1
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Villot C, Lao KU. Electronic structure theory on modeling short-range noncovalent interactions between amino acids. J Chem Phys 2023; 158:094301. [PMID: 36889981 DOI: 10.1063/5.0138032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
While short-range noncovalent interactions (NCIs) are proving to be of importance in many chemical and biological systems, these atypical bindings happen within the so-called van der Waals envelope and pose an enormous challenge for current computational methods. We introduce SNCIAA, a database of 723 benchmark interaction energies of short-range noncovalent interactions between neutral/charged amino acids originated from protein x-ray crystal structures at the "gold standard" coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory with a mean absolute binding uncertainty less than 0.1 kcal/mol. Subsequently, a systematic assessment of commonly used computational methods, such as the second-order Møller-Plesset theory (MP2), density functional theory (DFT), symmetry-adapted perturbation theory (SAPT), composite electronic-structure methods, semiempirical approaches, and the physical-based potentials with machine learning (IPML) on SNCIAA is carried out. It is shown that the inclusion of dispersion corrections is essential even though these dimers are dominated by electrostatics, such as hydrogen bondings and salt bridges. Overall, MP2, ωB97M-V, and B3LYP+D4 turned out to be the most reliable methods for the description of short-range NCIs even in strongly attractive/repulsive complexes. SAPT is also recommended in describing short-range NCIs only if the δMP2 correction has been included. The good performance of IPML for dimers at close-equilibrium and long-range conditions is not transferable to the short-range. We expect that SNCIAA will assist the development/improvement/validation of computational methods, such as DFT, force-fields, and ML models, in describing NCIs across entire potential energy surfaces (short-, intermediate-, and long-range NCIs) on the same footing.
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Affiliation(s)
- Corentin Villot
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| | - Ka Un Lao
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA
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2
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Rahimi AM, Jamali S, Bardhan JP, Lustig SR. Solvation Thermodynamics of Solutes in Water and Ionic Liquids Using the Multiscale Solvation-Layer Interface Condition Continuum Model. J Chem Theory Comput 2022; 18:5539-5558. [PMID: 36001344 DOI: 10.1021/acs.jctc.2c00248] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular assembly processes are generally driven by thermodynamic properties in solutions. Atomistic modeling can be very helpful in designing and understanding complex systems, except that bulk solvent is very inefficient to treat explicitly as discrete molecules. In this work, we develop and assess two multiscale solvation models for computing solvation thermodynamic properties. The new SLIC/CDC model combines continuum solvent electrostatics based on the solvent layer interface condition (SLIC) with new statistical thermodynamic models for hydrogen bonding and nonpolar modes: cavity formation, dispersion interactions, combinatorial mixing (CDC). Given the structures of 500 solutes, the SLIC/CDC model predicts Gibbs energies of solvation in water with an average accuracy better than 1 kcal/mol, when compared to experimental measurements, and better than 0.8 kcal/mol, when compared to explicit-solvent molecular dynamics simulations. The individual SLIC/CDC energy mode values agree quantitatively with those computed from explicit-solvent molecular dynamics. The previously published SLIC/SASA multiscale model combines the SLIC continuum electrostatic model with the solvent-accessible surface area (SASA) nonpolar energy mode. With our new, improved parametrization method, the SLIC/SASA model now predicts Gibbs energies of solvation with better than 1.4 kcal/mol average accuracy in aqueous systems, compared to experimental and explicit-solvent molecular dynamics, and better than 1.6 kcal/mol average accuracy in ionic liquids, compared to explicit-solvent molecular dynamics. Both models predict solvation entropies, and are the first implicit-solvation models capable of predicting solvation heat capacities.
