1
|
Tavares ABM, Albuquerque EL. A Quantum Chemistry Approach of Breast Cancer Drugs Bound to Human Serum Albumin. ADVANCED THEORY AND SIMULATIONS 2022. [DOI: 10.1002/adts.202100464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ana Beatriz M.L.A. Tavares
- Departamento de Biofísica Universidade Federal do Rio Grande do Norte Natal‐RN 59072‐970 Brazil
- Hospital das Clínicas Universidade Federal de Pernambuco Recife‐PE 50.670‐901 Brazil
| | | |
Collapse
|
2
|
Singh A, Khatun S, Pawar N, Gupta AN. Interactive patches over amyloid-β oligomers mediate fractal self-assembly. Phys Rev E 2021; 104:064404. [PMID: 35030868 DOI: 10.1103/physreve.104.064404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 11/18/2021] [Indexed: 06/14/2023]
Abstract
The monomeric units of intrinsically disordered proteins self-assemble into oligomers, protofilaments, and eventually fibrils which may turn into amyloid. The aggregation of these proteins is primarily studied in bulk with no restriction on their degrees of freedom. Herein we experimentally demonstrate that amyloid-β (Aβ) aggregation under diffusion-limited conditions leads to its fractal self-assembly. Confocal microscopy and scanning electron microscopy with energy dispersion x-ray analysis were used to confirm that the fractal self-assemblies were formed from Aβ rather than the salt present in the two supporting media: deionized water and phosphate buffered saline. The results from the molecular docking experiments implicated that electrostatic and hydrophobic patches on the solvent-accessible surface area of the Aβ oligomers mediate the fractal self-assembly. These implications were tested with laser light scattering experiments on the oligomers formed by breaking mature fibrils of Aβ through sonication, which were observed to self-assemble into fractals when sonicated solutions were drop casted. The electrostatic interactions modulate the fractal morphologies with pH of the solution, which leads to a morphological phase transition observed through the variation in their fractal dimension. These transitions provide experimental evidence for the existing theoretical framework in terms of different kinetic models. The higher surface-to-volume ratio of these fractal self-assemblies may have applications in drug delivery, biosensing, and other biomedical applications.
Collapse
Affiliation(s)
- Anurag Singh
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology Kharagpur, 721302, India
| | - Suparna Khatun
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology Kharagpur, 721302, India
| | - Nisha Pawar
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology Kharagpur, 721302, India
| | - Amar Nath Gupta
- Biophysics and Soft Matter Laboratory, Department of Physics, Indian Institute of Technology Kharagpur, 721302, India
| |
Collapse
|
3
|
Catacuzzeno L, Sforna L, Franciolini F, Eisenberg RS. Multiscale modeling shows that dielectric differences make NaV channels faster than KV channels. J Gen Physiol 2021; 153:211724. [PMID: 33502441 PMCID: PMC7845922 DOI: 10.1085/jgp.202012706] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/22/2020] [Accepted: 12/18/2020] [Indexed: 12/31/2022] Open
Abstract
The generation of action potentials in excitable cells requires different activation kinetics of voltage-gated Na (NaV) and K (KV) channels. NaV channels activate much faster and allow the initial Na+ influx that generates the depolarizing phase and propagates the signal. Recent experimental results suggest that the molecular basis for this kinetic difference is an amino acid side chain located in the gating pore of the voltage sensor domain, which is a highly conserved isoleucine in KV channels but an equally highly conserved threonine in NaV channels. Mutagenesis suggests that the hydrophobicity of this side chain in Shaker KV channels regulates the energetic barrier that gating charges cross as they move through the gating pore and control the rate of channel opening. We use a multiscale modeling approach to test this hypothesis. We use high-resolution molecular dynamics to study the effect of the mutation on polarization charge within the gating pore. We then incorporate these results in a lower-resolution model of voltage gating to predict the effect of the mutation on the movement of gating charges. The predictions of our hierarchical model are fully consistent with the tested hypothesis, thus suggesting that the faster activation kinetics of NaV channels comes from a stronger dielectric polarization by threonine (NaV channel) produced as the first gating charge enters the gating pore compared with isoleucine (KV channel).
