151
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Developing a molecular dynamics force field for both folded and disordered protein states. Proc Natl Acad Sci U S A 2018; 115:E4758-E4766. [PMID: 29735687 PMCID: PMC6003505 DOI: 10.1073/pnas.1800690115] [Citation(s) in RCA: 597] [Impact Index Per Article: 99.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Many proteins that perform important biological functions are completely or partially disordered under physiological conditions. Molecular dynamics simulations could be a powerful tool for the structural characterization of such proteins, but it has been unclear whether the physical models (force fields) used in simulations are sufficiently accurate. Here, we systematically compare the accuracy of a number of different force fields in simulations of both ordered and disordered proteins, finding that each force field has strengths and limitations. We then describe a force field that substantially improves on the state-of-the-art accuracy for simulations of disordered proteins without sacrificing accuracy for folded proteins, thus broadening the range of biological systems amenable to molecular dynamics simulations. Molecular dynamics (MD) simulation is a valuable tool for characterizing the structural dynamics of folded proteins and should be similarly applicable to disordered proteins and proteins with both folded and disordered regions. It has been unclear, however, whether any physical model (force field) used in MD simulations accurately describes both folded and disordered proteins. Here, we select a benchmark set of 21 systems, including folded and disordered proteins, simulate these systems with six state-of-the-art force fields, and compare the results to over 9,000 available experimental data points. We find that none of the tested force fields simultaneously provided accurate descriptions of folded proteins, of the dimensions of disordered proteins, and of the secondary structure propensities of disordered proteins. Guided by simulation results on a subset of our benchmark, however, we modified parameters of one force field, achieving excellent agreement with experiment for disordered proteins, while maintaining state-of-the-art accuracy for folded proteins. The resulting force field, a99SB-disp, should thus greatly expand the range of biological systems amenable to MD simulation. A similar approach could be taken to improve other force fields.
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152
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Borgohain G, Paul S. Atomistic level understanding of the stabilization of protein Trp cage in denaturing and mixed osmolyte solutions. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.03.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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153
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Uralcan B, Kim SB, Markwalter CE, Prud’homme RK, Debenedetti PG. A Computational Study of the Ionic Liquid-Induced Destabilization of the Miniprotein Trp-Cage. J Phys Chem B 2018; 122:5707-5715. [DOI: 10.1021/acs.jpcb.8b01722] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Betul Uralcan
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Sang Beom Kim
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Chester E. Markwalter
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Robert K. Prud’homme
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Pablo G. Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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154
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Tokunaga Y, Yamamori Y, Matubayasi N. Probabilistic analysis for identifying the driving force of protein folding. J Chem Phys 2018; 148:125101. [PMID: 29604891 DOI: 10.1063/1.5019410] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Toward identifying the driving force of protein folding, energetics was analyzed in water for Trp-cage (20 residues), protein G (56 residues), and ubiquitin (76 residues) at their native (folded) and heat-denatured (unfolded) states. All-atom molecular dynamics simulation was conducted, and the hydration effect was quantified by the solvation free energy. The free-energy calculation was done by employing the solution theory in the energy representation, and it was seen that the sum of the protein intramolecular (structural) energy and the solvation free energy is more favorable for a folded structure than for an unfolded one generated by heat. Probabilistic arguments were then developed to determine which of the electrostatic, van der Waals, and excluded-volume components of the interactions in the protein-water system governs the relative stabilities between the folded and unfolded structures. It was found that the electrostatic interaction does not correspond to the preference order of the two structures. The van der Waals and excluded-volume components were shown, on the other hand, to provide the right order of preference at probabilities of almost unity, and it is argued that a useful modeling of protein folding is possible on the basis of the excluded-volume effect.
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Affiliation(s)
- Yoshihiko Tokunaga
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Yu Yamamori
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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155
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Lee JG, Ryu JH, Kim SM, Park MY, Kim SH, Shin YG, Sohn JW, Kim HH, Park ZY, Seong JY, Kim JI. Replacement of the C-terminal Trp-cage of exendin-4 with a fatty acid improves therapeutic utility. Biochem Pharmacol 2018. [PMID: 29522713 DOI: 10.1016/j.bcp.2018.03.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Exendin-4, a 39 amino acid peptide isolated from the saliva of the Gila monster, plays an important role in regulating glucose homeostasis, and is used clinically for the treatment of type 2 diabetes. Exendin-4 shares 53% sequence identity with the incretin hormone glucagon-like peptide 1 (GLP-1) but, unlike GLP-1, is highly resistant to proteolytic enzymes such as dipeptidyl peptidase IV (DPP-IV) and neutral endopeptidase 24.11 (NEP 24.11). Herein, we focused on the structure and function of the C-terminal Trp-cage of exendin-4, and suggest that it may be structurally required for resistance to proteolysis by NEP 24.11. Using a series of substitutions and truncations of the C-terminal Trp-cage, we found that residues 1-33, including the N-terminal and helical regions of wild-type (WT) exendin-4, is the minimum motif required for both high peptidase resistance and potent activity toward the GLP-1 receptor comparable to WT exendin-4. To improve the therapeutic utility of C-terminally truncated exendin-4, we incorporated various fatty acids into exendin-4(1-33) in which Ser33 was substituted with Lys for acylation. Exendin-4(1-32)K-capric acid exhibited the most well balanced activity, with much improved therapeutic utility for regulating blood glucose and body weight relative to WT exendin-4.
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Affiliation(s)
- Jung Gi Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, 123, Cheomdangwagiro, Buk-gu, Gwangju 500-712, South Korea
| | - Jae Ha Ryu
- School of Life Sciences, Gwangju Institute of Science and Technology, 123, Cheomdangwagiro, Buk-gu, Gwangju 500-712, South Korea
| | - Seon-Myung Kim
- Rm. 206, Pilot Plant, Anygen, Gwangju Technopark, Cheomdankwagiro 333, Buk-gu, Gwangju 61008, South Korea
| | - Moon-Young Park
- Rm. 206, Pilot Plant, Anygen, Gwangju Technopark, Cheomdankwagiro 333, Buk-gu, Gwangju 61008, South Korea
| | - San-Ho Kim
- Rm. 206, Pilot Plant, Anygen, Gwangju Technopark, Cheomdankwagiro 333, Buk-gu, Gwangju 61008, South Korea
| | - Young G Shin
- College of Pharmacy, Chungnam National University, Daejeon, South Korea
| | - Jong-Woo Sohn
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Daejeon 34141, South Korea
| | - Ha Hyung Kim
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 156-756, South Korea
| | - Zee-Yong Park
- School of Life Sciences, Gwangju Institute of Science and Technology, 123, Cheomdangwagiro, Buk-gu, Gwangju 500-712, South Korea
| | - Jae Young Seong
- Graduate School of Medicine, Korea University, Anam-dong 5ga, Seongbuk-gu, Seoul 136-701, South Korea
| | - Jae Il Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, 123, Cheomdangwagiro, Buk-gu, Gwangju 500-712, South Korea; Rm. 206, Pilot Plant, Anygen, Gwangju Technopark, Cheomdankwagiro 333, Buk-gu, Gwangju 61008, South Korea.
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156
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Peter EK, Shea JE. An adaptive bias - hybrid MD/kMC algorithm for protein folding and aggregation. Phys Chem Chem Phys 2018. [PMID: 28650060 DOI: 10.1039/c7cp03035e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this paper, we present a novel hybrid Molecular Dynamics/kinetic Monte Carlo (MD/kMC) algorithm and apply it to protein folding and aggregation in explicit solvent. The new algorithm uses a dynamical definition of biases throughout the MD component of the simulation, normalized in relation to the unbiased forces. The algorithm guarantees sampling of the underlying ensemble in dependency of one average linear coupling factor 〈α〉τ. We test the validity of the kinetics in simulations of dialanine and compare dihedral transition kinetics with long-time MD-simulations. We find that for low 〈α〉τ values, kinetics are in good quantitative agreement. In folding simulations of TrpCage and TrpZip4 in explicit solvent, we also find good quantitative agreement with experimental results and prior MD/kMC simulations. Finally, we apply our algorithm to study growth of the Alzheimer Amyloid Aβ 16-22 fibril by monomer addition. We observe two possible binding modes, one at the extremity of the fibril (elongation) and one on the surface of the fibril (lateral growth), on timescales ranging from ns to 8 μs.
