1
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Suh D, Feng S, Lee H, Zhang H, Park S, Kim S, Lee J, Choi S, Im W. CHARMM-GUI Enhanced Sampler for various collective variables and enhanced sampling methods. Protein Sci 2022; 31:e4446. [PMID: 36124940 PMCID: PMC9601830 DOI: 10.1002/pro.4446] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 11/08/2022]
Abstract
Enhanced sampling methodologies modifying underlying Hamiltonians can be used for the systems with a rugged potential energy surface that makes it hard to observe convergence using conventional unbiased molecular dynamics (MD) simulations. We present CHARMM-GUI Enhanced Sampler, a web-based tool to prepare various enhanced sampling simulations inputs with user-selected collective variables (CVs). Enhanced Sampler provides inputs for the following nine methods: accelerated MD, Gaussian accelerated MD, conformational flooding, metadynamics, adaptive biasing force, steered MD, temperature replica exchange MD, replica exchange solute tempering 2, and replica exchange umbrella sampling for the method-implemented MD packages including AMBER, CHARMM, GENESIS, GROMACS, NAMD, and OpenMM. Users only need to select a group of atoms via intuitive web-implementation in order to define commonly used nine CVs of interest: center of mass based distance, angle, dihedral, root-mean-square-distance, radius of gyration, distance projected on axis, two types of angles projected on axis, and coordination numbers. The enhanced sampling methods are tested with several biological systems to illustrate their efficiency over conventional MD. Enhanced Sampler with carefully optimized system-dependent parameters will help users to get meaningful results from their enhanced sampling simulations.
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Affiliation(s)
- Donghyuk Suh
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and EngineeringLehigh UniversityBethlehemPennsylvaniaUSA
- Research Institute for Pharmaceutical Sciences, College of Pharmacy and Graduate School of Pharmaceutical SciencesEwha Womans UniversitySeoulRepublic of Korea
| | - Shasha Feng
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and EngineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Hwayoung Lee
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and EngineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Han Zhang
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and EngineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Sang‐Jun Park
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and EngineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Seonghan Kim
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and EngineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Jumin Lee
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and EngineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Sun Choi
- Research Institute for Pharmaceutical Sciences, College of Pharmacy and Graduate School of Pharmaceutical SciencesEwha Womans UniversitySeoulRepublic of Korea
| | - Wonpil Im
- Department of Biological Sciences, Chemistry, Bioengineering, and Computer Science and EngineeringLehigh UniversityBethlehemPennsylvaniaUSA
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2
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Love O, Pacheco Lima MC, Clark C, Cornillie S, Roalstad S, Cheatham TE. Evaluating the accuracy of the AMBER protein force fields in modeling dihydrofolate reductase structures: misbalance in the conformational arrangements of the flexible loop domains. J Biomol Struct Dyn 2022:1-15. [PMID: 35838167 PMCID: PMC9840716 DOI: 10.1080/07391102.2022.2098823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Protein flexible loop regions were once thought to be simple linkers between other more functional secondary structural elements. However, as it becomes clearer that these loop domains are critical players in a plethora of biological processes, accurate conformational sampling of 3D loop structures is vital to the advancement of drug design techniques and the overall growth of knowledge surrounding molecular systems. While experimental techniques provide a wealth of structural information, the resolution of flexible loop domains is sometimes low or entirely absent due to their complex and dynamic nature. This highlights an opportunity for de novo structure prediction using in silico methods with molecular dynamics (MDs). This study evaluates some of the AMBER protein force field's (ffs) ability to accurately model dihydrofolate reductase (DHFR) conformations, a protein complex characterized by specific arrangements and interactions of multiple flexible loops whose conformations are determined by the presence or absence of bound ligands and cofactors. Although the AMBER ffs, including ff19SB, studied well model most protein structures with rich secondary structure, results obtained here suggest the inability to significantly sample the expected DHFR loop-loop conformations - of the six distinct protein-ligand systems simulated, a majority lacked consistent stabilization of experimentally derived metrics definitive the three enzyme conformations. Although under-sampling and the chosen ff parameter combinations could be the cause, given past successes with these MD approaches for many protein systems, this suggests a potential misbalance in available ff parameters required to accurately predict the structure of multiple flexible loop regions present in proteins.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Olivia Love
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | | | - Casey Clark
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Sean Cornillie
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Shelly Roalstad
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Thomas E. Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
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3
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Jephthah S, Pesce F, Lindorff-Larsen K, Skepö M. Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity. J Chem Theory Comput 2021; 17:6634-6646. [PMID: 34524800 PMCID: PMC8515809 DOI: 10.1021/acs.jctc.1c00408] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Five peptides previously suggested to possess polyproline II (PPII) structure have here been investigated by using atomistic molecular dynamics simulations to compare how well four different force fields known for simulating intrinsically disordered proteins relatively well (Amber ff99SB-disp, Amber ff99SB-ILDN, CHARM36IDPSFF, and CHARMM36m) can capture this secondary structure element. The results revealed that all force fields sample PPII structures but to different extents and with different propensities toward other secondary structure elements, in particular, the β-sheet and "random coils". A cluster analysis of the simulations of histatin 5 also revealed that the conformational ensembles of the force fields are quite different. We compared the simulations to circular dichroism and nuclear magnetic resonance spectroscopy experiments and conclude that further experiments and methods for interpreting them are needed to assess the accuracy of force fields in determining PPII structure.
