification strategies are widely used to study charge-related functions and applications. However, these strategies often result in the loss of the positive charge on lysine, significantly impacting the charge-related properties of proteins. Herein, we report a strategy to preserve the positive charge and selectively convert amines in lysine side chains to amidines using nitriles and hydroxylamine under aqueous conditions. Various unprotected peptides and proteins were successfully modified with a high conversion rate. Moreover, the reactive amidine moiety and derived modification site enable subsequent secondary modifications. Notably, positive charges were retained during the modification. Therefore, positive charge-related protein properties, such as liquid-liquid phase separation behaviour of α-synuclein, were not affected. This strategy was subsequently applied to a lysine rich protein to develop an amidine-containing coacervate DNA complex with outstanding mechanical properties. Overall, our innovative strategy provides a new avenue to explore the characteristics of positively charged proteins.
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Affiliation(s)
- Pei-Yang He
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Yusai Zhou
- Engineering Research Center of Advanced Rare Earth Materials, (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Pu-Guang Chen
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Meng-Qian Zhang
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Jin-Jian Hu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Yeh-Jun Lim
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Hongjie Zhang
- Engineering Research Center of Advanced Rare Earth Materials, (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Kai Liu
- Engineering Research Center of Advanced Rare Earth Materials, (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Yan-Mei Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
- Beijing Institute for Brain Disorders, Beijing, 100069, P. R. China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, P. R. China
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2
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Liang J, Xu Z, Zhao Y. Improved Random Batch Ewald Method in Molecular Dynamics Simulations. J Phys Chem A 2022; 126:3583-3593. [PMID: 35635179 DOI: 10.1021/acs.jpca.2c01918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The random batch Ewald (RBE) is an efficient and accurate method for molecular dynamics (MD) simulations of physical systems at the nano/microscale. The method shows great potential to solve the computational bottleneck of long-range interactions, motivating a necessity to accelerate short-range components of the nonbonded interactions for a further speedup of MD simulations. In this work, we present an improved RBE method for the nonbonding interactions by introducing the random batch idea to constructing neighbor lists for the treatment of both the short-range part of the Ewald splitting and the Lennard-Jones potential. The efficiency that the novel neighbor list algorithm owes to the stochastic minibatch strategy can significantly reduce the total number of neighbors. We obtain the error estimate and convergence by theoretical analysis and implement the improved RBE method in the LAMMPS package. Benchmark simulations are performed to demonstrate the accuracy and stability of the algorithm. Numerical tests on computer performance by conducting large-scaled MD simulations for systems including up to 0.1 billion water molecules are run on massive clusters with up to 50000 CPU cores, demonstrating the attractive features such as the high parallel scalability and memory-saving of the method in comparison to the existing methods.
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Affiliation(s)
- Jiuyang Liang
- School of Mathematical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhenli Xu
- School of Mathematical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.,MOE-LSC, CMA-Shanghai and Shanghai Center for Applied Mathematics, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yue Zhao
- School of Mathematical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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3
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Yang CT, Chu LK. Protein dynamics of human serum albumin at hypothermic temperatures investigated by temperature jump. Phys Chem Chem Phys 2022; 24:11079-11085. [PMID: 35471209 DOI: 10.1039/d2cp00220e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Human serum albumin (HSA) is the most abundant protein in human plasma. Most protein dynamics studies of HSA have been performed above the hyperthermia temperature (>42 °C), so information on the dynamics under hypothermic conditions (<35 °C) is lacking. In this work, a tryptophan-based fluorescence temperature jump system was employed to investigate the thermally-induced dynamic process of HSA at a physiological concentration of ca. 45 mg mL-1 and pH = ca. 7 upon an instantaneous temperature increase from 25 °C to 30-43 °C. The observed kinetics manifested a three-state consecutive feature, . Upon analysis with the Arrhenius model, the rate coefficients k1 and k2 manifested piecewise temperature dependence, and the turning-point temperature was found to be ca. 34 °C, coinciding with the upper bound of hypothermic temperature. Meanwhile, the corresponding activation energies of the transitions at 34-43 °C were lower than those at 30-34 °C, suggesting that protein conformational adjustments at 34-43 °C were more feasible than those at hypothermic temperatures. These observations provided a fresh viewpoint on the relationship between the energetics of protein dynamics and the apparent functioning of a given protein at the molecular level.