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Affiliation(s)
- Emanuel K Peter
- Department of Pharmacy and Chemistry, Institute of Physical and Theoretical Chemistry, University of Regensburg, Germany
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157
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Husak A, Noichl BP, Šumanovac Ramljak T, Sohora M, Škalamera Đ, Budiša N, Basarić N. Photochemical formation of quinone methides from peptides containing modified tyrosine. Org Biomol Chem 2018; 14:10894-10905. [PMID: 27812591 DOI: 10.1039/c6ob02191c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We have demonstrated that quinone methide (QM) precursors can be introduced in the peptide structure and used as photoswitchable units for peptide modifications. QM precursor 1 was prepared from protected tyrosine in the Mannich reaction, and further used as a building block in peptide synthesis. Moreover, peptides containing tyrosine can be transformed into a photoactivable QM precursor by the Mannich reaction which can afford monosubstituted derivatives 2 or bis-substituted derivatives 3. Photochemical reactivity of modified tyrosine 1 and dipeptides 2 and 3 was studied by preparative irradiation in CH3OH where photodeamination and photomethanolysis occur. QM precursors incorporated in peptides undergo photomethanolysis with quantum efficiency ΦR = 0.1-0.2, wherein the peptide backbone does not affect their photochemical reactivity. QMs formed from dipeptides were detected by laser flash photolysis (λmax ≈ 400 nm, τ = 100 μs-20 ms) and their reactivity with nucleophiles was studied. Consequently, QM precursors derived from tyrosine can be a part of the peptide backbone which can be transformed into QMs upon electronic excitation, leading to the reactions of peptides with different reagents. This proof of principle showing the ability to photochemically trigger peptide modifications and interactions with other molecules can have numerous applications in organic synthesis, materials science, biology and medicine.
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Affiliation(s)
- Antonija Husak
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia.
| | - Benjamin P Noichl
- Institute for Chemistry, Technical University Berlin, Müller-Breslau-Str. 10, 10623 Berlin, Germany
| | - Tatjana Šumanovac Ramljak
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia.
| | - Margareta Sohora
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia.
| | - Đani Škalamera
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia.
| | - Nediljko Budiša
- Institute for Chemistry, Technical University Berlin, Müller-Breslau-Str. 10, 10623 Berlin, Germany
| | - Nikola Basarić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia.
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158
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Roussel G, Caudano Y, Matagne A, Sansom MS, Perpète EA, Michaux C. Peptide-surfactant interactions: A combined spectroscopic and molecular dynamics simulation approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 190:464-470. [PMID: 28961531 DOI: 10.1016/j.saa.2017.09.056] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 06/07/2023]
Abstract
In the present contribution, we report a combined spectroscopic and computational approach aiming to unravel at atomic resolution the effect of the anionic SDS detergent on the structure of two model peptides, the α-helix TrpCage and the β-stranded TrpZip. A detailed characterization of the specific amino acids involved is performed. Monomeric (single molecules) and micellar SDS species differently interact with the α-helix and β-stranded peptides, emphasizing the different mechanisms occurring below and above the critical aggregation concentration (CAC). Below the CAC, the α-helix peptide is fully unfolded, losing its hydrophobic core and its Asp-Arg salt bridge, while the β-stranded peptide keeps its native structure with its four Trp well oriented. Above the CAC, the SDS micelles have the same effect on both peptides, that is, destabilizing the tertiary structure while keeping their secondary structure. Our studies will be helpful to deepen our understanding of the action of the denaturant SDS on peptides and proteins.
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Affiliation(s)
- Guillaume Roussel
- Department of Physiology and Biophysics, University of California, D340 Medical Sciences I, Irvine, CA 92697-4560, USA
| | - Yves Caudano
- Research Centre in Physics of Matter and Radiation (PMR), University of Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institut de Chimie B6, University of Liège, Belgium
| | - Mark S Sansom
- Department of Biochemistry, University of Oxford, South Park Road, OX13QU Oxford, United Kingdom
| | - Eric A Perpète
- Laboratory of Physical Chemistry of Biomolecules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, 61, Rue de Bruxelles, 5000 Namur, Belgium
| | - Catherine Michaux
- Laboratory of Physical Chemistry of Biomolecules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, 61, Rue de Bruxelles, 5000 Namur, Belgium.
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159
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Kovalenko A, Gusarov S. Multiscale methods framework: self-consistent coupling of molecular theory of solvation with quantum chemistry, molecular simulations, and dissipative particle dynamics. Phys Chem Chem Phys 2018; 20:2947-2969. [DOI: 10.1039/c7cp05585d] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In this work, we will address different aspects of self-consistent field coupling of computational chemistry methods at different time and length scales in modern materials and biomolecular science.
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Affiliation(s)
- Andriy Kovalenko
- National Institute for Nanotechnology
- National Research Council of Canada
- Edmonton
- Canada
- Department of Mechanical Engineering
| | - Sergey Gusarov
- National Institute for Nanotechnology
- National Research Council of Canada
- Edmonton
- Canada
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160
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Andryushchenko VA, Chekmarev SF. Turbulence in protein folding: Vorticity, scaling and diffusion of probability flows. PLoS One 2017; 12:e0188659. [PMID: 29206845 PMCID: PMC5716548 DOI: 10.1371/journal.pone.0188659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 11/10/2017] [Indexed: 11/19/2022] Open
Abstract
Recently, when studying folding of a SH3 domain, we discovered that the flows of transitions between protein states can be surprisingly similar to turbulent fluid flows. This similarity was not restricted by a vortex pattern of the flow fields but extended to a spatial correlation of flow fluctuations, resulting, in particular, in the structure functions such as in the Kolmogorov theory of homogeneous and isotropic turbulence. Here, we undertake a detailed analysis of spatial distribution of folding flows and their similarity to turbulent fluid flows. Using molecular dynamics simulations, we study folding of another benchmark system—Trp-cage miniprotein, which has different content of secondary structure elements and mechanism of folding. Calculating the probability fluxes of transitions in a three-dimensional space of collective variables, we have found that similar to the SH3 domain, the structure functions of the second and third orders correspond to the Kolmogorov functions. The spatial distributions of the probability fluxes are self-similar with a fractal dimension, and the fractal index decreases toward the native state, indicating that the flow becomes more turbulent as the native state is approached. We also show that the process of folding can be viewed as Brownian diffusion in the space of probability fluxes. The diffusion coefficient plays a role of the key parameter that defines the structures functions, similar to the rate of dissipation of kinetic energy in hydrodynamic turbulence. The obtained results, first, show that the very complex dynamics of protein folding allows a simple characterization in terms of scaling and diffusion of probability fluxes, and, secondly, they suggest that the turbulence phenomena similar to hydrodynamic turbulence are not specific of folding of a particular protein but are common to protein folding.
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Affiliation(s)
- Vladimir A. Andryushchenko
- Institute of Thermophysics, SB RAS, Novosibirsk, Russia
- Department of Physics, Novosibirsk State University, Novosibirsk, Russia
| | - Sergei F. Chekmarev
- Institute of Thermophysics, SB RAS, Novosibirsk, Russia
- Department of Physics, Novosibirsk State University, Novosibirsk, Russia
- * E-mail:
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161
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Blinov N, Khorvash M, Wishart DS, Cashman NR, Kovalenko A. Initial Structural Models of the Aβ42 Dimer from Replica Exchange Molecular Dynamics Simulations. ACS OMEGA 2017; 2:7621-7636. [PMID: 31457321 PMCID: PMC6645216 DOI: 10.1021/acsomega.7b00805] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 10/26/2017] [Indexed: 05/27/2023]
Abstract
Experimental characterization of the molecular structure of small amyloid (A)β oligomers that are currently considered as toxic agents in Alzheimer's disease is a formidably difficult task due to their transient nature and tendency to aggregate. Such structural information is of importance because it can help in developing diagnostics and an effective therapy for the disease. In this study, molecular simulations and protein-protein docking are employed to explore a possible connection between the structure of Aβ monomers and the properties of the intermonomer interface in the Aβ42 dimer. A structurally diverse ensemble of conformations of the monomer was sampled in microsecond timescale implicit solvent replica exchange molecular dynamics simulations. Representative structures with different solvent exposure of hydrophobic residues and secondary structure content were selected to build structural models of the dimer. Analysis of these models reveals that formation of an intramonomer salt bridge (SB) between Asp23 and Lys28 residues can prevent the building of a hydrophobic interface between the central hydrophobic clusters (CHCs) of monomers upon dimerization. This structural feature of the Aβ42 dimer is related to the difference in packing of hydrophobic residues in monomers with the Asp23-Lys28 SB in on and off states, in particular, to a lower propensity to form hydrophobic contacts between the CHC domain and C-terminal residues in monomers with a formed SB. These findings could have important implications for understanding the difference between aggregation pathways of Aβ monomers leading to neurotoxic oligomers or inert fibrillar structures.