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Affiliation(s)
- Stéphanie Jephthah
- Division of Theoretical Chemistry, Lund University, SE-221 00 Lund, Sweden
| | - Francesco Pesce
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Marie Skepö
- Division of Theoretical Chemistry, Lund University, SE-221 00 Lund, Sweden
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4
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Tian C, Kasavajhala K, Belfon KAA, Raguette L, Huang H, Migues AN, Bickel J, Wang Y, Pincay J, Wu Q, Simmerling C. ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution. J Chem Theory Comput 2019; 16:528-552. [PMID: 31714766 DOI: 10.1021/acs.jctc.9b00591] [Citation(s) in RCA: 843] [Impact Index Per Article: 168.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular dynamics (MD) simulations have become increasingly popular in studying the motions and functions of biomolecules. The accuracy of the simulation, however, is highly determined by the molecular mechanics (MM) force field (FF), a set of functions with adjustable parameters to compute the potential energies from atomic positions. However, the overall quality of the FF, such as our previously published ff99SB and ff14SB, can be limited by assumptions that were made years ago. In the updated model presented here (ff19SB), we have significantly improved the backbone profiles for all 20 amino acids. We fit coupled φ/ψ parameters using 2D φ/ψ conformational scans for multiple amino acids, using as reference data the entire 2D quantum mechanics (QM) energy surface. We address the polarization inconsistency during dihedral parameter fitting by using both QM and MM in aqueous solution. Finally, we examine possible dependency of the backbone fitting on side chain rotamer. To extensively validate ff19SB parameters, and to compare to results using other Amber models, we have performed a total of ∼5 ms MD simulations in explicit solvent. Our results show that after amino-acid-specific training against QM data with solvent polarization, ff19SB not only reproduces the differences in amino-acid-specific Protein Data Bank (PDB) Ramachandran maps better but also shows significantly improved capability to differentiate amino-acid-dependent properties such as helical propensities. We also conclude that an inherent underestimation of helicity is present in ff14SB, which is (inexactly) compensated for by an increase in helical content driven by the TIP3P bias toward overly compact structures. In summary, ff19SB, when combined with a more accurate water model such as OPC, should have better predictive power for modeling sequence-specific behavior, protein mutations, and also rational protein design. Of the explicit water models tested here, we recommend use of OPC with ff19SB.
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Affiliation(s)
- Chuan Tian
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Koushik Kasavajhala
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Kellon A A Belfon
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Lauren Raguette
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - He Huang
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Angela N Migues
- Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - John Bickel
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Yuzhang Wang
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Jorge Pincay
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Qin Wu
- Center for Functional Nanomaterials , Brookhaven National Laboratory , Upton , New York 11973 , United States
| | - Carlos Simmerling
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
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5
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Graham KA, Byrne A, Son R, Andersen NH. Reversing the typical pH stability profile of the Trp-cage. Biopolymers 2019; 110:e23260. [PMID: 30779444 DOI: 10.1002/bip.23260] [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] [Received: 10/15/2018] [Revised: 12/14/2018] [Accepted: 01/07/2019] [Indexed: 12/18/2022]
Abstract
The Trp-cage, an 18-20 residue miniprotein, has emerged as a primary test system for evaluating computational fold prediction and folding rate determination efforts. As it turns out, a number of stabilizing interactions in the Trp-cage folded state have a strong pH dependence; all prior Trp-cage mutants have been destabilized under carboxylate-protonating conditions. Notable among the pH dependent stabilizing interactions within the Trp-cage are: (1) an Asp as the helix N-cap, (2) an H-bonded Asp9/Arg16 salt bridge, (3) an interaction between the chain termini which are in close spatial proximity, and (4) additional side chain interactions with Asp9. In the present study, we have prepared Trp-cage species that are significantly more stable at pH 2.5 (rather than 7) and quantitated the contribution of each interaction listed above. The Trp-cage structure remains constant with the pH change. The study has also provided measures of the stabilizing contribution of indole ring shielding from surface exposure and the destabilizing effects of an ionized Asp at the C-terminus of an α-helix.