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Affiliation(s)
- Chih-Tsun Yang
- Department of Chemistry, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu 300044, Taiwan.
| | - Li-Kang Chu
- Department of Chemistry, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu 300044, Taiwan.
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4
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Xu Z, He Z, Quan X, Sun D, Miao Z, Yu H, Yang S, Chen Z, Zeng J, Zhou J. Molecular simulations of charged complex fluids: A review. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.11.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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5
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Heilmann N, Wolf M, Kozlowska M, Sedghamiz E, Setzler J, Brieg M, Wenzel W. Sampling of the conformational landscape of small proteins with Monte Carlo methods. Sci Rep 2020; 10:18211. [PMID: 33097750 PMCID: PMC7585447 DOI: 10.1038/s41598-020-75239-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/12/2020] [Indexed: 12/24/2022] Open
Abstract
Computer simulation provides an increasingly realistic picture of large-scale conformational change of proteins, but investigations remain fundamentally constrained by the femtosecond timestep of molecular dynamics simulations. For this reason, many biologically interesting questions cannot be addressed using accessible state-of-the-art computational resources. Here, we report the development of an all-atom Monte Carlo approach that permits the modelling of the large-scale conformational change of proteins using standard off-the-shelf computational hardware and standard all-atom force fields. We demonstrate extensive thermodynamic characterization of the folding process of the α-helical Trp-cage, the Villin headpiece and the β-sheet WW-domain. We fully characterize the free energy landscape, transition states, energy barriers between different states, and the per-residue stability of individual amino acids over a wide temperature range. We demonstrate that a state-of-the-art intramolecular force field can be combined with an implicit solvent model to obtain a high quality of the folded structures and also discuss limitations that still remain.
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Affiliation(s)
- Nana Heilmann
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Moritz Wolf
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Mariana Kozlowska
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Elaheh Sedghamiz
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Julia Setzler
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Martin Brieg
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Wolfgang Wenzel
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
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6
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Gautam RP, Pan H, Chalyavi F, Tucker MJ, Barile CJ. Nanostructured Ni-Cu Electrocatalysts for the Oxygen Evolution Reaction. Catal Sci Technol 2020; 10:4960-4967. [PMID: 33796262 PMCID: PMC8009306 DOI: 10.1039/d0cy00427h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ni-based materials are promising electrocatalysts for the oxygen evolution reaction (OER) for water splitting in alkaline media. We report the synthesis and OER electrocatalysis of both Ni-Cu nanoparticles (20-50 nm in diameter) and Ni-Cu nanoclusters (<20 metal atoms). Analysis of mass spectral data from matrix-assisted laser desorption/ionization and electrospray ionization techniques demonstrates that discrete heterobimetallic Ni-Cu nanoclusters capped with glutathione ligands were successfully synthesized. Ni-Cu nanoclusters with a 52:48 mol % Ni:Cu metal composition display an OER onset overpotential of 50 mV and an overpotential of 150 mV at 10 mA cm-2, which makes this catalyst one of the most efficient nonprecious metal OER catalysts. The durability of the nanocluster catalysts on carbon electrodes can be extended by appending them to electrodes modified with TiO2 nanoparticles. Infrared spectroscopy results indicate that the aggregation dynamics of the glutathione ligands change during catalysis. Taken together, these results help explain the reactivity of a novel class of nanostructured Ni-Cu OER catalysts, which are underexplored alternatives to more commonly studied Ni-Fe, Ni-Co, and Ni-Mn materials.