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Affiliation(s)
- Ali Mehdizadeh Rahimi
- Department of Mechanical and Industrial Engineering, Northeastern University, 360 Huntington Ave., Boston Massachusetts 02115, United States
| | - Safa Jamali
- Department of Mechanical and Industrial Engineering, Northeastern University, 360 Huntington Ave., Boston Massachusetts 02115, United States
| | - Jaydeep P Bardhan
- Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, Washington 99354, United States
| | - Steven R Lustig
- Department of Chemical Engineering, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115, United States
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3
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Egawa D, Ogiso T, Nishikata K, Yamamoto K, Itoh T. Structural Insights into the Loss-of-Function R288H Mutant of Human PPARγ. Biol Pharm Bull 2021; 44:1196-1201. [PMID: 34471047 DOI: 10.1248/bpb.b21-00253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Peroxisome proliferator-activated receptor gamma (PPARγ) is a nuclear receptor and the molecular target of thiazolidinedione-class antidiabetic drugs. It has been reported that the loss of function R288H mutation in the human PPARγ ligand-binding domain (LBD) may be associated with the onset of colon cancer. A previous in vitro study showed that this mutation dampens 15-deoxy-Δ12,14-prostaglandin J2 (15d-PGJ2, a natural PPARγ agonist)-dependent transcriptional activation; however, it is poorly understood why the function of the R288H mutant is impaired and what role this arginine (Arg) residue plays. In this study, we found that the apo-form of R288H PPARγ mutant displays several altered conformational arrangements of the amino acid side chains in LBD: 1) the loss of a salt bridge between Arg288 and Glu295 leads to increased helix 3 movement; 2) closer proximity of Gln286 and His449 via a hydrogen bond, and closer proximity of Cys285 and Phe363 via hydrophobic interaction, stabilize the helix 3-helix 11 interaction; and 3) there is steric hindrance between Cys285/Gln286/Ser289/His449 and the flexible ligands 15d-PGJ2, 6-oxotetracosahexaenoic acid (6-oxoTHA), and 17-oxodocosahexaenoic acid (17-oxoDHA). These results suggest why Arg288 plays an important role in ligand binding and why the R288H mutation is disadvantageous for flexible ligand binding.
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Affiliation(s)
- Daichi Egawa
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University
| | - Taku Ogiso
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University
| | - Kimina Nishikata
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University
| | - Keiko Yamamoto
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University
| | - Toshimasa Itoh
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University
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4
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Tiwari MK, Murarka RK. Interaction strength of osmolytes with the anion of a salt-bridge determines its stability. Phys Chem Chem Phys 2021; 23:5527-5539. [PMID: 33651069 DOI: 10.1039/d0cp05378c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In order to understand the role of osmolytes in regulating physicochemical behavior of proteins, we investigated the influence of protein destabilizing (urea and guanidinium chloride) and stabilizing osmolytes (TMAO, glycerol, and betaine) on a model salt-bridge (SB) formed between structural analogues of arginine and glutamate/aspartate sidechains in a solvent continuum using first-principles quantum chemical calculations based on DFT and MP2 methods. The binding strength of the osmolyte with the SB is found to be in the order of betaine > TMAO > Gdm+ > glycerol > urea. The osmolytes (TMAO and betaine) that preferentially bind to the SB cation have a marginal influence on SB stability. Also, pure π-π stacking interaction between Gdm+ and the SB cation plays an insignificant role in destabilizing the SB. In fact, the interaction strength of osmolytes with the SB anion mainly determines the stability of SB. For instance, a competition between Gdm+ and the SB cation to bind with the SB anion is responsible for instability and subsequent dissociation of the SB. The competition provided by other osmolytes is too weak to break the SB. Exploiting this information, we designed three structural derivatives of Gdm+, all having a stronger interaction with SB anion, and thereby show a stronger SB dissociation potential. Furthermore, we find an excellent linear anti-correlation between SB interaction energy and the energy of interaction between osmolyte and the SB anion, which suggests that by knowing only the strength of osmolyteacetate interaction, one can predict the influence of osmolytes on the salt-bridge instability. This information is useful in fine-tuning the SB dissociation power of Gdm+, which has a practical significance in obtaining the mechanistic insight into the influence of GdmCl on protein stability. Our results also provide a basis for understanding the chemistry of other ion-pairs formed between a cationic hydrogen donor and an anionic acceptor.
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Affiliation(s)
- Mrityunjay K Tiwari
- A Department of Chemistry Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri, Bhopal, MP 462066, India.
| | - Rajesh K Murarka
- A Department of Chemistry Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri, Bhopal, MP 462066, India.