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Affiliation(s)
| | - Aimee Byrne
- Department of Chemistry, University of Washington, Seattle, Washington
| | - Ruth Son
- Department of Chemistry, University of Washington, Seattle, Washington
| | - Niels H Andersen
- Department of Chemistry, University of Washington, Seattle, Washington
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6
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Hagler AT. Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics. J Comput Aided Mol Des 2018; 33:205-264. [DOI: 10.1007/s10822-018-0134-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/18/2018] [Indexed: 01/04/2023]
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7
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Cerutti DS, Debiec KT, Case DA, Chong LT. Links between the charge model and bonded parameter force constants in biomolecular force fields. J Chem Phys 2018; 147:161730. [PMID: 29096508 DOI: 10.1063/1.4985866] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The ff15ipq protein force field is a fixed charge model built by automated tools based on the two charge sets of the implicitly polarized charge method: one set (appropriate for vacuum) for deriving bonded parameters and the other (appropriate for aqueous solution) for running simulations. The duality is intended to treat water-induced electronic polarization with an understanding that fitting data for bonded parameters will come from quantum mechanical calculations in the gas phase. In this study, we compare ff15ipq to two alternatives produced with the same fitting software and a further expanded data set but following more conventional methods for tailoring bonded parameters (harmonic angle terms and torsion potentials) to the charge model. First, ff15ipq-Qsolv derives bonded parameters in the context of the ff15ipq solution phase charge set. Second, ff15ipq-Vac takes ff15ipq's bonded parameters and runs simulations with the vacuum phase charge set used to derive those parameters. The IPolQ charge model and associated protocol for deriving bonded parameters are shown to be an incremental improvement over protocols that do not account for the material phases of each source of their fitting data. Both force fields incorporating the polarized charge set depict stable globular proteins and have varying degrees of success modeling the metastability of short (5-19 residues) peptides. In this particular case, ff15ipq-Qsolv increases stability in a number of α-helices, correctly obtaining 70% helical character in the K19 system at 275 K and showing appropriately diminishing content up to 325 K, but overestimating the helical fraction of AAQAA3 by 50% or more, forming long-lived α-helices in simulations of a β-hairpin, and increasing the likelihood that the disordered p53 N-terminal peptide will also form a helix. This may indicate a systematic bias imparted by the ff15ipq-Qsolv parameter development strategy, which has the hallmarks of strategies used to develop other popular force fields, and may explain some of the need for manual corrections in this force fields' evolution. In contrast, ff15ipq-Vac incorrectly depicts globular protein unfolding in numerous systems tested, including Trp cage, villin, lysozyme, and GB3, and does not perform any better than ff15ipq or ff15ipq-Qsolv in tests on short peptides. We analyze the free energy surfaces of individual amino acid dipeptides and the electrostatic potential energy surfaces of each charge model to explain the differences.
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Affiliation(s)
- David S Cerutti
- Department of Chemistry and Chemical Biology, Rutgers University, 174 Frelinghueysen Road, Piscataway, New Jersey 08854-8066, USA
| | - Karl T Debiec
- Epic Systems, 1979 Milky Way, Verona, Wisconsin 53593, USA
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, 174 Frelinghueysen Road, Piscataway, New Jersey 08854-8066, USA
| | - Lillian T Chong
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
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8
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Strandberg E, Grau-Campistany A, Wadhwani P, Bürck J, Rabanal F, Ulrich AS. Helix Fraying and Lipid-Dependent Structure of a Short Amphipathic Membrane-Bound Peptide Revealed by Solid-State NMR. J Phys Chem B 2018; 122:6236-6250. [DOI: 10.1021/acs.jpcb.8b02661] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Erik Strandberg
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Ariadna Grau-Campistany
- Secció de Química Orgànica, Departament de Química Inorgànica i Orgànica, Facultat de Química, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Parvesh Wadhwani
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Jochen Bürck
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Francesc Rabanal
- Secció de Química Orgànica, Departament de Química Inorgànica i Orgànica, Facultat de Química, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Anne S. Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), P.O. Box 3640, 76021 Karlsruhe, Germany
- KIT, Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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9
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Onufriev AV, Izadi S. Water models for biomolecular simulations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1347] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Alexey V. Onufriev
- Department of Physics; Virginia Tech; Blacksburg VA USA
- Department of Computer Science; Virginia Tech; Blacksburg VA USA
- Center for Soft Matter and Biological Physics; Virginia Tech; Blacksburg VA USA