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Affiliation(s)
| | - Hanqing Pan
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - Farzaneh Chalyavi
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - Matthew J. Tucker
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
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7
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Hofmann SM, Frost CV, Podewin T, Gailer M, Weber E, Zacharias M, Zinth W, Hoffmann-Röder A. Folding and Unfolding of the Short Light-Triggered β-Hairpin Peptide AzoChignolin Occurs within 100 ns. J Phys Chem B 2020; 124:5113-5121. [PMID: 32479079 DOI: 10.1021/acs.jpcb.0c02021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To map the underlying molecular mechanisms of folding dynamics in proteins, light-operated peptides have emerged as promising tools. In this study, we reveal the complete sequence of light-induced structural changes of AzoChignolin, a short β-hairpin peptide containing an azobenzene photoswitch in its loop region. Light-triggered structural changes were monitored by time-resolved IR spectroscopy. Formation and destruction of the hairpin structure is very fast and occurs within 100 ns for AzoChignolin in methanol. Atomistic molecular dynamics simulations using two explicit solvents, methanol and water, revealed the underlying molecular processes and allowed us to gain further insight into the reaction mechanism. Despite its rapid reaction time, hairpin formation in these solvents is not force-driven by the molecular switch but proceeded via formation of interstrand hydrogen bonds and contacts between aromatic residues. Moreover, the combined experimental and theoretical study demonstrates that the solvent (methanol vs water) does not dictate the velocity of β-hairpin formation in the AzoChignolin peptide comprising only a few hydrophobic residues in the strands.
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Affiliation(s)
- Stefan M Hofmann
- BioMolecular Optics and Center for Integrated Protein Science, Faculty of Physics, Ludwig-Maximilians-Universität München, Oettingenstr. 67, München 80538, Germany
| | - Christina V Frost
- TUM Department of Physics T38, Technical University of Munich, James-Franck-Str. 1, Garching 85748, Germany
| | - Tom Podewin
- Department of Organic Chemistry and Center for Integrated Protein Science, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, München 81377, Germany
| | - Manuel Gailer
- Department of Organic Chemistry and Center for Integrated Protein Science, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, München 81377, Germany
| | - Elisa Weber
- BioMolecular Optics and Center for Integrated Protein Science, Faculty of Physics, Ludwig-Maximilians-Universität München, Oettingenstr. 67, München 80538, Germany
| | - Martin Zacharias
- TUM Department of Physics T38, Technical University of Munich, James-Franck-Str. 1, Garching 85748, Germany
| | - Wolfgang Zinth
- BioMolecular Optics and Center for Integrated Protein Science, Faculty of Physics, Ludwig-Maximilians-Universität München, Oettingenstr. 67, München 80538, Germany
| | - Anja Hoffmann-Röder
- Department of Organic Chemistry and Center for Integrated Protein Science, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, München 81377, Germany
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8
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Sofronov O, Giubertoni G, Pérez de Alba Ortíz A, Ensing B, Bakker HJ. Peptide Side-COOH Groups Have Two Distinct Conformations under Biorelevant Conditions. J Phys Chem Lett 2020; 11:3466-3472. [PMID: 32293901 PMCID: PMC7212517 DOI: 10.1021/acs.jpclett.0c00711] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
The carboxyl (COOH) side chain groups of amino acids, such as aspartic acid, play an important role in biochemical processes, including enzymatic proton transport. In many theoretical studies, it was found that the (bio)chemical reactivity of the carboxyl group strongly depends on the conformation of this group. Interestingly, up to now there has been no experimental investigation of the geometry and the stability of different COOH conformers under biorelevant conditions. Here, we investigate the conformational isomerism of the side chain COOH group of N-acetyl aspartic acid amide using polarization-resolved two-dimensional infrared spectroscopy. We find that the carboxyl group shows two distinct near-planar conformers (syn and anti) when dissolved in water at room temperature. Both conformers are significantly populated in aqueous solution (75 ± 10% and 25 ± 10% for syn and anti, respectively). Molecular dynamics simulations show that the anti conformer interacts more strongly with water molecules than the syn conformer, explaining why this conformer is significantly present in aqueous solution.