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5
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Protein dynamics of five FMN binding protein isomers revealed by residue electrostatic energies between ionic residues: correlation coefficients. CHEMICAL PAPERS 2020. [DOI: 10.1007/s11696-020-01128-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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6
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McManus TJ, Wells SA, Walker AB. Salt bridge impact on global rigidity and thermostability in thermophilic citrate synthase. Phys Biol 2019; 17:016002. [PMID: 31220825 DOI: 10.1088/1478-3975/ab2b5c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
It has been suggested that structural rigidity is connected to thermostability, e.g. in enzymes from thermophilic microorganisms. We examine the importance of correctly handling salt bridges, and interactions which we term 'strong polars', when constructing the constraint network for global rigidity analysis in these systems. Through a comparison of rigidity in citrate synthases, we clarify the relationship between rigidity and thermostability. In particular, with our corrected handling of strong polar interactions, the difference in rigidity between mesophilic and thermophilic structures is detected more clearly than in previous studies. The increase in rigidity did not detract from the functional flexibility of the active site in all systems once their respective temperature range had been reached. We then examine the distribution of salt bridges in thermophiles that were previously unaccounted for in flexibility studies. We show that in hyperthermophiles these have stabilising roles in the active site; occuring in close proximity to key residues involved in catalysis and binding of the protein.
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Affiliation(s)
- T J McManus
- Department of Physics, University of Bath, Bath, BA2 7AY, United Kingdom
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7
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Okiyama Y, Watanabe C, Fukuzawa K, Mochizuki Y, Nakano T, Tanaka S. Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson-Boltzmann Equation: II. Protein and Its Ligand-Binding System Studies. J Phys Chem B 2018; 123:957-973. [PMID: 30532968 DOI: 10.1021/acs.jpcb.8b09326] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, the electronic properties of bioactive proteins were analyzed using an ab initio fragment molecular orbital (FMO) methodology in solution: coupling with an implicit solvent model based on the Poisson-Boltzmann surface area called as FMO-PBSA. We investigated the solvent effects on practical and heterogeneous targets with uneven exposure to solvents unlike deoxyribonucleic acid analyzed in our recent study. Interfragment interaction energy (IFIE) and its decomposition analyses by FMO-PBSA revealed solvent-screening mechanisms that affect local stability inside ubiquitin protein: the screening suppresses excessiveness in bare charge-charge interactions and enables an intuitive IFIE analysis. The electrostatic character and associated solvation free energy also give consistent results as a whole to previous studies on the explicit solvent model. Moreover, by using the estrogen receptor alpha (ERα) protein bound to ligands, we elucidated the importance of specific interactions that depend on the electric charge and activatability as agonism/antagonism of the ligand while estimating the influences of the implicit solvent on the ligand and helix-12 bindings. The predicted ligand-binding affinities of bioactive compounds to ERα also show a good correlation with their in vitro activities. The FMO-PBSA approach would thus be a promising tool both for biological and pharmaceutical research targeting proteins.
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Affiliation(s)
- Yoshio Okiyama
- Institute of Industrial Science , The University of Tokyo , 4-6-1 Komaba , Meguro-ku, Tokyo 153-8505 , Japan.,Division of Medicinal Safety Science , National Institute of Health Sciences , 3-25-26 Tonomachi , Kawasaki-ku, Kawasaki , Kanagawa 210-9501 , Japan
| | - Chiduru Watanabe
- Institute of Industrial Science , The University of Tokyo , 4-6-1 Komaba , Meguro-ku, Tokyo 153-8505 , Japan.,RIKEN Center for Biosystems Dynamics Research , 1-7-22 Suehiro-cho , Tsurumi-ku, Yokohama , Kanagawa 230-0045 , Japan
| | - Kaori Fukuzawa
- Institute of Industrial Science , The University of Tokyo , 4-6-1 Komaba , Meguro-ku, Tokyo 153-8505 , Japan.,Faculty of Pharmaceutical Sciences , Hoshi University , 2-4-41 Ebara , Shinagawa-ku, Tokyo 142-8501 , Japan
| | - Yuji Mochizuki