| | - Saeed Izadi
- Early Stage Pharmaceutical Development; Genentech Inc.; South San Francisco, CA USA
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10
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Ni G, Wang Y, Cummins S, Walton S, Mounsey K, Liu X, Wei MQ, Wang T. Inhibitory mechanism of peptides with a repeating hydrophobic and hydrophilic residue pattern on interleukin-10. Hum Vaccin Immunother 2016; 13:518-527. [PMID: 27686406 DOI: 10.1080/21645515.2016.1238537] [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: 10/20/2022] Open
Abstract
Interleukin 10 (IL-10) is a cytokine that is able to downregulate inflammation. Its overexpression is directly associated with the difficulty in the clearance of chronic viral infections, such as chronic hepatitis B, hepatitis C and HIV infection, and infection-related cancer. IL-10 signaling blockade has been proposed as a promising way of clearing chronic viral infection and preventing tumor growth in animal models. Recently, we have reported that peptides with a helical repeating pattern of hydrophobic and hydrophilic residues are able to inhibit IL-10 significantly both in vitro and in vivo. 1 In this work, we seek to further study the inhibiting mechanism of these peptides using sequence-modified peptides. As evidenced by both experimental and molecular dynamics simulation in concert the N-terminal hydrophobic peptide constructed with repeating hydrophobic and hydrophilic pattern of residues is more likely to inhibit IL10. In addition, the sequence length and the ability of protonation are also important for inhibition activity.
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Affiliation(s)
- Guoying Ni
- a Genecology Research Centre , University of the Sunshine Coast , Maroochydore , DC , Australia.,b School of Medical Science, Griffith Health Institute , Griffith University , Gold Coast , Australia
| | - Yuejian Wang
- c Cancer Research Institute, Foshan First People's Hospital , Foshan , Guangdong , China
| | - Scott Cummins
- a Genecology Research Centre , University of the Sunshine Coast , Maroochydore , DC , Australia
| | - Shelley Walton
- d Inflammation and Healing Research Cluster, School of Health and Sport Sciences , University of Sunshine Coast , Maroochydore , DC , Australia
| | - Kate Mounsey
- d Inflammation and Healing Research Cluster, School of Health and Sport Sciences , University of Sunshine Coast , Maroochydore , DC , Australia
| | - Xiaosong Liu
- c Cancer Research Institute, Foshan First People's Hospital , Foshan , Guangdong , China.,d Inflammation and Healing Research Cluster, School of Health and Sport Sciences , University of Sunshine Coast , Maroochydore , DC , Australia
| | - Ming Q Wei
- b School of Medical Science, Griffith Health Institute , Griffith University , Gold Coast , Australia
| | - Tianfang Wang
- a Genecology Research Centre , University of the Sunshine Coast , Maroochydore , DC , Australia
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11
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Anderson JM, Jurban B, Huggins KNL, Shcherbakov AA, Shu I, Kier B, Andersen NH. Nascent Hairpins in Proteins: Identifying Turn Loci and Quantitating Turn Contributions to Hairpin Stability. Biochemistry 2016; 55:5537-5553. [DOI: 10.1021/acs.biochem.6b00732] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jordan M. Anderson
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Brice Jurban
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Kelly N. L. Huggins
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | | | - Irene Shu
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Brandon Kier
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Niels H. Andersen
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
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12
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Debiec KT, Cerutti DS, Baker LR, Gronenborn AM, Case DA, Chong LT. Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model. J Chem Theory Comput 2016; 12:3926-47. [PMID: 27399642 PMCID: PMC4980686 DOI: 10.1021/acs.jctc.6b00567] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
We present the AMBER
ff15ipq force field for proteins, the second-generation
force field developed using the Implicitly Polarized Q (IPolQ) scheme
for deriving implicitly polarized atomic charges in the presence of
explicit solvent. The ff15ipq force field is a complete rederivation
including more than 300 unique atomic charges, 900 unique torsion
terms, 60 new angle parameters, and new atomic radii for polar hydrogens.
The atomic charges were derived in the context of the SPC/Eb water model, which yields more-accurate rotational diffusion of
proteins and enables direct calculation of nuclear magnetic resonance
(NMR) relaxation parameters from molecular dynamics simulations. The
atomic radii improve the accuracy of modeling salt bridge interactions
relative to contemporary fixed-charge force fields, rectifying a limitation
of ff14ipq that resulted from its use of pair-specific Lennard-Jones
radii. In addition, ff15ipq reproduces penta-alanine J-coupling constants
exceptionally well, gives reasonable agreement with NMR relaxation
rates, and maintains the expected conformational propensities of structured
proteins/peptides, as well as disordered peptides—all on the
microsecond (μs) time scale, which is a critical regime for
drug design applications. These encouraging results demonstrate the
power and robustness of our automated methods for deriving new force
fields. All parameters described here and the mdgx program used to
fit them are included in the AmberTools16 distribution.