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Affiliation(s)
| | | | - Alberto Pérez de Alba Ortíz
- Amsterdam
Center for Multiscale Modeling and Van ’t Hoff Institute for
Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Bernd Ensing
- Amsterdam
Center for Multiscale Modeling and Van ’t Hoff Institute for
Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Huib J. Bakker
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
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9
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Melien R, Garidel P, Hinderberger D, Blech M. Thermodynamic Unfolding and Aggregation Fingerprints of Monoclonal Antibodies Using Thermal Profiling. Pharm Res 2020; 37:78. [DOI: 10.1007/s11095-020-02792-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/28/2020] [Indexed: 01/05/2023]
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10
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Davis CM, Zanetti-Polzi L, Gruebele M, Amadei A, Dyer RB, Daidone I. A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy. Chem Sci 2018; 9:9002-9011. [PMID: 30647892 PMCID: PMC6301204 DOI: 10.1039/c8sc03786h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/02/2018] [Indexed: 11/23/2022] Open
Abstract
We break the barrier between simulation and experiment by comparing identical computed and experimental infrared observables.
For small molecule reaction kinetics, computed reaction coordinates often mimic experimentally measured observables quite accurately. Although nowadays simulated and measured biomolecule kinetics can be compared on the same time scale, a gap between computed and experimental observables remains. Here we directly compared temperature-jump experiments and molecular dynamics simulations of protein folding dynamics using the same observable: the time-dependent infrared spectrum. We first measured the stability and folding kinetics of the fastest-folding β-protein, the GTT35 WW domain, using its structurally specific infrared spectrum. The relaxation dynamics of the peptide backbone, β-sheets, turn, and random coil were measured independently by probing the amide I′ region at different frequencies. Next, the amide I′ spectra along folding/unfolding molecular dynamics trajectories were simulated by accurate mixed quantum/classical calculations. The simulated time dependence and spectral amplitudes at the exact experimental probe frequencies provided relaxation and folding rates in agreement with experimental observations. The calculations validated by experiment yield direct structural evidence for a rate-limiting reaction step where an intermediate state with either the first or second hairpin is formed. We show how folding switches from a more homogeneous (apparent two-state) process at high temperature to a more heterogeneous process at low temperature, where different parts of the WW domain fold at different rates.
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Affiliation(s)
- Caitlin M Davis
- Department of Chemistry and Department of Physics , University of Illinois at Urbana-Champaign , IL 61801 , USA.,Department of Chemistry , Emory University , Atlanta , GA 30322 , USA .
| | - Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences , University of L'Aquila , 67010 L'Aquila , Italy .
| | - Martin Gruebele
- Department of Chemistry and Department of Physics , University of Illinois at Urbana-Champaign , IL 61801 , USA.,Center for Biophysics and Quantitative Biology , University of Illinois at Urbana-Champaign , IL 61801 , USA
| | - Andrea Amadei
- Department of Chemical and Technological Sciences , University of Rome "Tor Vergata" , 00133 Rome , Italy
| | - R Brian Dyer
- Department of Chemistry , Emory University , Atlanta , GA 30322 , USA .
| | - Isabella Daidone
- Department of Physical and Chemical Sciences , University of L'Aquila , 67010 L'Aquila , Italy .