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Affiliation(s)
- Nikolay Blinov
- Department
of Mechanical Engineering, University of
Alberta, Edmonton, Alberta T6G 1H9, Canada
- National
Institute for Nanotechnology, National Research
Council of Canada, Edmonton, Alberta T6G 2M9, Canada
| | - Massih Khorvash
- Department
of Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - David S. Wishart
- Departments
of Computing Science and Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E8, Canada
| | - Neil R. Cashman
- Department
of Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Andriy Kovalenko
- Department
of Mechanical Engineering, University of
Alberta, Edmonton, Alberta T6G 1H9, Canada
- National
Institute for Nanotechnology, National Research
Council of Canada, Edmonton, Alberta T6G 2M9, Canada
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162
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Amitay M, Goldstein M. Evaluating the peptide structure prediction capabilities of a purely ab-initio method. Protein Eng Des Sel 2017; 30:723-727. [PMID: 29040794 DOI: 10.1093/protein/gzx052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 09/08/2017] [Indexed: 01/25/2023] Open
Abstract
DEEPSAM is a relatively new global optimization algorithm aimed to predict the structure of bio-molecules from sequence, without any additional preliminary assumption. It is an evolutionary algorithm whose mutation operators are built by hybridizing the diffusion equation method, molecular dynamics simulated annealing, and a quasi-Newton local minimization method. The goal of this study was to evaluate the structure prediction capabilities of DEEPSAM by running it upon NMR structures of linear peptides (10-20 residues). The results indicate that DEEPSAM successfully predicted the conformations of these peptides, using modest computing resources.
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Affiliation(s)
- M Amitay
- Department of Bioinformatics, Jerusalem College of Technology, Havaad Haleumi 21, Jerusalem 9372115, Israel
| | - M Goldstein
- Department of Computer Science, Jerusalem College of Technology, Havaad Haleumi 21, Jerusalem 9372115, Israel
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163
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164
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Sieradzan AK, Lipska AG, Lubecka EA. Shielding effect in protein folding. J Mol Graph Model 2017; 79:118-132. [PMID: 29161634 DOI: 10.1016/j.jmgm.2017.10.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 10/19/2017] [Accepted: 10/20/2017] [Indexed: 01/01/2023]
Abstract
One of the most important interactions responsible for protein folding and stability are hydrogen bonds between peptide groups. There is a constant competition between the water molecules and peptide groups in a hydrogen bond formation. Also side-chains take part in this process by reducing hydration of peptide group (shielding effect) that promotes the protein folding. In this paper, a new approach to take into account a shielding effect is presented. A modification of the energy function is derived and incorporated into the UNited RESidue (UNRES) force field. Canonical Molecular Dynamics and Replica Exchange Molecular Dynamics with UNRES force field is applied to study the influence of this effect on protein structure, folding kinetics and free energy landscapes. The results of test calculations suggest that even small contribution of this effect into energy function changes force field behavior as well as speeds up the folding process significantly.
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Affiliation(s)
- Adam K Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Agnieszka G Lipska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Emilia A Lubecka
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; Institute of Informatics, University of Gdańsk, Wita Stwosza 57, 80-308 Gdańsk, Poland
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165
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Zhao D, Song R, Li W, Ma J, Dong H, Li S. Accurate Prediction of NMR Chemical Shifts in Macromolecular and Condensed-Phase Systems with the Generalized Energy-Based Fragmentation Method. J Chem Theory Comput 2017; 13:5231-5239. [DOI: 10.1021/acs.jctc.7b00380] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dongbo Zhao
- Key
Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute
of Theoretical and Computational Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
- Kuang
Yaming Honors School, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Ruiheng Song
- Kuang
Yaming Honors School, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Wei Li
- Key
Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute
of Theoretical and Computational Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Jing Ma
- Key
Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute
of Theoretical and Computational Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Hao Dong
- Kuang
Yaming Honors School, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Shuhua Li
- Key
Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute
of Theoretical and Computational Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
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166
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Goyal S, Chattopadhyay A, Kasavajhala K, Priyakumar UD. Role of Urea–Aromatic Stacking Interactions in Stabilizing the Aromatic Residues of the Protein in Urea-Induced Denatured State. J Am Chem Soc 2017; 139:14931-14946. [DOI: 10.1021/jacs.7b05463] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Siddharth Goyal
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - Aditya Chattopadhyay
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - Koushik Kasavajhala
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - U. Deva Priyakumar
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
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167
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Andryushchenko VA, Chekmarev SF. Temperature evolution of Trp-cage folding pathways: An analysis by dividing the probability flux field into stream tubes. J Biol Phys 2017; 43:565-583. [PMID: 28983809 DOI: 10.1007/s10867-017-9470-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 09/01/2017] [Indexed: 11/25/2022] Open
Abstract
Owing to its small size and very fast folding rate, the Trp-cage miniprotein has become a benchmark system to study protein folding. Two folding pathways were found to be characteristic of this protein: pathway I, in which the hydrophobic collapse precedes the formation of α-helix, and pathway II, in which the events occur in the reverse order. At the same time, the relative contribution of these pathways at different temperatures as well as the nature of transition from one pathway to the other remain unclear. To gain insight into this issue, we employ a recently proposed hydrodynamic description of protein folding, in which the process of folding is considered as a motion of a "folding fluid" (Chekmarev et al., Phys. Rev. Lett. 100(1), 018107 2008). Using molecular dynamics simulations, we determine the field of probability fluxes of transitions in a space of collective variables and divide it into stream tubes. Each tube contains a definite fraction of the total folding flow and can be associated with a certain pathway. Specifically, three temperatures were considered, T = 285K, T = 315K, and T = 325K. We have found that as the temperature increases, the contribution of pathway I, which is approximately 90% of the total folding flow at T = 285K, decreases to approximately 10% at T = 325K, i.e., pathway II becomes dominant. At T = 315K, both pathways contribute approximately equally. All these temperatures are found below the calculated melting point, which suggests that the Trp-cage folding mechanism is determined by kinetic factors rather than thermodynamics.
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Affiliation(s)
- Vladimir A Andryushchenko
- Institute of Thermophysics, SB RAS, 630090, Novosibirsk, Russia
- Department of Physics, Novosibirsk State University, 630090, Novosibirsk, Russia
| | - Sergei F Chekmarev
- Institute of Thermophysics, SB RAS, 630090, Novosibirsk, Russia.
- Department of Physics, Novosibirsk State University, 630090, Novosibirsk, Russia.
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168
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Ion-induced alterations of the local hydration environment elucidate Hofmeister effect in a simple classical model of Trp-cage miniprotein. J Mol Model 2017; 23:298. [PMID: 28956172 DOI: 10.1007/s00894-017-3471-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 09/10/2017] [Indexed: 10/18/2022]
Abstract
Protein stability is known to be influenced by the presence of Hofmeister active ions in the solution. In addition to direct ion-protein interactions, this influence manifests through the local alterations of the interfacial water structure induced by the anions and cations present in this region. In our earlier works it was pointed out that the effects of Hofmeister active salts on the stability of Trp-cage miniprotein can be modeled qualitatively using non-polarizable force fields. These simulations reproduced the structure-stabilization and structure-destabilization effects of selected kosmotropic and chaotropic salts, respectively. In the present study we use the same model system to elucidate atomic processes behind the chaotropic destabilization and kosmotropic stabilization of the miniprotein. We focus on changes of the local hydration environment of the miniprotein upon addition of NaClO4 and NaF salts to the solution. The process is separated into two parts. In the first, 'promotion' phase, the protein structure is fixed, and the local hydration properties induced by the simultaneous presence of protein and ions are investigated, with a special focus on the interaction of Hofmeister active anions with the charged and polar sites. In the second, 'rearrangement' phase we follow changes of the hydration of ions and the protein, accompanying the conformational relaxation of the protein. We identify significant factors of an enthalpic and entropic nature behind the ion-induced free energy changes of the protein-water system, and also propose a possible atomic mechanism consistent with the Collins's rule, for the chaotropic destabilization and kosmotropic stabilization of protein conformation.