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Affiliation(s)
- Karl T Debiec
- Molecular Biophysics and Structural Biology Graduate Program, University of Pittsburgh and Carnegie Mellon University , Pittsburgh, Pennsylvania, United States.,Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - David S Cerutti
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - Lewis R Baker
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University , New Brunswick, New Jersey 08854, United States
| | - Lillian T Chong
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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13
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Harder E, Damm W, Maple J, Wu C, Reboul M, Xiang JY, Wang L, Lupyan D, Dahlgren MK, Knight JL, Kaus JW, Cerutti DS, Krilov G, Jorgensen WL, Abel R, Friesner RA. OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins. J Chem Theory Comput 2015; 12:281-96. [PMID: 26584231 DOI: 10.1021/acs.jctc.5b00864] [Citation(s) in RCA: 2047] [Impact Index Per Article: 227.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The parametrization and validation of the OPLS3 force field for small molecules and proteins are reported. Enhancements with respect to the previous version (OPLS2.1) include the addition of off-atom charge sites to represent halogen bonding and aryl nitrogen lone pairs as well as a complete refit of peptide dihedral parameters to better model the native structure of proteins. To adequately cover medicinal chemical space, OPLS3 employs over an order of magnitude more reference data and associated parameter types relative to other commonly used small molecule force fields (e.g., MMFF and OPLS_2005). As a consequence, OPLS3 achieves a high level of accuracy across performance benchmarks that assess small molecule conformational propensities and solvation. The newly fitted peptide dihedrals lead to significant improvements in the representation of secondary structure elements in simulated peptides and native structure stability over a number of proteins. Together, the improvements made to both the small molecule and protein force field lead to a high level of accuracy in predicting protein-ligand binding measured over a wide range of targets and ligands (less than 1 kcal/mol RMS error) representing a 30% improvement over earlier variants of the OPLS force field.
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Affiliation(s)
- Edward Harder
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Wolfgang Damm
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Jon Maple
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Chuanjie Wu
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Mark Reboul
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Jin Yu Xiang
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Lingle Wang
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Dmitry Lupyan
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Markus K Dahlgren
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Jennifer L Knight
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Joseph W Kaus
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - David S Cerutti
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Goran Krilov
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - William L Jorgensen
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
| | - Robert Abel
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Richard A Friesner
- Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States
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14
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Kumar A, Campitelli P, Thorpe MF, Ozkan SB. Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics. Proteins 2015; 83:2279-92. [PMID: 26476100 DOI: 10.1002/prot.24947] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/11/2015] [Accepted: 09/29/2015] [Indexed: 12/26/2022]
Abstract
The most successful protein structure prediction methods to date have been template-based modeling (TBM) or homology modeling, which predicts protein structure based on experimental structures. These high accuracy predictions sometimes retain structural errors due to incorrect templates or a lack of accurate templates in the case of low sequence similarity, making these structures inadequate in drug-design studies or molecular dynamics simulations. We have developed a new physics based approach to the protein refinement problem by mimicking the mechanism of chaperons that rehabilitate misfolded proteins. The template structure is unfolded by selectively (targeted) pulling on different portions of the protein using the geometric based technique FRODA, and then refolded using hierarchically restrained replica exchange molecular dynamics simulations (hr-REMD). FRODA unfolding is used to create a diverse set of topologies for surveying near native-like structures from a template and to provide a set of persistent contacts to be employed during re-folding. We have tested our approach on 13 previous CASP targets and observed that this method of folding an ensemble of partially unfolded structures, through the hierarchical addition of contact restraints (that is, first local and then nonlocal interactions), leads to a refolding of the structure along with refinement in most cases (12/13). Although this approach yields refined models through advancement in sampling, the task of blind selection of the best refined models still needs to be solved. Overall, the method can be useful for improved sampling for low resolution models where certain of the portions of the structure are incorrectly modeled.