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11
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Hazel AJ, Walters ET, Rowley CN, Gumbart JC. Folding free energy landscapes of β-sheets with non-polarizable and polarizable CHARMM force fields. J Chem Phys 2018; 149:072317. [PMID: 30134731 DOI: 10.1063/1.5025951] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Molecular dynamics (MD) simulations of peptides and proteins offer atomic-level detail into many biological processes, although the degree of insight depends on the accuracy of the force fields used to represent them. Protein folding is a key example in which the accurate reproduction of folded-state conformations of proteins and kinetics of the folding processes in simulation is a longstanding goal. Although there have been a number of recent successes, challenges remain in capturing the full complexity of folding for even secondary-structure elements. In the present work, we have used all-atom MD simulations to study the folding properties of one such element, the C-terminal β-hairpin of the B1 domain of streptococcal protein G (GB1). Using replica-exchange umbrella sampling simulations, we examined the folding free energy of two fixed-charge CHARMM force fields, CHARMM36 and CHARMM22*, as well as a polarizable force field, the CHARMM Drude-2013 model, which has previously been shown to improve the folding properties of α-helical peptides. The CHARMM22* and Drude-2013 models are in rough agreement with experimental studies of GB1 folding, while CHARMM36 overstabilizes the β-hairpin. Additional free-energy calculations show that small adjustments to the atomic polarizabilities in the Drude-2013 model can improve both the backbone solubility and folding properties of GB1 without significantly affecting the model's ability to properly fold α-helices. We also identify a non-native salt bridge in the β-turn region that overstabilizes the β-hairpin in the C36 model. Finally, we demonstrate that tryptophan fluorescence is insufficient for capturing the full β-hairpin folding pathway.
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Affiliation(s)
- Anthony J Hazel
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Evan T Walters
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador A1B3X7, Canada
| | - Christopher N Rowley
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador A1B3X7, Canada
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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12
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Kisley L, Miller KA, Davis CM, Guin D, Murphy EA, Gruebele M, Leckband DE. Soluble Zwitterionic Poly(sulfobetaine) Destabilizes Proteins. Biomacromolecules 2018; 19:3894-3901. [PMID: 30064224 DOI: 10.1021/acs.biomac.8b01120] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The widespread interest in neutral, water-soluble polymers such as poly(ethylene glycol) (PEG) and poly(zwitterions) such as poly(sulfobetaine) (pSB) for biomedical applications is due to their widely assumed low protein binding. Here we demonstrate that pSB chains in solution can interact with proteins directly. Moreover, pSB can reduce the thermal stability and increase the protein folding cooperativity relative to proteins in buffer or in PEG solutions. Polymer-dependent changes in the tryptophan fluorescence spectra of three structurally-distinct proteins reveal that soluble, 100 kDa pSB interacts directly with all three proteins and changes both the local polarity near tryptophan residues and the protein conformation. Thermal denaturation studies show that the protein melting temperatures decrease by as much as ∼1.9 °C per weight percent of polymer and that protein folding cooperativity increases by as much as ∼130 J mol-1 K-1 per weight percent of polymer. The exact extent of the changes is protein-dependent, as some proteins exhibit increased stability, whereas others experience decreased stability at high soluble pSB concentrations. These results suggest that pSB is not universally protein-repellent and that its efficacy in biotechnological applications will depend on the specific proteins used.
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13
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Iglesias-Bexiga M, Szczepaniak M, Sánchez de Medina C, Cobos ES, Godoy-Ruiz R, Martinez JC, Muñoz V, Luque I. Protein Folding Cooperativity and Thermodynamic Barriers of the Simplest β-Sheet Fold: A Survey of WW Domains. J Phys Chem B 2018; 122:11058-11071. [PMID: 29985628 DOI: 10.1021/acs.jpcb.8b05198] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Theory and experiments have shown that microsecond folding proteins exhibit characteristic thermodynamic properties that reflect the limited cooperativity of folding over marginal barriers (downhill folding). Those studies have mostly focused on proteins with large α-helical contents and small size, which tend to be the fastest folders. A key open question is whether such properties are also present in the fastest all-β proteins. We address this issue by investigating the unfolding thermodynamics of a collection of WW domains as representatives of the simplest β-sheet fold. WW domains are small microsecond folders, although they do not fold as fast as their α-helical counterparts. In previous work on the NEDD4-WW4 domain, we reported deviations from two-state thermodynamics that were less apparent and thus suggestive of an incipient downhill scenario. Here we investigate the unfolding thermodynamics of four other WW domains (NEDD4-WW3, YAP65-WW1(L30K), FBP11-WW1, and FBP11-WW2) by performing all of the thermodynamic tests for downhill folding that have been previously developed on α-helical proteins. This set of five WW domains shares low sequence identity and include examples from two specificity classes, thus providing a comprehensive survey. Thermodynamic analysis of the four new WW domains consistently reveals all of the properties of downhill folding equilibria, which are in all cases more marked than what we found before in NEDD4-WW4. Our results show that fast-folding all-β proteins do share limited cooperativity and gradual unfolding thermodynamics with fast α-helical proteins and suggest that the free energy barrier to folding of natural proteins is mostly determined by size and fold topology and much less by the specific amino acid sequence.