- Institute of Industrial Science , The University of Tokyo , 4-6-1 Komaba , Meguro-ku, Tokyo 153-8505 , Japan.,Department of Chemistry and Research Center for Smart Molecules, Faculty of Science , Rikkyo University , 3-34-1 Nishi-ikebukuro , Toshima-ku, Tokyo 171-8501 , Japan
| | - Tatsuya Nakano
- Institute of Industrial Science , The University of Tokyo , 4-6-1 Komaba , Meguro-ku, Tokyo 153-8505 , Japan.,Division of Medicinal Safety Science , National Institute of Health Sciences , 3-25-26 Tonomachi , Kawasaki-ku, Kawasaki , Kanagawa 210-9501 , Japan
| | - Shigenori Tanaka
- Graduate School of System Informatics , Kobe University , 1-1 Rokkodai, Nada-ku, Kobe , Hyogo 657-8501 , Japan
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8
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Smith MS, Billings WM, Whitby FG, Miller MB, Price JL. Enhancing a long-range salt bridge with intermediate aromatic and nonpolar amino acids. Org Biomol Chem 2018; 15:5882-5886. [PMID: 28678274 DOI: 10.1039/c7ob01198a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction of a positively charged amino acid residue with a negatively charged residue (i.e. a salt bridge) can contribute substantially to protein conformational stability, especially when two ionic groups are in close proximity. At longer distances, this stabilizing effect tends to drop off precipitously. However, several lines of evidence suggest that salt-bridge interaction could persist at longer distances if an aromatic amino acid residue were positioned between the anion and cation. Here we explore this possibility in the context of a peptide in which a Lys residue occupies the i + 8 position relative to an i-position Glu on the solvent-exposed surface of a helix-bundle homotrimer. Variable temperature circular dichroism (CD) experiments indicate that an i + 4-position Trp enables a favorable long-range interaction between Glu and the i + 8 Lys. A substantial portion of this effect relies on the presence of a hydrogen-bond donor on the arene; however, non-polar arenes, a cyclic hydrocarbon, and an acyclic Leu side-chain can also enhance the long-range salt bridge, possibly by excluding water and ions from the space between Glu and Lys.
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Affiliation(s)
- Mason S Smith
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
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9
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Lake PT, McCullagh M. Implicit Solvation Using the Superposition Approximation (IS-SPA): An Implicit Treatment of the Nonpolar Component to Solvation for Simulating Molecular Aggregation. J Chem Theory Comput 2017; 13:5911-5924. [PMID: 29120632 DOI: 10.1021/acs.jctc.7b00698] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nonpolar solute-solvent interactions are the driving force for aggregation in important chemical and biological phenomena including protein folding, peptide self-assembly, and oil-water emulsion formation. Currently, the most accurate and computationally efficient description of these processes requires an explicit treatment of all solvent and solute atoms. Previous computationally feasible implicit solvent models, such as solute surface area approaches, are unsuccessful at capturing aggregation features including both structural and energetic trends while more theoretically rigorous approaches, such as Reference Interaction Site Model (RISM), are accurate but extremely computationally demanding. Our approach, denoted Implicit Solvation using the Superposition Approximation (IS-SPA), builds on previous theory utilizing the Kirkwood superposition approximation to approximate the mean force of the solvent from solute parameters. We introduce and verify a parabolic first solvation shell truncation of atomic solvation, fitting water distributions around a molecule, and a Monte Carlo integration of the mean solvent force. These extensions allow this method to be implemented as an efficient nonpolar implicit solvent model for molecular simulation. The approximations in IS-SPA are first explored and justified for the homodimerization of an array of different sized Lennard-Jones spheres. The accuracy and transferability of the approach are demonstrated by its ability to capture the position and relative energies of the desolvation barrier and free energy minimum of alkane homodimers. The model is then shown to reproduce the phase separation and solubility of cyclohexane and water. These promising results, coupled with 2 orders of magnitude speed-up for dilute systems as compared to explicit solvent simulations, demonstrate that IS-SPA is an appealing approach to boost the time- and length-scale of molecular aggregation simulations.