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Affiliation(s)
- Avishek Kumar
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona
| | - Paul Campitelli
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona
| | - M F Thorpe
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona.,Rudolf Peierls Center for Theoretical Physics, University of Oxford, Oxford, OX1 3NP, United Kingdom
| | - S Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona
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15
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Neelamraju S, Oakley MT, Johnston RL. Chiral effects on helicity studied via the energy landscape of short (d, l)-alanine peptides. J Chem Phys 2015; 143:165103. [DOI: 10.1063/1.4933428] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sridhar Neelamraju
- School of Chemistry, University of Birmingham, Edgbaston B15 2TT, United Kingdom
| | - Mark T. Oakley
- School of Chemistry, University of Birmingham, Edgbaston B15 2TT, United Kingdom
| | - Roy L. Johnston
- School of Chemistry, University of Birmingham, Edgbaston B15 2TT, United Kingdom
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16
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Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. J Chem Theory Comput 2015; 11:3696-713. [PMID: 26574453 DOI: 10.1021/acs.jctc.5b00255] [Citation(s) in RCA: 6521] [Impact Index Per Article: 724.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein secondary structure balance and dynamics from earlier force fields like ff99, but weaknesses in side chain rotamer and backbone secondary structure preferences have been identified. Here, we performed a complete refit of all amino acid side chain dihedral parameters, which had been carried over from ff94. The training set of conformations included multidimensional dihedral scans designed to improve transferability of the parameters. Improvement in all amino acids was obtained as compared to ff99SB. Parameters were also generated for alternate protonation states of ionizable side chains. Average errors in relative energies of pairs of conformations were under 1.0 kcal/mol as compared to QM, reduced 35% from ff99SB. We also took the opportunity to make empirical adjustments to the protein backbone dihedral parameters as compared to ff99SB. Multiple small adjustments of φ and ψ parameters were tested against NMR scalar coupling data and secondary structure content for short peptides. The best results were obtained from a physically motivated adjustment to the φ rotational profile that compensates for lack of ff99SB QM training data in the β-ppII transition region. Together, these backbone and side chain modifications (hereafter called ff14SB) not only better reproduced their benchmarks, but also improved secondary structure content in small peptides and reproduction of NMR χ1 scalar coupling measurements for proteins in solution. We also discuss the Amber ff12SB parameter set, a preliminary version of ff14SB that includes most of its improvements.
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Affiliation(s)
- James A Maier
- Graduate Program in Biochemistry and Structural Biology, ‡Department of Chemistry, and §Laufer Center for Physical and Quantitative Biology, Stony Brook University , Stony Brook, New York 11794, United States
| | - Carmenza Martinez
- Graduate Program in Biochemistry and Structural Biology, ‡Department of Chemistry, and §Laufer Center for Physical and Quantitative Biology, Stony Brook University , Stony Brook, New York 11794, United States
| | - Koushik Kasavajhala
- Graduate Program in Biochemistry and Structural Biology, ‡Department of Chemistry, and §Laufer Center for Physical and Quantitative Biology, Stony Brook University , Stony Brook, New York 11794, United States
| | - Lauren Wickstrom
- Graduate Program in Biochemistry and Structural Biology, ‡Department of Chemistry, and §Laufer Center for Physical and Quantitative Biology, Stony Brook University , Stony Brook, New York 11794, United States
| | - Kevin E Hauser
- Graduate Program in Biochemistry and Structural Biology, ‡Department of Chemistry, and §Laufer Center for Physical and Quantitative Biology, Stony Brook University , Stony Brook, New York 11794, United States
| | - Carlos Simmerling
- Graduate Program in Biochemistry and Structural Biology, ‡Department of Chemistry, and §Laufer Center for Physical and Quantitative Biology, Stony Brook University , Stony Brook, New York 11794, United States
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17
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Bea RDLS, Petraglia AF, Johnson LELD. Synthesis, antimicrobial activity and toxicity of analogs of the scorpion venom BmKn peptides. Toxicon 2015; 101:79-84. [PMID: 25982541 DOI: 10.1016/j.toxicon.2015.05.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 05/06/2015] [Accepted: 05/12/2015] [Indexed: 12/16/2022]
Abstract
Two analogs of the natural peptide BmKn1 and four of BmKn2 found in the venom of the scorpion Buthus martensii Karsh have been synthesized and tested to compare their antimicrobial and hemolytic activity with the natural ones. Modifications of the natural sequence were done on the hydrophobic side of the alpha helix by increasing the size and hydrophobicity of the residues with alanine (BmKn2A1), valine (BmKn2V1) and leucine (BmKn2L1) respectively, and on the hydrophilic side by increasing the charge from +2 to +3 with two lysines (BmKn2K7). In order to study observed peptide aggregation, two peptides with one (BmKn1-6Lys) and two (BmKn1L2K2) positive charges respectively in the hydrophobic side have been also designed. Results show that the valine substituted analog BmKn2V1 and lysine substituted analog BmKn2K7 have in general, the highest antibiotic and hemolytic activity of the group. Introduction of one positive charge on the hydrophobic side shows a significant increase in antibacterial activity compared with the original sequence except for Bacillus and Enterobacter where, unexpectedly, the activity flats-off. In contrast, the analog with two positive charges has minimal antibacterial or hemolytic activity.