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Affiliation(s)
- Manuel Iglesias-Bexiga
- Department of Physical Chemistry and Institute of Biotechnology , University of Granada , Granada 18010 , Spain
| | - Malwina Szczepaniak
- Centro Nacional de Biotecnología , Consejo Superior de Investigaciones Científicas (CSIC) , Darwin 3 , 28049 Madrid , Spain
| | - Celia Sánchez de Medina
- Centro Nacional de Biotecnología , Consejo Superior de Investigaciones Científicas (CSIC) , Darwin 3 , 28049 Madrid , Spain
| | - Eva S Cobos
- Department of Physical Chemistry and Institute of Biotechnology , University of Granada , Granada 18010 , Spain
| | - Raquel Godoy-Ruiz
- Department of Chemistry & Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
| | - Jose C Martinez
- Department of Physical Chemistry and Institute of Biotechnology , University of Granada , Granada 18010 , Spain
| | - Victor Muñoz
- Centro Nacional de Biotecnología , Consejo Superior de Investigaciones Científicas (CSIC) , Darwin 3 , 28049 Madrid , Spain.,Department of Bioengineering , University of California Merced , Merced , California 95343 , United States
| | - Irene Luque
- Department of Physical Chemistry and Institute of Biotechnology , University of Granada , Granada 18010 , Spain
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14
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Zanetti-Polzi L, Davis CM, Gruebele M, Dyer RB, Amadei A, Daidone I. Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation. FEBS Lett 2017; 591:3265-3275. [PMID: 28881468 DOI: 10.1002/1873-3468.12836] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/21/2017] [Accepted: 08/31/2017] [Indexed: 11/06/2022]
Abstract
We present a calculation of the amide I' infrared (IR) spectra of the folded, unfolded, and intermediate states of the WW domain Fip35, a model system for β-sheet folding. Using an all-atom molecular dynamics simulation in which multiple folding and unfolding events take place we identify six conformational states and then apply perturbed matrix method quantum-mechanical calculations to determine their amide I' IR spectra. Our analysis focuses on two states previously identified as Fip35 folding intermediates and suggests that a three-stranded core similar to the folded state core is the main source of the spectroscopic differences between the two intermediates. In particular, we propose a hypothesis for why folding via one of these intermediates was not experimentally observed by IR T-jump.
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Affiliation(s)
| | - Caitlin M Davis
- Departments of Chemistry and Physics, University of Illinois at Urbana-Champaign, IL, USA
| | - Martin Gruebele
- Departments of Chemistry and Physics, University of Illinois at Urbana-Champaign, IL, USA.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, IL, USA
| | - R Brian Dyer
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Andrea Amadei
- Department of Chemical and Technological Sciences, University of Rome "Tor Vergata", Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, Italy
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15
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Abaskharon RM, Gai F. Meandering Down the Energy Landscape of Protein Folding: Are We There Yet? Biophys J 2017; 110:1924-32. [PMID: 27166801 DOI: 10.1016/j.bpj.2016.03.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/18/2016] [Accepted: 03/22/2016] [Indexed: 12/11/2022] Open
Abstract
As judged by a single publication metric, the activity in the protein folding field has been declining over the past 5 years, after enjoying a decade-long growth. Does this development indicate that the field is sunsetting or is this decline only temporary? Upon surveying a small territory of its landscape, we find that the protein folding field is still quite active and many important findings have emerged from recent experimental studies. However, it is also clear that only continued development of new techniques and methods, especially those enabling dissection of the fine details and features of the protein folding energy landscape, will fuel this old field to move forward.