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Affiliation(s)
- Peter T Lake
- Department of Chemistry, Colorado State University , Fort Collins, Colorado 80523, United States
| | - Martin McCullagh
- Department of Chemistry, Colorado State University , Fort Collins, Colorado 80523, United States
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10
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Bezsudnova EY, Petrova TE, Popinako AV, Antonov MY, Stekhanova TN, Popov VO. Intramolecular hydrogen bonding in the polyextremophilic short-chain dehydrogenase from the archaeon Thermococcus sibiricus and its close structural homologs. Biochimie 2015; 118:82-9. [PMID: 26300061 DOI: 10.1016/j.biochi.2015.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 08/19/2015] [Indexed: 01/27/2023]
Abstract
The short-chain alcohol dehydrogenase from the archaeon Thermococcus sibiricus (TsAdh319) exhibits adaptation to different kinds of stress: high temperature, high salinity, and the presence of organic solvents and denaturants. Previously a comparison of TsAdh319 with close structural homologs revealed an abnormally large number of charged residues on the surface of TsAdh319 tetramer. We further focused on the analysis of hydrogen bonding of TsAdh319 and its structural homologs from thermophilic and mesophilic organisms as a structural factor of adaptation to extreme environment. The calculation and analysis of the dynamics of hydrogen bonds of different kind were performed. In particular, the intramolecular hydrogen bonds of different kind according to their location and the type of a.a. residues involved in the bond were analyzed. TsAdh319 showed the greatest contribution of charged residues to the formation of surface hydrogen bonds, inner hydrogen bonding, and the bonds between different subunits compared to its structural homologs. Molecular dynamics simulations revealed that, of three enzyme molecules analyzed, TsAdh319 shows the least change in the number of hydrogen bonds of different kinds upon a temperature shift from 27 to 85 °C. The greatest changes were observed for a homologous enzyme from a mesophilic host. Only guanidine hydrochloride being a charged agent was able to deactivate TsAdh319. We suggest that the percentage of charged residues plays a key role in the resistance of TsAdh319 to environmental stress. The analysis shows that salt bridges in TsAdh319 serve as a universal instrument of stabilization under different extreme conditions.
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Affiliation(s)
- Ekaterina Yu Bezsudnova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky pr. 33, bld. 2, 119071, Moscow, Russian Federation.
| | - Tatiana E Petrova
- Institute of Mathematical Problems of Biology, RAS, Institutskaya str. 4, Pushchino, 142290, Russian Federation
| | - Anna V Popinako
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky pr. 33, bld. 2, 119071, Moscow, Russian Federation
| | - Mikhail Yu Antonov
- M.K. Ammosov North-Eastern Federal University, Belinskiy str., 58, Suite 312, Yakutsk, 677980, Republic of Sakha (Yakutia), Russian Federation
| | - Tatiana N Stekhanova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky pr. 33, bld. 2, 119071, Moscow, Russian Federation
| | - Vladimir O Popov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky pr. 33, bld. 2, 119071, Moscow, Russian Federation; Dep. "Protein Factory", NBICS Center, National Research Centre "Kurchatov Institute", Akad. Kurchatova sqr., 1, Moscow, 123182, Russian Federation
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11
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Vener MV, Odinokov AV, Wehmeyer C, Sebastiani D. The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations. J Chem Phys 2015; 142:215106. [DOI: 10.1063/1.4922165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M. V. Vener
- Mendeleev University of Chemical Technology, Moscow, Russia
| | - A. V. Odinokov
- Photochemistry Center of the Russian Academy of Sciences, Moscow, Russia
| | | | - D. Sebastiani
- Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
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12
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Pluhařová E, Marsalek O, Schmidt B, Jungwirth P. Peptide salt bridge stability: from gas phase via microhydration to bulk water simulations. J Chem Phys 2013; 137:185101. [PMID: 23163393 DOI: 10.1063/1.4765052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The salt bridge formation and stability in the terminated lysine-glutamate dipeptide is investigated in water clusters of increasing size up to the limit of bulk water. Proton transfer dynamics between the acidic and basic side chains is described by DFT-based Born-Oppenheimer molecular dynamics simulations. While the desolvated peptide prefers to be in its neutral state, already the addition of a single water molecule can trigger proton transfer from the glutamate side chain to the lysine side chain, leading to a zwitterionic salt bridge state. Upon adding more water molecules we find that stabilization of the zwitterionic state critically depends on the number of hydrogen bonds between side chain termini, the water molecules, and the peptidic backbone. Employing classical molecular dynamics simulations for larger clusters, we observed that the salt bridge is weakened upon additional hydration. Consequently, long-lived solvent shared ion pairs are observed for about 30 water molecules while solvent separated ion pairs are found when at least 40 or more water molecules hydrate the dipeptide. These results have implications for the formation and stability of salt bridges at partially dehydrated surfaces of aqueous proteins.
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Affiliation(s)
- Eva Pluhařová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, Prague 6, CZ-16610, Czech Republic.