Collapse
Affiliation(s)
- Luigi Catacuzzeno
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Luigi Sforna
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Fabio Franciolini
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Robert S Eisenberg
- Department of Physiology and Biophysics, Rush University, Chicago, IL.,Department of Applied Mathematics, Illinois Institute of Technology, Chicago, IL
| |
Collapse
|
4
|
Świderek K, Porter AJ, Upfold CM, Williams IH. Influence of Dielectric Environment upon Isotope Effects on Glycoside Heterolysis: Computational Evaluation and Atomic Hessian Analysis. J Am Chem Soc 2020; 142:1556-1563. [PMID: 31887034 DOI: 10.1021/jacs.9b11988] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Isotope effects depend upon the polarity of the bulk medium in which a chemical process occurs. Implicit solvent calculations with molecule-shaped cavities show that the equilibrium isotope effect (EIE) for heterolysis of the glycosidic bonds in 5'-methylthioadenosine and in 2-(p-nitrophenoxy)tetrahydropyran, both in water, are very sensitive in the range 2 ≤ ε ≤ 10 to the relative permittivity of the continuum surrounding the oxacarbenium ion. However, different implementations of nominally the same PCM method can lead to opposite trends being predicted for the same molecule. Computational modeling of the influence of the inhomogeneous effective dielectric surrounding a substrate within the protein environment of an enzymic reaction requires an explicit treatment. The EIE (KH/KD) for transfer of cyclopentyl, cyclohexyl, tetrahydrofuranyl and tetrahydropyranyl cations from water to cyclohexane is predicted by B3LYP/6-31+G(d) calculations with implicit solvation and confirmed by B3LYP/6-31+G(d)/OPLS-AA calculations with averaging over many explicit solvation configurations. Atomic Hessian analysis, whereby the full Hessian is reduced to the elements belonging to a single atom at the site of isotopic substitution, reveals a remarkable result for both implicit and explicit solvation: the influence of the solvent environment on these EIEs is essentially captured completely by only a 3 × 3 block of the Hessian, although these values must correctly reflect the influence of the whole environment. QM/MM simulation with ensemble averaging has an important role to play in assisting the meaningful interpretation of observed isotope effects for chemical reactions both in solution and catalyzed by enzymes.
Collapse
Affiliation(s)
- Katarzyna Świderek
- Departament de Química Física i Analítica , Universitat Jaume I , 12071 Castellón , Spain.,Department of Chemistry , University of Bath , Bath BA2 7AY , United Kingdom
| | - Alexander J Porter
- Department of Chemistry , University of Bath , Bath BA2 7AY , United Kingdom
| | - Catherine M Upfold
- Department of Chemistry , University of Bath , Bath BA2 7AY , United Kingdom
| | - Ian H Williams
- Department of Chemistry , University of Bath , Bath BA2 7AY , United Kingdom
| |
Collapse
|
5
|
Glancy JH, Lee DM, Read EO, Williams IH. Computational simulation of mechanism and isotope effects on acetal heterolysis as a model for glycoside hydrolysis. PURE APPL CHEM 2019. [DOI: 10.1515/pac-2019-0221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Abstract
DFT calculations for the equilibrium isotope effect for deuterium substitution at the anomeric centre Cα in 2-(p-nitrophenoxy)tetrahydropyran with continuum solvation show significant variation in the range of relative permittivity 2 ≤ ε ≤ 10. One-dimensional scans of potential energy (with implicit solvation by water) or of free energy (from QM/MM potentials of mean force with explicit aqueous solvation with a hybrid AM1/OPLS method) for heterolysis of the bond between Cα and the nucleofuge do not show a transition state. A two-dimensional free-energy surface that considers also the distance between Cα and a nucleophilic water indicates a pre-association DN*ANint
‡ mechanism with a transition state involving nucleophilic attack upon an ion-pair intermediate, and this is supported by good agreement between the mean values of the calculated and experimental α-D KIEs. However, the magnitudes of the standard deviations about the mean values for the making and breaking C–O bonds suggest that the transition state is rather plastic, with Cα–Onu≈2 ± 0.4 Å and Cα–Olg≈3 ± 0.5 Å. Not only is nucleophilic solvent assistance necessary, but there is also evidence for electrophilic assistance through specific hydrogen bonding to the nucleofuge.