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Affiliation(s)
- Rachel M Abaskharon
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania; The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania.
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16
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Qiao X, Liu Y, Luo L, Chen L, Zhao C, Ai X. Effects of naturally occurring charged mutations on the structure, stability, and binding of the Pin1 WW domain. Biochem Biophys Res Commun 2017; 487:470-476. [PMID: 28431929 DOI: 10.1016/j.bbrc.2017.04.093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 04/18/2017] [Indexed: 11/26/2022]
Abstract
Pin1 is a peptidyl-prolyl cis-trans isomerase, whose WW domain specifically recognizes the pSer/Thr-Pro motif. Pin1 is involved in multiple phosphorylation events that regulate the activities of various substrates, and Pin1 deregulation has been reported in various diseases, including cancer and Alzheimer's disease. The WW domain of Pin1 has been used as a small model protein to investigate the folding mechanisms of the β-sheet structure by studying the effect of mutations or its naturally occurring variants. However, only a few studies have investigated the structure and binding of Pin1 WW mutants. In the present work, two naturally occurring Pin1 WW variants, namely, G20D and S16R, derived from the cynomolgus monkey and African green monkey, respectively, were selected to investigate the influence of charge mutation on the structure, stability, and binding properties of the Pin1 WW domain. Analysis using a combination of nuclear magnetic resonance (NMR) and chemical shift-based calculations revealed that the G20D and S16R mutants had high structural similarity to the wild-type Pin1 WW domain. However, the presence of a charge mutation significantly decreased the stability of the Pin1 WW domain. Both the wild-type and G20D forms of the Pin1 WW domain utilized a three-site mode to bind to a phosphorylated Tau peptide, pT231, whereas the S16R mutant binds to the pT231 peptide either in a non-specific manner or through a totally different binding mechanism. Correspondingly, the wild-type and two mutant Pin1 WW domains showed different binding affinities to the Tau phosphopeptide. Considering that the WW domain participates in the catalytic activity of the Pin1 isomerase, our study represents a novel approach for studying Pin1 function through the analysis of its naturally occurring mutants.
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Affiliation(s)
- Xiaoya Qiao
- School of Chemical Engineering, Xiangtan University, Xiangtan 411105, PR China; Division of Energy Research Resources, National Laboratory for Clean Energy, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, PR China
| | - Ying Liu
- Division of Virology & Immunology, National Center for AIDS/STD Control and Prevention, Beijing 102206, PR China
| | - Liting Luo
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Lei Chen
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Caixian Zhao
- School of Chemical Engineering, Xiangtan University, Xiangtan 411105, PR China.
| | - Xuanjun Ai
- Division of Energy Research Resources, National Laboratory for Clean Energy, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, PR China.
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17
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Davis CM, Reddish MJ, Dyer RB. Dual time-resolved temperature-jump fluorescence and infrared spectroscopy for the study of fast protein dynamics. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 178:185-191. [PMID: 28189834 PMCID: PMC5346054 DOI: 10.1016/j.saa.2017.01.069] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 01/27/2017] [Accepted: 01/31/2017] [Indexed: 05/30/2023]
Abstract
Time-resolved temperature-jump (T-jump) coupled with fluorescence and infrared (IR) spectroscopy is a powerful technique for monitoring protein dynamics. Although IR spectroscopy of the polypeptide amide I mode is more technically challenging, it offers complementary information because it directly probes changes in the protein backbone, whereas, fluorescence spectroscopy is sensitive to the environment of specific side chains. With the advent of widely tunable quantum cascade lasers (QCL) it is possible to efficiently probe multiple IR frequencies with high sensitivity and reproducibility. Here we describe a dual time-resolved T-jump fluorescence and IR spectrometer and its application to study protein folding dynamics. A Q-switched Ho:YAG laser provides the T-jump source for both time-resolved IR and fluorescence spectroscopy, which are probed by a QCL and Ti:Sapphire laser, respectively. The Ho:YAG laser simultaneously pumps the time-resolved IR and fluorescence spectrometers. The instrument has high sensitivity, with an IR absorbance detection limit of <0.2mOD and a fluorescence sensitivity of 2% of the overall fluorescence intensity. Using a computer controlled QCL to rapidly tune the IR frequency it is possible to create a T-jump induced difference spectrum from 50ns to 0.5ms. This study demonstrates the power of the dual time-resolved T-jump fluorescence and IR spectroscopy to resolve complex folding mechanisms by complementary IR absorbance and fluorescence measurements of protein dynamics.