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13
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14
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Cheng RP, Wang WR, Girinath P, Yang PA, Ahmad R, Li JH, Hart P, Kokona B, Fairman R, Kilpatrick C, Argiros A. Effect of Glutamate Side Chain Length on Intrahelical Glutamate–Lysine Ion Pairing Interactions. Biochemistry 2012; 51:7157-72. [DOI: 10.1021/bi300655z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Richard P. Cheng
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Wei-Ren Wang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Prashant Girinath
- Department of Chemistry, University
at Buffalo, The State University of New York, Buffalo, New York 14260-3000, United States
| | - Po-An Yang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Raheel Ahmad
- Department of Chemistry, University
at Buffalo, The State University of New York, Buffalo, New York 14260-3000, United States
| | - Jhe-Hao Li
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Pier Hart
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041, United
States
| | - Bashkim Kokona
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041, United
States
| | - Robert Fairman
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041, United
States
| | - Casey Kilpatrick
- Department of Chemistry, University
at Buffalo, The State University of New York, Buffalo, New York 14260-3000, United States
| | - Annmarie Argiros
- Department of Chemistry, University
at Buffalo, The State University of New York, Buffalo, New York 14260-3000, United States
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15
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Designing electrostatic interactions in biological systems via charge optimization or combinatorial approaches: insights and challenges with a continuum electrostatic framework. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1252-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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16
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Francis DM, Różycki B, Koveal D, Hummer G, Page R, Peti W. Structural basis of p38α regulation by hematopoietic tyrosine phosphatase. Nat Chem Biol 2011; 7:916-24. [PMID: 22057126 DOI: 10.1038/nchembio.707] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 08/30/2011] [Indexed: 12/14/2022]
Abstract
MAP kinases regulate essential cellular events, including cell growth, differentiation and inflammation. The solution structure of a complete MAPK-MAPK-regulatory protein complex, p38α-HePTP, was determined, enabling a comprehensive investigation of the molecular basis of specificity and fidelity in MAPK regulation. Structure determination was achieved by combining NMR spectroscopy and small-angle X-ray scattering data with a new ensemble calculation-refinement procedure. We identified 25 residues outside of the HePTP kinase interaction motif necessary for p38α recognition. The complex adopts an extended conformation in solution and rarely samples the conformation necessary for kinase deactivation. Complex formation also does not affect the N-terminal lobe, the activation loop of p38α or the catalytic domain of HePTP. Together, these results show how the downstream tyrosine phosphatase HePTP regulates p38α and provide for fundamentally new insights into MAPK regulation and specificity.
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Affiliation(s)
- Dana M Francis
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island, USA
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17
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Francis DM, Różycki B, Tortajada A, Hummer G, Peti W, Page R. Resting and active states of the ERK2:HePTP complex. J Am Chem Soc 2011; 133:17138-41. [PMID: 21985012 DOI: 10.1021/ja2075136] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The MAP kinase ERK2 (ERK2, extracellular signal-regulated kinase 2) is regulated by numerous phosphatases that tightly control its activity. For example, the hematopoietic tyrosine phosphatase (HePTP) negatively regulates T cell activation in lymphocytes via ERK2 dephosphorylation. However, only very limited structural information is available for these biologically important complexes. Here, we use small-angle X-ray scattering combined with EROS ensemble refinement to characterize the structures of the resting and active states of ERK2:HePTP complexes. Our data show that the resting state ERK2:HePTP complex adopts a highly extended, dynamic conformation that becomes compact and ordered in the active state complex. This work experimentally demonstrates that these complexes undergo significant dynamic structural changes in solution and provides the first structural insight into an active state MAPK complex.