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169
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Baker EG, Bartlett GJ, Porter Goff KL, Woolfson DN. Miniprotein Design: Past, Present, and Prospects. Acc Chem Res 2017; 50:2085-2092. [PMID: 28832117 DOI: 10.1021/acs.accounts.7b00186] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The design and study of miniproteins, that is, polypeptide chains <40 amino acids in length that adopt defined and stable 3D structures, is resurgent. Miniproteins offer possibilities for reducing the complexity of larger proteins and so present new routes to studying sequence-to-structure and sequence-to-stability relationships in proteins generally. They also provide modules for protein design by pieces and, with this, prospects for building more-complex or even entirely new protein structures. In addition, miniproteins are useful scaffolds for templating functional domains, for example, those involved in protein-protein interactions, catalysis, and biomolecular binding, leading to potential applications in biotechnology and medicine. Here we select examples from almost four decades of miniprotein design, development, and dissection. Simply because of the word limit for this Account, we focus on miniproteins that are cooperatively folded monomers in solution and not stabilized by cross-linking or metal binding. In these cases, the optimization of noncovalent interactions is even more critical for the maintenance of the folded states than in larger proteins. Our chronology and catalogue highlights themes in miniproteins, which we explore further and begin to put on a firmer footing through an analysis of the miniprotein structures that have been deposited in the Protein Data Bank (PDB) thus far. Specifically, and compared with larger proteins, miniproteins generally have a lower proportion of residues in regular secondary structure elements (α helices, β strands, and polyproline-II helices) and, concomitantly, more residues in well-structured loops. This allows distortions of the backbone enabling mini-hydrophobic cores to be made. This also contrasts with larger proteins, which can achieve hydrophobic cores through tertiary contacts between distant regions of sequence. On average, miniproteins have a higher proportion of aromatic residues than larger proteins, and specifically electron-rich Trp and Tyr, which are often found in combination with Pro and Arg to render networks of CH-π or cation-π interactions. Miniproteins also have a higher proportion of the long-chain charged amino acids (Arg, Glu, and Lys), which presumably reflects salt-bridge formation and their greater surface area-to-volume ratio. Together, these amino-acid preferences appear to support greater densities of noncovalent interactions in miniproteins compared with larger proteins. We anticipate that with recent developments such as parametric protein design, it will become increasingly routine to use computation to generate and evaluate models for miniproteins in silico ahead of experimental studies. This could include accessing new structures comprising secondary structure elements linked in previously unseen configurations. The improved understanding of the noncovalent interactions that stabilize the folded states of such miniproteins that we are witnessing through both in-depth bioinformatics analyses and experimental testing will feed these computational protein designs. With this in mind, we can expect a new and exciting era for miniprotein design, study, and application.
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Affiliation(s)
- Emily G. Baker
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Gail J. Bartlett
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | | | - Derek N. Woolfson
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- School
of Biochemistry, University of Bristol, Biomedical Sciences Building, University
Walk, Bristol BS8 1TD, U.K
- BrisSynBio
and the Bristol BioDesign Institute, University of Bristol, Life Sciences
Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
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170
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Cieplak AS. Protein folding, misfolding and aggregation: The importance of two-electron stabilizing interactions. PLoS One 2017; 12:e0180905. [PMID: 28922400 PMCID: PMC5603215 DOI: 10.1371/journal.pone.0180905] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022] Open
Abstract
Proteins associated with neurodegenerative diseases are highly pleiomorphic and may adopt an all-α-helical fold in one environment, assemble into all-β-sheet or collapse into a coil in another, and rapidly polymerize in yet another one via divergent aggregation pathways that yield broad diversity of aggregates’ morphology. A thorough understanding of this behaviour may be necessary to develop a treatment for Alzheimer’s and related disorders. Unfortunately, our present comprehension of folding and misfolding is limited for want of a physicochemical theory of protein secondary and tertiary structure. Here we demonstrate that electronic configuration and hyperconjugation of the peptide amide bonds ought to be taken into account to advance such a theory. To capture the effect of polarization of peptide linkages on conformational and H-bonding propensity of the polypeptide backbone, we introduce a function of shielding tensors of the Cα atoms. Carrying no information about side chain-side chain interactions, this function nonetheless identifies basic features of the secondary and tertiary structure, establishes sequence correlates of the metamorphic and pH-driven equilibria, relates binding affinities and folding rate constants to secondary structure preferences, and manifests common patterns of backbone density distribution in amyloidogenic regions of Alzheimer’s amyloid β and tau, Parkinson’s α-synuclein and prions. Based on those findings, a split-intein like mechanism of molecular recognition is proposed to underlie dimerization of Aβ, tau, αS and PrPC, and divergent pathways for subsequent association of dimers are outlined; a related mechanism is proposed to underlie formation of PrPSc fibrils. The model does account for: (i) structural features of paranuclei, off-pathway oligomers, non-fibrillar aggregates and fibrils; (ii) effects of incubation conditions, point mutations, isoform lengths, small-molecule assembly modulators and chirality of solid-liquid interface on the rate and morphology of aggregation; (iii) fibril-surface catalysis of secondary nucleation; and (iv) self-propagation of infectious strains of mammalian prions.
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Affiliation(s)
- Andrzej Stanisław Cieplak
- Department of Chemistry, Bilkent University, Ankara, Turkey
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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171
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De S, Chi B, Granier T, Qi T, Maurizot V, Huc I. Designing cooperatively folded abiotic uni- and multimolecular helix bundles. Nat Chem 2017; 10:51-57. [PMID: 29256508 DOI: 10.1038/nchem.2854] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 07/27/2017] [Indexed: 01/09/2023]
Abstract
Abiotic foldamers, that is foldamers that have backbones chemically remote from peptidic and nucleotidic skeletons, may give access to shapes and functions different to those of peptides and nucleotides. However, design methodologies towards abiotic tertiary and quaternary structures are yet to be developed. Here we report rationally designed interactional patterns to guide the folding and assembly of abiotic helix bundles. Computational design facilitated the introduction of hydrogen-bonding functionalities at defined locations on the aromatic amide backbones that promote cooperative folding into helix-turn-helix motifs in organic solvents. The hydrogen-bond-directed aggregation of helices not linked by a turn unit produced several thermodynamically and kinetically stable homochiral dimeric and trimeric bundles with structures that are distinct from the designed helix-turn-helix. Relative helix orientation within the bundles may be changed from parallel to tilted on subtle solvent variations. Altogether, these results prefigure the richness and uniqueness of abiotic tertiary structure behaviour.
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Affiliation(s)
- Soumen De
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
| | - Bo Chi
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
| | - Thierry Granier
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
| | - Ting Qi
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
| | - Victor Maurizot
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
| | - Ivan Huc
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
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172
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Su Z, Mahmoudinobar F, Dias CL. Effects of Trimethylamine-N-oxide on the Conformation of Peptides and its Implications for Proteins. PHYSICAL REVIEW LETTERS 2017; 119:108102. [PMID: 28949191 DOI: 10.1103/physrevlett.119.108102] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Indexed: 05/16/2023]
Abstract
To provide insights into the stabilizing mechanisms of trimethylamine-N-oxide (TMAO) on protein structures, we perform all-atom molecular dynamics simulations of peptides and the Trp-cage miniprotein. The effects of TMAO on the backbone and charged residues of peptides are found to stabilize compact conformations, whereas effects of TMAO on nonpolar residues lead to peptide swelling. This suggests competing mechanisms of TMAO on proteins, which accounts for hydrophobic swelling, backbone collapse, and stabilization of charge-charge interactions. These mechanisms are observed in Trp cage.