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Affiliation(s)
- Caitlin M Davis
- Department of Chemistry, Emory University, Atlanta, GA 30322, United States
| | - Michael J Reddish
- Department of Chemistry, Emory University, Atlanta, GA 30322, United States
| | - R Brian Dyer
- Department of Chemistry, Emory University, Atlanta, GA 30322, United States.
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18
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Hsu CH, Park S, Mortenson DE, Foley BL, Wang X, Woods RJ, Case DA, Powers ET, Wong CH, Dyson HJ, Kelly JW. The Dependence of Carbohydrate-Aromatic Interaction Strengths on the Structure of the Carbohydrate. J Am Chem Soc 2016; 138:7636-48. [PMID: 27249581 DOI: 10.1021/jacs.6b02879] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Interactions between proteins and carbohydrates are ubiquitous in biology. Therefore, understanding the factors that determine their affinity and selectivity are correspondingly important. Herein, we have determined the relative strengths of intramolecular interactions between a series of monosaccharides and an aromatic ring close to the glycosylation site in an N-glycoprotein host. We employed the enhanced aromatic sequon, a structural motif found in the reverse turns of some N-glycoproteins, to facilitate face-to-face monosaccharide-aromatic interactions. A protein host was used because the dependence of the folding energetics on the identity of the monosaccharide can be accurately measured to assess the strength of the carbohydrate-aromatic interaction. Our data demonstrate that the carbohydrate-aromatic interaction strengths are moderately affected by changes in the stereochemistry and identity of the substituents on the pyranose rings of the sugars. Galactose seems to make the weakest and allose the strongest sugar-aromatic interactions, with glucose, N-acetylglucosamine (GlcNAc) and mannose in between. The NMR solution structures of several of the monosaccharide-containing N-glycoproteins were solved to further understand the origins of the similarities and differences between the monosaccharide-aromatic interaction energies. Peracetylation of the monosaccharides substantially increases the strength of the sugar-aromatic interaction in the context of our N-glycoprotein host. Finally, we discuss our results in light of recent literature regarding the contribution of electrostatics to CH-π interactions and speculate on what our observations imply about the absolute conservation of GlcNAc as the monosaccharide through which N-linked glycans are attached to glycoproteins in eukaryotes.
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Affiliation(s)
- Che-Hsiung Hsu
- Department of Molecular and Experimental Medicine, The Scripps Research Institute , La Jolla, California 92037, United States.,Department of Chemistry, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Sangho Park
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - David E Mortenson
- Department of Molecular and Experimental Medicine, The Scripps Research Institute , La Jolla, California 92037, United States
| | - B Lachele Foley
- Complex Carbohydrate Research Center, University of Georgia , 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Xiaocong Wang
- Complex Carbohydrate Research Center, University of Georgia , 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia , 315 Riverbend Road, Athens, Georgia 30602, United States
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854, United States
| | - Evan T Powers
- Department of Chemistry, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Chi-Huey Wong
- Department of Chemistry, The Scripps Research Institute , La Jolla, California 92037, United States.,Genomics Research Center, Academia Sinica , Taipei 115, Taiwan.,The Skaggs Institute for Chemical Biology , La Jolla, California 92037, United States
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Jeffery W Kelly
- Department of Molecular and Experimental Medicine, The Scripps Research Institute , La Jolla, California 92037, United States.,Department of Chemistry, The Scripps Research Institute , La Jolla, California 92037, United States.,The Skaggs Institute for Chemical Biology , La Jolla, California 92037, United States
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