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Affiliation(s)
- Dana M Francis
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island 02912, USA
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18
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Bardhan JP. Nonlocal continuum electrostatic theory predicts surprisingly small energetic penalties for charge burial in proteins. J Chem Phys 2011; 135:104113. [PMID: 21932882 DOI: 10.1063/1.3632995] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the energetics of burying charges, ion pairs, and ionizable groups in a simple protein model using nonlocal continuum electrostatics. Our primary finding is that the nonlocal response leads to markedly reduced solvent screening, comparable to the use of application-specific protein dielectric constants. Employing the same parameters as used in other nonlocal studies, we find that for a sphere of radius 13.4 Å containing a single +1e charge, the nonlocal solvation free energy varies less than 18 kcal/mol as the charge moves from the surface to the center, whereas the difference in the local Poisson model is ∼35 kcal/mol. Because an ion pair (salt bridge) generates a comparatively more rapidly varying Coulomb potential, energetics for salt bridges are even more significantly reduced in the nonlocal model. By varying the central parameter in nonlocal theory, which is an effective length scale associated with correlations between solvent molecules, nonlocal-model energetics can be varied from the standard local results to essentially zero; however, the existence of the reduction in charge-burial penalties is quite robust to variations in the protein dielectric constant and the correlation length. Finally, as a simple exploratory test of the implications of nonlocal response, we calculate glutamate pK(a) shifts and find that using standard protein parameters (ε(protein) = 2-4), nonlocal results match local-model predictions with much higher dielectric constants. Nonlocality may, therefore, be one factor in resolving discrepancies between measured protein dielectric constants and the model parameters often used to match titration experiments. Nonlocal models may hold significant promise to deepen our understanding of macromolecular electrostatics without substantially increasing computational complexity.
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Affiliation(s)
- Jaydeep P Bardhan
- Department of Molecular Biophysics and Physiology, Rush University Medical Center, Chicago, Illinois 60612, USA.
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Secundo F, Fialà S, Fraaije MW, de Gonzalo G, Meli M, Zambianchi F, Ottolina G. Effects of water miscible organic solvents on the activity and conformation of the baeyer-villiger monooxygenases from Thermobifida fusca and Acinetobacter calcoaceticus: A comparative study. Biotechnol Bioeng 2010; 108:491-9. [DOI: 10.1002/bit.22963] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 09/03/2010] [Accepted: 09/16/2010] [Indexed: 11/06/2022]
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The energetic contribution of induced electrostatic asymmetry to DNA bending by a site-specific protein. J Mol Biol 2010; 406:285-312. [PMID: 21167173 DOI: 10.1016/j.jmb.2010.12.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 11/30/2010] [Accepted: 12/04/2010] [Indexed: 11/21/2022]
Abstract
DNA bending can be promoted by reducing the net negative electrostatic potential around phosphates on one face of the DNA, such that electrostatic repulsion among phosphates on the opposite face drives bending toward the less negative surface. To provide the first assessment of energetic contribution to DNA bending when electrostatic asymmetry is induced by a site-specific DNA binding protein, we manipulated the electrostatics in the EcoRV endonuclease-DNA complex by mutation of cationic side chains that contact DNA phosphates and/or by replacement of a selected phosphate in each strand with uncharged methylphosphonate. Reducing the net negative charge at two symmetrically located phosphates on the concave DNA face contributes -2.3 kcal mol(-1) to -0.9 kcal mol(-1) (depending on position) to complex formation. In contrast, reducing negative charge on the opposing convex face produces a penalty of +1.3 kcal mol(-1). Förster resonance energy transfer experiments show that the extent of axial DNA bending (about 50°) is little affected in modified complexes, implying that modification affects the energetic cost but not the extent of DNA bending. Kinetic studies show that the favorable effects of induced electrostatic asymmetry on equilibrium binding derive primarily from a reduced rate of complex dissociation, suggesting stabilization of the specific complex between protein and markedly bent DNA. A smaller increase in the association rate may suggest that the DNA in the initial encounter complex is mildly bent. The data imply that protein-induced electrostatic asymmetry makes a significant contribution to DNA bending but is not itself sufficient to drive full bending in the specific EcoRV-DNA complex.
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Aleksandrov A, Polydorides S, Archontis G, Simonson T. Predicting the Acid/Base Behavior of Proteins: A Constant-pH Monte Carlo Approach with Generalized Born Solvent. J Phys Chem B 2010; 114:10634-48. [DOI: 10.1021/jp104406x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexey Aleksandrov
- Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France, and Department of Physics, University of Cyprus, PO20537, CY1678, Nicosia, Cyprus
| | - Savvas Polydorides
- Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France, and Department of Physics, University of Cyprus, PO20537, CY1678, Nicosia, Cyprus
| | - Georgios Archontis
- Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France, and Department of Physics, University of Cyprus, PO20537, CY1678, Nicosia, Cyprus
| | - Thomas Simonson
- Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France, and Department of Physics, University of Cyprus, PO20537, CY1678, Nicosia, Cyprus
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