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Affiliation(s)
| | - Adam Fine Petraglia
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis TN 38112, USA
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18
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Cerutti DS, Swope WC, Rice J, Case DA. ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins. J Chem Theory Comput 2014; 10:4515-4534. [PMID: 25328495 PMCID: PMC4196740 DOI: 10.1021/ct500643c] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Indexed: 01/25/2023]
Abstract
We present the ff14ipq force field, implementing the previously published IPolQ charge set for simulations of complete proteins. Minor modifications to the charge derivation scheme and van der Waals interactions between polar atoms are introduced. Torsion parameters are developed through a generational learning approach, based on gas-phase MP2/cc-pVTZ single-point energies computed of structures optimized by the force field itself rather than the quantum benchmark. In this manner, we sacrifice information about the true quantum minima in order to ensure that the force field maintains optimal agreement with the MP2/cc-pVTZ benchmark for the ensembles it will actually produce in simulations. A means of making the gas-phase torsion parameters compatible with solution-phase IPolQ charges is presented. The ff14ipq model is an alternative to ff99SB and other Amber force fields for protein simulations in programs that accommodate pair-specific Lennard-Jones combining rules. The force field gives strong performance on α-helical and β-sheet oligopeptides as well as globular proteins over microsecond time scale simulations, although it has not yet been tested in conjunction with lipid and nucleic acid models. We show how our choices in parameter development influence the resulting force field and how other choices that may have appeared reasonable would actually have led to poorer results. The tools we developed may also aid in the development of future fixed-charge and even polarizable biomolecular force fields.
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Affiliation(s)
- David S. Cerutti
- Department
of Chemistry and
Chemical Biology and BioMaPS Institute, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854-8066, United States
| | - William C. Swope
- Department
of Chemistry and
Chemical Biology and BioMaPS Institute, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854-8066, United States
| | - Julia
E. Rice
- Department
of Chemistry and
Chemical Biology and BioMaPS Institute, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854-8066, United States
| | - David A. Case
- Department
of Chemistry and
Chemical Biology and BioMaPS Institute, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854-8066, United States
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19
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Nguyen H, Roe DR, Simmerling C. Improved Generalized Born Solvent Model Parameters for Protein Simulations. J Chem Theory Comput 2013; 9:2020-2034. [PMID: 25788871 DOI: 10.1021/ct3010485] [Citation(s) in RCA: 341] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The generalized Born (GB) model is one of the fastest implicit solvent models and it has become widely adopted for Molecular Dynamics (MD) simulations. This speed comes with tradeoffs, and many reports in the literature have pointed out weaknesses with GB models. Because the quality of a GB model is heavily affected by empirical parameters used in calculating solvation energy, in this work we have refit these parameters for GB-Neck, a recently developed GB model, in order to improve the accuracy of both the solvation energy and effective radii calculations. The data sets used for fitting are significantly larger than those used in the past. Comparing to other pairwise GB models like GB-OBC and the original GB-Neck, the new GB model (GB-Neck2) has better agreement to Poisson-Boltzmann (PB) in terms of reproducing solvation energies for a variety of systems ranging from peptides to proteins. Secondary structure preferences are also in much better agreement with those obtained from explicit solvent MD simulations. We also obtain near-quantitative reproduction of experimental structure and thermal stability profiles for several model peptides with varying secondary structure motifs. Extension to non-protein systems will be explored in the future.
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Affiliation(s)
- Hai Nguyen
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794 ; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794
| | - Daniel R Roe
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794 ; Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, 84112
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794 ; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794
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20
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Vitalis A, Caflisch A. 50 Years of Lifson-Roig Models: Application to Molecular Simulation Data. J Chem Theory Comput 2011; 8:363-73. [PMID: 26592894 DOI: 10.1021/ct200744s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Simple helix-coil transition theories have been indispensable tools in the analysis of data reporting on the reversible folding of α-helical polypeptides. They provide a transferable means to not only characterize different systems but to also compare different techniques, viz., experimental probes monitoring helix-coil transitions in vitro or biomolecular force fields in silico. This article addresses several issues with the application of Lifson-Roig theory to helix-coil transition data. We use computer simulation to generate two sets of ensembles for the temperature-controlled, reversible folding of the 21-residue, alanine-rich FS peptide. Ensembles differ in the rigidity of backbone bond angles and are analyzed using two distinct descriptors of helicity. The analysis unmasks an underlying phase diagram that is surprisingly complex. The complexities give rise to fitted nucleation and propagation parameters that are difficult to interpret and that are inconsistent with the distribution of isolated residues in the α-helical basin. We show that enthalpies of helix formation are more robustly determined using van't Hoff analysis of simple measures of helicity rather than fitted propagation parameters. To overcome some of these issues, we design a simple variant of the Lifson-Roig model that recovers physical interpretability of the obtained parameters by allowing bundle formation to be described in simple fashion. The relevance of our results is discussed in relation to the applicability of Lifson-Roig models to both in silico and in vitro data.