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Affiliation(s)
- Zhaoqian Su
- Physics Department, New Jersey Institute of Technology, Newark, 07102-1982 New Jersey, USA
| | - Farbod Mahmoudinobar
- Physics Department, New Jersey Institute of Technology, Newark, 07102-1982 New Jersey, USA
| | - Cristiano L Dias
- Physics Department, New Jersey Institute of Technology, Newark, 07102-1982 New Jersey, USA
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173
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Harada R, Shigeta Y. Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins. J Comput Chem 2017; 38:2671-2674. [PMID: 28861895 DOI: 10.1002/jcc.25060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/11/2017] [Accepted: 08/14/2017] [Indexed: 11/12/2022]
Abstract
Parallel cascade selection molecular dynamics (PaCS-MD) is an enhanced conformational sampling method for searching structural transition pathways from a given reactant to a product. Recently, a temperature-aided PaCS-MD (Vinod et al., Eur. Biophys. J. 2016, 45, 463) has been proposed as its extension, in which the temperatures were introduced as additional parameters in conformational resampling, whereas the temperature is fixed in the original PaCS-MD. In the present study, temperature-shuffled PaCS-MD is proposed as a further extension of temperature-aided PaCS-MD in which the temperatures are shuffled among different replicas at the beginning of each cycle of conformational resampling. To evaluate their conformational sampling efficiencies, the original, temperature-aided, and temperature-shuffled PaCS-MD were applied to a protein-folding process of Trp-cage, and their minimum computational costs to identify the native state were addressed. Through the evaluation, it was confirmed that temperature-shuffled PaCS-MD remarkably accelerated the protein-folding process of Trp-cage compared with the other methods. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Ryuhei Harada
- Division of Life Science, Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Yasuteru Shigeta
- Division of Life Science, Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
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174
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Tabassum N, Tae HS, Jia X, Kaas Q, Jiang T, Adams DJ, Yu R. Role of Cys I-Cys III Disulfide Bond on the Structure and Activity of α-Conotoxins at Human Neuronal Nicotinic Acetylcholine Receptors. ACS OMEGA 2017; 2:4621-4631. [PMID: 30023726 PMCID: PMC6044955 DOI: 10.1021/acsomega.7b00639] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/04/2017] [Indexed: 06/08/2023]
Abstract
α-Conotoxins preferentially antagonize muscle and neuronal nicotinic acetylcholine receptors (nAChRs). Native α-conotoxins have two disulfide links, CI-CIII and CII-CIV, and owing to the inherent properties of disulfide bonds, α-conotoxins have been systematically engineered to improve their chemical and biological properties. In this study, we explored the possibility of simplifying the disulfide framework of α-conotoxins Vc1.1, BuIA, ImI, and AuIB, by introducing [C2H,C8F] modification to the CI-CIII bond. We therefore explored the possibility of using hydrophobic packing of standard amino acid side chains to replace disulfide bonds as an alternative strategy to nonnatural amino acid cross-links. The impact of CI-CIII disulfide bond replacement on the conformation of the α-conotoxins was investigated using molecular dynamics (MD) simulations and nuclear magnetic resonance chemical shift index study. Two-electrode voltage clamp techniques and MD simulations were used to study the impact of disulfide bond deletion on the activities of the peptides at human neuronal nAChRs. All disulfide-deleted variants except ImI[C2H,C8F] had reduced potency for inhibiting nAChRs. Our results suggest that the CI-CIII disulfide bond is important to stabilize the secondary structure of α-conotoxins as well as their interaction with neuronal nAChR targets. Results from this study enrich our understanding of the function of the CI-CIII disulfide bond and are useful in guiding future structural engineering of the α-conotoxins.
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Affiliation(s)
- Nargis Tabassum
- Key
Laboratory of Marine Drugs, Chinese Ministry of Education, School
of Medicine and Pharmacy, Ocean University
of China, Qingdao 266003, China
- Laboratory
for Marine Drugs and Bioproducts of Qingdao National Laboratory for
Marine Science and Technology, Qingdao 266003, China
| | - Han-Shen Tae
- Illawarra
Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Xinying Jia
- The Centre for Advanced Imaging and Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072 Australia
| | - Quentin Kaas
- The Centre for Advanced Imaging and Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072 Australia
| | - Tao Jiang
- Key
Laboratory of Marine Drugs, Chinese Ministry of Education, School
of Medicine and Pharmacy, Ocean University
of China, Qingdao 266003, China
| | - David J. Adams
- Illawarra
Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Rilei Yu
- Key
Laboratory of Marine Drugs, Chinese Ministry of Education, School
of Medicine and Pharmacy, Ocean University
of China, Qingdao 266003, China
- Laboratory
for Marine Drugs and Bioproducts of Qingdao National Laboratory for
Marine Science and Technology, Qingdao 266003, China
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175
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Seibert J, Bannwarth C, Grimme S. Biomolecular Structure Information from High-Speed Quantum Mechanical Electronic Spectra Calculation. J Am Chem Soc 2017; 139:11682-11685. [DOI: 10.1021/jacs.7b05833] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jakob Seibert
- Mulliken Center for Theoretical
Chemistry, University of Bonn, D-53115 Bonn, Germany
| | - Christoph Bannwarth
- Mulliken Center for Theoretical
Chemistry, University of Bonn, D-53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical
Chemistry, University of Bonn, D-53115 Bonn, Germany
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176
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Shao Q, Zhu W. Effective Conformational Sampling in Explicit Solvent with Gaussian Biased Accelerated Molecular Dynamics. J Chem Theory Comput 2017; 13:4240-4252. [DOI: 10.1021/acs.jctc.7b00242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Qiang Shao
- Drug
Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi
Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weiliang Zhu
- Drug
Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi
Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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177
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Holub JM. Small Scaffolds, Big Potential: Developing Miniature Proteins as Therapeutic Agents. Drug Dev Res 2017; 78:268-282. [PMID: 28799168 DOI: 10.1002/ddr.21408] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 07/26/2017] [Indexed: 12/14/2022]
Abstract
Preclinical Research Miniature proteins are a class of oligopeptide characterized by their short sequence lengths and ability to adopt well-folded, three-dimensional structures. Because of their biomimetic nature and synthetic tractability, miniature proteins have been used to study a range of biochemical processes including fast protein folding, signal transduction, catalysis and molecular transport. Recently, miniature proteins have been gaining traction as potential therapeutic agents because their small size and ability to fold into defined tertiary structures facilitates their development as protein-based drugs. This research overview discusses emerging developments involving the use of miniature proteins as scaffolds to design novel therapeutics for the treatment and study of human disease. Specifically, this review will explore strategies to: (i) stabilize miniature protein tertiary structure; (ii) optimize biomolecular recognition by grafting functional epitopes onto miniature protein scaffolds; and (iii) enhance cytosolic delivery of miniature proteins through the use of cationic motifs that facilitate endosomal escape. These objectives are discussed not only to address challenges in developing effective miniature protein-based drugs, but also to highlight the tremendous potential miniature proteins hold for combating and understanding human disease. Drug Dev Res 78 : 268-282, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Justin M Holub
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
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178
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Tennyson RL, Walker SN, Ikeda T, Harris RS, McNaughton BR. Evaluation of sequence variability in HIV-1 gp41 C-peptide helix-grafted proteins. Bioorg Med Chem 2017; 26:1220-1224. [PMID: 28811070 DOI: 10.1016/j.bmc.2017.07.064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 07/24/2017] [Accepted: 07/31/2017] [Indexed: 12/11/2022]
Abstract
Many therapeutically-relevant protein-protein interactions (PPIs) have been reported that feature a helix and helix-binding cleft at the interface. Given this, different approaches to disrupting such PPIs have been developed. While short peptides (<15 amino acids) typically do not fold into a stable helix, researchers have reported chemical approaches to constraining helix structure. However, these approaches rely on laborious, and often expensive, chemical synthesis and purification. Our premise is that protein-based solutions that stabilize a therapeutically-relevant helix offer a number of advantages. In contrast to chemically constrained helical peptides, or minimal/miniature proteins, which must be synthesized (at great expense and labor), a protein can be expressed in a cellular system (like all current protein therapeutics). If selected properly, the protein scaffold can stabilize the therapeutically-relevant helix. We recently reported a protein engineering strategy, which we call "helix-grafted display", and applied it to the challenge of suppressing HIV entry. We have reported helix-grafted display proteins that inhibit formation of an intramolecular PPI involving HIV gp41 C-peptide helix, and HIV gp41 N-peptide trimer, which contain C-peptide helix-binding clefts. Here, we used yeast display to screen a library of grafted C-peptide helices for N-peptide trimer recognition. Using 'hits' from yeast display library screening, we evaluated the effect helix mutations have on structure, expression, stability, function (target recognition), and suppression of HIV entry.
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Affiliation(s)
- Rachel L Tennyson
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Susanne N Walker
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Terumasa Ikeda
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, USA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, USA
| | - Brian R McNaughton
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA; Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, USA.
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179
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Wu HN, Jiang F, Wu YD. Significantly Improved Protein Folding Thermodynamics Using a Dispersion-Corrected Water Model and a New Residue-Specific Force Field. J Phys Chem Lett 2017; 8:3199-3205. [PMID: 28651056 DOI: 10.1021/acs.jpclett.7b01213] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
An accurate potential energy model is crucial for biomolecular simulations. Despite many recent improvements of classical protein force fields, there are remaining key issues: much weaker temperature dependence of folding/unfolding equilibrium and overly collapsed unfolded or disordered states. For the latter problem, a new water model (TIP4P-D) has been proposed to correct the significantly underestimated water dispersion interactions. Here, using TIP4P-D, we reveal problems in current force fields through failures in folding model systems (a polyalanine peptide, Trp-cage, and the GB1 hairpin). By using residue-specific parameters to achieve better match between amino acid sequences and native structures and adding a small H-bond correction to partially compensate the missing many-body effects in α-helix formation, the new RSFF2+ force field with the TIP4P-D water model can excellently reproduce experimental melting curves of both α-helical and β-hairpin systems. The RSFF2+/TIP4P-D method also gives less collapsed unfolded structures and describes well folded proteins simultaneously.
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Affiliation(s)
- Hao-Nan Wu
- Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School , Shenzhen 518055, China
| | - Fan Jiang
- Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School , Shenzhen 518055, China
| | - Yun-Dong Wu
- Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School , Shenzhen 518055, China
- College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
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180
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Giussani A, Marcheselli J, Mukamel S, Garavelli M, Nenov A. On the Simulation of Two-dimensional Electronic Spectroscopy of Indole-containing Peptides. Photochem Photobiol 2017; 93:1368-1380. [PMID: 28380692 DOI: 10.1111/php.12770] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 02/27/2017] [Indexed: 01/27/2023]
Abstract
A benchmark study of low-cost multiconfigurational CASSCF/CASPT2 schemes for computing the electronic structure of indole is presented. This facilitates the simulation of near-ultraviolet (UV) pump visible (VIS) probe (i.e. two-color) two-dimensional electronic spectra (2DES) of homo- and hetero-aggregates as well as for processing of multiple snapshots from molecular dynamics simulations. Fingerprint excited-state absorption signatures of indole are identified in a broad spectral window between 10 and 25 k cm-1 . The 18-24 k cm-1 spectral window which has no absorption of the monomer and noninteracting aggregates is ideally suited to embed charge-transfer signatures in stacked aggregates. The small peptide Trp-cage, containing a tryptophan and a tyrosine amino acids, having indole and phenol as side chains, respectively, serves to prove the concept. Clear charge-transfer signatures are found in the proposed spectral window for an interchromophore distance of 5 Å making near-UV pump VIS probe 2DES a suitable technique for resolving closely packed aggregates. We demonstrate that 2DES utilizing ultra-short pulses has the potential to resolve the nature of the spectroscopically resolved electronic states and that the line shapes of the excited-state absorption signals can be correlated to the polarity of the relevant states.
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Affiliation(s)
- Angelo Giussani
- Dipartimento di Chimica "G. Ciamician", Università degli Studi di Bologna, Bologna, Italy
| | | | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, CA
| | - Marco Garavelli
- Dipartimento di Chimica "G. Ciamician", Università degli Studi di Bologna, Bologna, Italy.,Dipartimento di Chimica Industriale "Toso Montanari", Universita degli Studi di Bologna, Bologna, Italy
| | - Artur Nenov
- Dipartimento di Chimica "G. Ciamician", Università degli Studi di Bologna, Bologna, Italy.,Dipartimento di Chimica Industriale "Toso Montanari", Universita degli Studi di Bologna, Bologna, Italy
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181
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Chalyavi F, Hogle DG, Tucker MJ. Tyrosine as a Non-perturbing Site-Specific Vibrational Reporter for Protein Dynamics. J Phys Chem B 2017; 121:6380-6389. [DOI: 10.1021/acs.jpcb.7b04999] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Farzaneh Chalyavi
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - David G. Hogle
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - Matthew J. Tucker
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557, United States
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182
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Harada R, Shigeta Y. How Does the Number of Initial Structures Affect the Conformational Sampling Efficiency and Quality in Parallel Cascade Selection Molecular Dynamics (PaCS-MD)? CHEM LETT 2017. [DOI: 10.1246/cl.170207] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577
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183
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Baker EG, Williams C, Hudson KL, Bartlett GJ, Heal JW, Porter Goff KL, Sessions RB, Crump MP, Woolfson DN. Engineering protein stability with atomic precision in a monomeric miniprotein. Nat Chem Biol 2017; 13:764-770. [PMID: 28530710 DOI: 10.1038/nchembio.2380] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 02/27/2017] [Indexed: 02/04/2023]
Abstract
Miniproteins simplify the protein-folding problem, allowing the dissection of forces that stabilize protein structures. Here we describe PPα-Tyr, a designed peptide comprising an α-helix buttressed by a polyproline II helix. PPα-Tyr is water soluble and monomeric, and it unfolds cooperatively with a midpoint unfolding temperature (TM) of 39 °C. NMR structures of PPα-Tyr reveal proline residues docked between tyrosine side chains, as designed. The stability of PPα is sensitive to modifications in the aromatic residues: replacing tyrosine with phenylalanine, i.e., changing three solvent-exposed hydroxyl groups to protons, reduces the TM to 20 °C. We attribute this result to the loss of CH-π interactions between the aromatic and proline rings, which we probe by substituting the aromatic residues with nonproteinogenic side chains. In analyses of natural protein structures, we find a preference for proline-tyrosine interactions over other proline-containing pairs, and observe abundant CH-π interactions in biologically important complexes between proline-rich ligands and SH3 and similar domains.
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Affiliation(s)
- Emily G Baker
- School of Chemistry, University of Bristol, Bristol, UK
| | - Christopher Williams
- School of Chemistry, University of Bristol, Bristol, UK.,BrisSynBio, University of Bristol, Bristol, UK
| | | | | | - Jack W Heal
- School of Chemistry, University of Bristol, Bristol, UK
| | | | - Richard B Sessions
- BrisSynBio, University of Bristol, Bristol, UK.,School of Biochemistry, University of Bristol, Bristol, UK
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Bristol, UK.,BrisSynBio, University of Bristol, Bristol, UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, UK.,BrisSynBio, University of Bristol, Bristol, UK.,School of Biochemistry, University of Bristol, Bristol, UK
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184
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Evers A, Haack T, Lorenz M, Bossart M, Elvert R, Henkel B, Stengelin S, Kurz M, Glien M, Dudda A, Lorenz K, Kadereit D, Wagner M. Design of Novel Exendin-Based Dual Glucagon-like Peptide 1 (GLP-1)/Glucagon Receptor Agonists. J Med Chem 2017; 60:4293-4303. [DOI: 10.1021/acs.jmedchem.7b00174] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Andreas Evers
- R&D, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Torsten Haack
- R&D, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Martin Lorenz
- R&D, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Martin Bossart
- R&D, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Ralf Elvert
- R&D, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Bernd Henkel
- R&D, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Siegfried Stengelin
- R&D, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Michael Kurz
- R&D, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Maike Glien
- R&D, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Angela Dudda
- R&D, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Katrin Lorenz
- R&D, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Dieter Kadereit
- R&D, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Michael Wagner
- R&D, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
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185
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186
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Koole C, Reynolds CA, Mobarec JC, Hick C, Sexton PM, Sakmar TP. Genetically encoded photocross-linkers determine the biological binding site of exendin-4 peptide in the N-terminal domain of the intact human glucagon-like peptide-1 receptor (GLP-1R). J Biol Chem 2017; 292:7131-7144. [PMID: 28283573 PMCID: PMC5409479 DOI: 10.1074/jbc.m117.779496] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/09/2017] [Indexed: 12/25/2022] Open
Abstract
The glucagon-like peptide-1 receptor (GLP-1R) is a key therapeutic target in the management of type II diabetes mellitus, with actions including regulation of insulin biosynthesis and secretion, promotion of satiety, and preservation of β-cell mass. Like most class B G protein-coupled receptors (GPCRs), there is limited knowledge linking biological activity of the GLP-1R with the molecular structure of an intact, full-length, and functional receptor·ligand complex. In this study, we have utilized genetic code expansion to site-specifically incorporate the photoactive amino acid p-azido-l-phenylalanine (azF) into N-terminal residues of a full-length functional human GLP-1R in mammalian cells. UV-mediated photolysis of azF was then carried out to induce targeted photocross-linking to determine the proximity of the azido group in the mutant receptor with the peptide exendin-4. Cross-linking data were compared directly with the crystal structure of the isolated N-terminal extracellular domain of the GLP-1R in complex with exendin(9-39), revealing both similarities as well as distinct differences in the mode of interaction. Generation of a molecular model to accommodate the photocross-linking constraints highlights the potential influence of environmental conditions on the conformation of the receptor·peptide complex, including folding dynamics of the peptide and formation of dimeric and higher order oligomeric receptor multimers. These data demonstrate that crystal structures of isolated receptor regions may not give a complete reflection of peptide/receptor interactions and should be combined with additional experimental constraints to reveal peptide/receptor interactions occurring in the dynamic, native, and full-length receptor state.