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Affiliation(s)
- Andreas Vitalis
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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21
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Kim W, Yamato I, Ando T. Alanine-based peptides containing polar residues presumably favour α-helical structure entropically. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2010.543975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Wankee Kim
- a Quantum Bio-Informatics Center, Tokyo University of Science , 2641 Yamazaki, Noda-Shi, Chiba, 278-8510, Japan
| | - Ichiro Yamato
- b Department of Biological Science and Technology , Tokyo University of Science , 2641 Yamazaki, Noda-Shi, Chiba, 278-8510, Japan
| | - Tadashi Ando
- b Department of Biological Science and Technology , Tokyo University of Science , 2641 Yamazaki, Noda-Shi, Chiba, 278-8510, Japan
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22
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Williams DV, Byrne A, Stewart J, Andersen NH. Optimal salt bridge for Trp-cage stabilization. Biochemistry 2011; 50:1143-52. [PMID: 21222485 DOI: 10.1021/bi101555y] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gai and co-workers [Bunagan, M. R., et al. (2006) J. Phys. Chem. B 110, 3759-3763] reported computational design studies suggesting that a D9E mutation would stabilize the Trp-cage. Experimental studies for this mutation were reported in 2008 [Hudaky, P., et al. (2008) Biochemistry 47, 1007-1016]; the authors suggested that [D9E]-TC5b presented a more compact and melting resistant structure because of the "optimal distance between the two sides of the molecule". Nonetheless, the authors reported essentially the same circular dichroism (CD) melting temperature, 38 ± 0.3 °C, for TC5b and its [D9E] mutant. In this study, a more stable Trp-cage, DAYAQ WLKDG GPSSG RPPPS, was examined by nuclear magnetic resonance and CD with the following mutations: [D9E], [D9R,R16E], [R16O], [D9E,R16O], [R16K], and [D9E,R16K]. Of these, the [D9E] mutant displayed the smallest acidification-induced change in the apparent T(m). In analogy to the prior study, the CD melts of TC10b and its [D9E] mutant were, however, very similar; all of the other mutations were significantly fold destabilizing by all measures. A detailed analysis indicates that the original D9-R16 salt bridge is optimal with regard to fold cooperativity and fold stabilization. Evidence of salt bridge formation is also provided for a swapped pair, the [D9R,R16E] mutant. Model systems reveal that an ionized aspartate at the C-terminus of a helix significantly decreases intrinsic helicity, a requirement for Trp-cage fold stability. The CD evidence that was cited as supporting increased fold stability for [D9E]-TC5b at higher temperatures appears to be a reflection of increased helix stability in both the folded and unfolded states rather than a more favorable salt bridge. Our study also provides evidence of other Trp-cage stabilizing roles of the R16 side chain.
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Affiliation(s)
- D Victoria Williams
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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23
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Shu I, Stewart JM, Scian M, Kier BL, Andersen NH. β-Sheet 13C structuring shifts appear only at the H-bonded sites of hairpins. J Am Chem Soc 2011; 133:1196-9. [PMID: 21214243 DOI: 10.1021/ja1088953] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The (13)C chemical shifts measured for designed β-hairpins indicate that the structuring shifts (upfield for Cα and C', downfield for Cβ) previously reported as diagnostic for β-structuring in proteins appear only at the H-bonded strand residues. The resulting periodicity of structuring shift magnitudes is not, however, a consequence of H-bonding status; rather, it reflects a previously unrecognized alternation in the backbone torsion angles of β-strands. This feature of hairpins is also likely to be present in proteins. The study provides reference values for the expectation shifts for (13)C sites in β-structures that should prove useful in the characterization of the folding equilibria of β-sheet models.
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Affiliation(s)
- Irene Shu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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24
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Stewart JM, Lin JC, Andersen NH. Lysine and arginine residues do not increase the helicity of alanine-rich peptide helices. Chem Commun (Camb) 2008:4765-7. [PMID: 18830486 DOI: 10.1039/b807101b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The helix-disfavoring, versus alanine, propagation values of lysine (0.8) and arginine (1.0) residues placed centrally in an (Ala)(9) unit have been measured by (13)C NMR.
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Affiliation(s)
- James M Stewart
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
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