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Affiliation(s)
- Cassandra Koole
- From the Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065
| | - Christopher A Reynolds
- the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Juan C Mobarec
- the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Caroline Hick
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia, and
| | - Patrick M Sexton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia, and
| | - Thomas P Sakmar
- From the Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065,
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187
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D'Souza A, Wu X, Yeow EKL, Bhattacharjya S. Designed Heme-Cage β-Sheet Miniproteins. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702472] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Areetha D'Souza
- School of Biological Sciences; Nanyang Technological University; Singapore 637551 Singapore
| | - Xiangyang Wu
- School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore 637371 Singapore
| | - Edwin Kok Lee Yeow
- School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore 637371 Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences; Nanyang Technological University; Singapore 637551 Singapore
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188
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D'Souza A, Wu X, Yeow EKL, Bhattacharjya S. Designed Heme-Cage β-Sheet Miniproteins. Angew Chem Int Ed Engl 2017; 56:5904-5908. [PMID: 28440962 DOI: 10.1002/anie.201702472] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Indexed: 01/21/2023]
Abstract
The structure and function of naturally occurring proteins are governed by a large number of amino acids (≥100). The design of miniature proteins with desired structures and functions not only substantiates our knowledge about proteins but can also contribute to the development of novel applications. Excellent progress has been made towards the design of helical proteins with diverse functions. However, the development of functional β-sheet proteins remains challenging. Herein, we describe the construction and characterization of four-stranded β-sheet miniproteins made up of about 19 amino acids that bind heme inside a hydrophobic binding pocket or "heme cage" by bis-histidine coordination in an aqueous environment. The designed miniproteins bound to heme with high affinity comparable to that of native heme proteins. Atomic-resolution structures confirmed the presence of a four-stranded β-sheet fold. The heme-protein complexes also exhibited high stability against thermal and chaotrope-induced unfolding.
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Affiliation(s)
- Areetha D'Souza
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Xiangyang Wu
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Edwin Kok Lee Yeow
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
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189
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Protein Stability and Unfolding Following Glycine Radical Formation. Molecules 2017; 22:molecules22040655. [PMID: 28422069 PMCID: PMC6154654 DOI: 10.3390/molecules22040655] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/12/2017] [Accepted: 04/13/2017] [Indexed: 02/02/2023] Open
Abstract
Glycine (Gly) residues are particularly susceptible to hydrogen abstraction; which results in the formation of the capto-dative stabilized Cα-centered Gly radical (GLR) on the protein backbone. We examined the effect of GLR formation on the structure of the Trp cage; tryptophan zipper; and the villin headpiece; three fast-folding and stable miniproteins; using all-atom (OPLS-AA) molecular dynamics simulations. Radicalization changes the conformation of the GLR residue and affects both neighboring residues but did not affect the stability of the Trp zipper. The stability of helices away from the radical center in villin were also affected by radicalization; and GLR in place of Gly15 caused the Trp cage to unfold within 1 µs. These results provide new evidence on the destabilizing effects of protein oxidation by reactive oxygen species.
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190
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Meshkin H, Zhu F. Thermodynamics of Protein Folding Studied by Umbrella Sampling along a Reaction Coordinate of Native Contacts. J Chem Theory Comput 2017; 13:2086-2097. [PMID: 28355066 DOI: 10.1021/acs.jctc.6b01171] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Spontaneous transitions between the native and non-native protein conformations are normally rare events that hardly take place in typical unbiased molecular dynamics simulations. It was recently demonstrated that such transitions can be well described by a reaction coordinate, Q, that represents the collective fraction of the native contacts between the protein atoms. Here we attempt to use this reaction coordinate to enhance the conformational sampling. We perform umbrella sampling simulations with biasing potentials on Q for two model proteins, Trp-Cage and BBA, using the CHARMM force field. Hamiltonian replica exchange is implemented in these simulations to further facilitate the sampling. The simulations appear to have reached satisfactory convergence, resulting in unbiased free energies as a function of Q. In addition to the native structure, multiple folded conformations are identified in the reconstructed equilibrium ensemble. Some conformations without any native contacts nonetheless have rather compact geometries and are stabilized by hydrogen bonds not present in the native structure. Whereas the enhanced sampling along Q reasonably reproduces the equilibrium conformational space, we also find that the folding of an α-helix in Trp-Cage is a slow degree of freedom orthogonal to Q and therefore cannot be accelerated by biasing the reaction coordinate. Overall, we conclude that whereas Q is an excellent parameter to analyze the simulations, it is not necessarily a perfect reaction coordinate for enhanced sampling, and better incorporation of other slow degrees of freedom may further improve this reaction coordinate.
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Affiliation(s)
- Hamed Meshkin
- Department of Physics, Indiana University Purdue University Indianapolis , 402 North Blackford Street, Indianapolis, Indiana 46202, United States
| | - Fangqiang Zhu
- Department of Physics, Indiana University Purdue University Indianapolis , 402 North Blackford Street, Indianapolis, Indiana 46202, United States
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191
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192
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Katouda M, Nakajima T. MPI/OpenMP hybrid parallel algorithm for resolution of identity second-order Møller-Plesset perturbation calculation of analytical energy gradient for massively parallel multicore supercomputers. J Comput Chem 2017; 38:489-507. [PMID: 28133838 DOI: 10.1002/jcc.24701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 11/16/2016] [Accepted: 11/16/2016] [Indexed: 11/09/2022]
Abstract
A massively parallel algorithm of the analytical energy gradient calculations based the resolution of identity Møller-Plesset perturbation (RI-MP2) method from the restricted Hartree-Fock reference is presented for geometry optimization calculations and one-electron property calculations of large molecules. This algorithm is designed for massively parallel computation on multicore supercomputers applying the Message Passing Interface (MPI) and Open Multi-Processing (OpenMP) hybrid parallel programming model. In this algorithm, the two-dimensional hierarchical MP2 parallelization scheme is applied using a huge number of MPI processes (more than 1000 MPI processes) for acceleration of the computationally demanding O(N5 ) step such as calculations of occupied-occupied and virtual-virtual blocks of MP2 one-particle density matrix and MP2 two-particle density matrices. The new parallel algorithm performance is assessed using test calculations of several large molecules such as buckycatcher C60 @C60 H28 (144 atoms, 1820 atomic orbitals (AOs) for def2-SVP basis set, and 3888 AOs for def2-TZVP), nanographene dimer (C96 H24 )2 (240 atoms, 2928 AOs for def2-SVP, and 6432 AOs for cc-pVTZ), and trp-cage protein 1L2Y (304 atoms and 2906 AOs for def2-SVP) using up to 32,768 nodes and 262,144 central processing unit (CPU) cores of the K computer. The results of geometry optimization calculations of trp-cage protein 1L2Y at the RI-MP2/def2-SVP level using the 3072 nodes and 24,576 cores of the K computer are presented and discussed to assess the efficiency of the proposed algorithm. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Michio Katouda
- Computational Molecular Science Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe, 650-0047, Japan
| | - Takahito Nakajima
- Computational Molecular Science Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe, 650-0047, Japan
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193
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Kim SB, Sparano EM, Singh RS, Debenedetti PG. Microscopic Origin of Hysteresis in Water Sorption on Protein Matrices. J Phys Chem Lett 2017; 8:1185-1190. [PMID: 28234480 DOI: 10.1021/acs.jpclett.7b00184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Despite the importance of water sorption isotherms for a fundamental understanding of protein-water interactions, the microscopic origin of hysteresis between the adsorption and desorption branches is not well understood. Using our recently developed simulation technique, we compute the water sorption isotherms of two proteins, lysozyme and Trp-cage, a miniprotein. We explicitly compare protein-water interactions in adsorption and desorption processes, by analyzing local hydration in terms of hydrogen bonding, water density, and solvent-accessible surface area. We find that significant differences in hydration behavior between adsorption and desorption manifest themselves at the individual amino acid level, in particular around polar or charged residues. We confirm this observation by demonstrating that Trp-cage's hysteresis can be significantly reduced by mutating charged residues to alanine, a neutral and nonpolar amino acid.
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Affiliation(s)
- Sang Beom Kim
- Department of Chemical and Biological Engineering, Princeton University , Princeton, New Jersey 08544, United States
| | - Evan M Sparano
- Department of Chemical and Biological Engineering, Princeton University , Princeton, New Jersey 08544, United States
| | - Rakesh S Singh
- Department of Chemical and Biological Engineering, Princeton University , Princeton, New Jersey 08544, United States
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University , Princeton, New Jersey 08544, United States
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194
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Harada R, Shigeta Y. Efficient Conformational Search Based on Structural Dissimilarity Sampling: Applications for Reproducing Structural Transitions of Proteins. J Chem Theory Comput 2017; 13:1411-1423. [PMID: 28170260 DOI: 10.1021/acs.jctc.6b01112] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Structural Dissimilarity Sampling (SDS) is proposed as an efficient conformational search method to promote structural transitions essential for the biological functions of proteins. In SDS, initial structures are selected based on structural dissimilarity, and conformational resampling is repeated. Conformational resampling is performed as follows: (I) arrangement of initial structures for a diverse distribution at the edge of a conformational subspace and (II) promotion of the structural transitions with multiple short-time molecular dynamics (MD) simulations restarting from the diversely distributed initial structures. Cycles of (I) and (II) are repeated to intensively promote structural transitions because conformational resampling from the initial structures would quickly expand conformational distributions toward unvisited conformational subspaces. As a demonstration, SDS was first applied to maltodextrin binding protein (MBP) in explicit water to reproduce structural transitions between the open and closed states of MBP. Structural transitions of MBP were successfully reproduced with SDS in nanosecond-order simulation times. Starting from both the open and closed forms, SDS successfully reproduced the structural transitions within 25 cycles (a total of 250 ns of simulation time). For reference, a conventional long-time (500 ns) MD simulation under NPT (300 K and 1 bar) starting from the open form failed to reproduce the structural transition. In addition to the open-closed motions of MBP, SDS was applied to folding processes of the fast-folding proteins (chignolin, Trp-cage, and villin) and successfully sampled their native states. To confirm how the selections of initial structures affected conformational sampling efficiency, numbers of base sets for characterizing structural dissimilarity of initial structures were addressed in distinct trials of SDS. The parameter searches showed that the conformational sampling efficiency was relatively insensitive with respect to the numbers of base sets, indicating the robustness of SDS for actual applications.
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Affiliation(s)
- Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba , Tennodai 1-1-1, Tsukuba, Ibaraki 305-8577, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba , Tennodai 1-1-1, Tsukuba, Ibaraki 305-8577, Japan
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195
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Gapsys V, de Groot BL. pmx Webserver: A User Friendly Interface for Alchemistry. J Chem Inf Model 2017; 57:109-114. [DOI: 10.1021/acs.jcim.6b00498] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vytautas Gapsys
- Computational Biomolecular
Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany
| | - Bert L. de Groot
- Computational Biomolecular
Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany
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196
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Kitazawa S, Fossat MJ, McCallum SA, Garcia AE, Royer CA. NMR and Computation Reveal a Pressure-Sensitive Folded Conformation of Trp-Cage. J Phys Chem B 2017; 121:1258-1267. [DOI: 10.1021/acs.jpcb.6b11810] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Soichiro Kitazawa
- Biological
Sciences, Rensselaer Polytechnic Institute, Troy, New York
| | - Martin J. Fossat
- Biological
Sciences, Rensselaer Polytechnic Institute, Troy, New York
- Laboratoire Charles
Coulomb UMR 5221 CNRS-UM, Montpellier, France
| | - Scott A. McCallum
- Center
for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| | - Angel E. Garcia
- Department
of Physics, Rensselaer Polytechnic Institute, Troy, New York
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197
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Wang LP, Song C. Geometry optimization made simple with translation and rotation coordinates. J Chem Phys 2017; 144:214108. [PMID: 27276946 DOI: 10.1063/1.4952956] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The effective description of molecular geometry is important for theoretical studies of intermolecular interactions. Here we introduce a new translation-rotation-internal coordinate (TRIC) system which explicitly includes the collective translations and rotations of molecules, or parts of molecules such as monomers or ligands, as degrees of freedom. The translations are described as the centroid position and the orientations are represented with the exponential map parameterization of quaternions. When TRIC is incorporated into geometry optimization calculations, the performance is consistently superior to existing coordinate systems for a diverse set of systems including water clusters, organic semiconductor donor-acceptor complexes, and small proteins, all of which are characterized by nontrivial intermolecular interactions. The method also introduces a new way to scan the molecular orientations while allowing orthogonal degrees of freedom to relax. Our findings indicate that an explicit description of molecular translation and rotation is a natural way to traverse the many-dimensional potential energy surface.
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Affiliation(s)
- Lee-Ping Wang
- Department of Chemistry, University of California, 1 Shields Ave., Davis, California 95616, USA
| | - Chenchen Song
- Department of Chemistry and the PULSE Institute, Stanford University, Stanford, California 94305, USA
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198
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Nishimoto Y, Fedorov DG. Three-body expansion of the fragment molecular orbital method combined with density-functional tight-binding. J Comput Chem 2017; 38:406-418. [DOI: 10.1002/jcc.24693] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/14/2016] [Accepted: 11/17/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Yoshio Nishimoto
- Fukui Institute for Fundamental Chemistry, Kyoto University; 34-4 Takano Nishihiraki-cho Sakyo-ku Kyoto 606-8103 Japan
| | - Dmitri G. Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat); National Institute of Advanced Industrial Science and Technology (AIST); 1-1-1 Umezono Tsukuba Ibaraki 305-8568 Japan
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199
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Strømland Ø, Handegård ØS, Govasli ML, Wen H, Halskau Ø. Peptides derived from α-lactalbumin membrane binding helices oligomerize in presence of lipids and disrupt bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1029-1039. [PMID: 28069414 DOI: 10.1016/j.bbamem.2017.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 12/02/2016] [Accepted: 01/04/2017] [Indexed: 11/16/2022]
Abstract
Helix A and -C of α-lactalbumin, a loosely folded amphitropic protein, perturb lipid monolayers by the formation of amyloid pore-like structures. To investigate whether these helices are able to disrupt fully formed bilayers, we designed peptides comprised of Helix A and -C, and investigated their membrane-perturbing properties. The peptides, designated A-Cage-C and A-Lnk-C, were prepared with tryptophan sites in the helical and the spacer segments in order to monitor which part were involved in membrane association under given conditions. The peptides associate with and disrupt negatively charged bilayers in a pH-dependent manner and α-helical tendencies increased upon membrane association. Both helices and the spacer segment were involved in membrane binding in the case of A-Lnk-C, and there are indications that the two helixes act in synergy to affect the membrane. However, the helices and the spacer segment could not intercalate when present as A-Cage-C at neutral conditions. At acidic pH, both helices could intercalate, but not the central spacer segment. AFM performed on bilayers under aqueous conditions revealed oligomers formed by the peptides. The presence of bilayers and acidic pHs were both drivers for the formation of these, suggestive of models for peptide oligomerization where segments of the peptide are stacked in an electrostatically favorable manner by the surface. Of the two peptides, A-Lnk-C was the more prolific oligomerizer, and also formed amyloid-fibril like structures at acidic pH and elevated concentrations. Our results suggest the peptides perturb membranes not through pore-like structures, but possibly by a thinning mechanism.
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Affiliation(s)
- Øyvind Strømland
- Department of Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5008 Bergen, Norway
| | - Ørjan S Handegård
- Department of Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5008 Bergen, Norway
| | - Morten L Govasli
- Department of Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5008 Bergen, Norway
| | - Hanzhen Wen
- Department of Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5008 Bergen, Norway
| | - Øyvind Halskau
- Department of Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5008 Bergen, Norway.
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Kumar A, Ranbhor R, Patel K, Ramakrishnan V, Durani S. Automated protein design: Landmarks and operational principles. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 125:24-35. [PMID: 27979438 DOI: 10.1016/j.pbiomolbio.2016.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/06/2016] [Indexed: 11/25/2022]
Abstract
Protein design has an eventful history spanning over three decades, with handful of success stories reported, and numerous failures not reported. Design practices have benefited tremendously from improvements in computer hardware and advances in scientific algorithms. Though protein folding problem still remains unsolved, the possibility of having multiple sequence solutions for a single fold makes protein design a more tractable problem than protein folding. One of the most significant advancement in this area is the implementation of automated design algorithms on pre-defined templates or completely new folds, optimized through deterministic and heuristic search algorithms. This progress report provides a succinct presentation of important landmarks in automated design attempts, followed by brief account of operational principles in automated design methods.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, University of Toronto, ON, M5S3H6, Canada.
| | | | | | - Vibin Ramakrishnan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781039, India.
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Technology, Bombay, 400076, India
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