Collapse
Affiliation(s)
- John H. Glancy
- Department of Chemistry , University of Bath , Bath BA2 7AY , UK
| | - Daniel M. Lee
- Department of Chemistry , University of Bath , Bath BA2 7AY , UK
| | - Emily O. Read
- Department of Chemistry , University of Bath , Bath BA2 7AY , UK
| | - Ian H. Williams
- Department of Chemistry , University of Bath , Bath BA2 7AY , UK
| |
Collapse
|
6
|
Vandebroek L, De Zitter E, Ly HGT, Conić D, Mihaylov T, Sap A, Proost P, Pierloot K, Van Meervelt L, Parac-Vogt TN. Protein-Assisted Formation and Stabilization of Catalytically Active Polyoxometalate Species. Chemistry 2018; 24:10099-10108. [PMID: 29797738 DOI: 10.1002/chem.201802052] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/17/2018] [Indexed: 01/24/2023]
Abstract
The effect of the protein environment on the formation and stabilization of an elusive catalytically active polyoxometalate (POM) species, K6 [Hf(α2 -P2 W17 O61 )] (1), is reported. In the co-crystal of hen egg-white lysozyme (HEWL) with 1, the catalytically active monomeric species is observed, originating from the dimeric 1:2 POM form, while it is intrinsically unstable under physiological pH conditions. The protein-assisted dissociation of the dimeric POM was rationalized by means of DFT calculations. The dissociation process is unfavorable in bulk water, but becomes favorable in the protein-POM complex due to the low dielectric response at the protein surface. The crystal structure shows that the monomeric form is stabilized by electrostatic and water-mediated hydrogen bonding interactions with the protein. It interacts at three distinct sites, close to the aspartate-containing hydrolysis sites, demonstrating high selectivity towards peptide bonds containing this residue.
Collapse
Affiliation(s)
- Laurens Vandebroek
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F box 2404, 3001, Leuven, Belgium
| | - Elke De Zitter
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F box 2404, 3001, Leuven, Belgium
| | - Hong Giang Thi Ly
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F box 2404, 3001, Leuven, Belgium
| | - Dragan Conić
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F box 2404, 3001, Leuven, Belgium
| | - Tzvetan Mihaylov
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F box 2404, 3001, Leuven, Belgium
| | - Annelies Sap
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F box 2404, 3001, Leuven, Belgium
| | - Paul Proost
- Department of Microbiology and Immunology, Rega Institute, Herestraat 49 box 1042, 3000, Leuven, Belgium
| | - Kristine Pierloot
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F box 2404, 3001, Leuven, Belgium
| | - Luc Van Meervelt
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F box 2404, 3001, Leuven, Belgium
| | - Tatjana N Parac-Vogt
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F box 2404, 3001, Leuven, Belgium
| |
Collapse
|
7
|
Wahle CW, Martini KM, Hollenbeck DM, Langner A, Ross DS, Hamilton JF, Thurston GM. Model for screened, charge-regulated electrostatics of an eye lens protein: Bovine gammaB-crystallin. Phys Rev E 2017; 96:032415. [PMID: 29346981 PMCID: PMC5830141 DOI: 10.1103/physreve.96.032415] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Indexed: 06/07/2023]
Abstract
We model screened, site-specific charge regulation of the eye lens protein bovine gammaB-crystallin (γB) and study the probability distributions of its proton occupancy patterns. Using a simplified dielectric model, we solve the linearized Poisson-Boltzmann equation to calculate a 54×54 work-of-charging matrix, each entry being the modeled voltage at a given titratable site, due to an elementary charge at another site. The matrix quantifies interactions within patches of sites, including γB charge pairs. We model intrinsic pK values that would occur hypothetically in the absence of other charges, with use of experimental data on the dependence of pK values on aqueous solution conditions, the dielectric model, and literature values. We use Monte Carlo simulations to calculate a model grand-canonical partition function that incorporates both the work-of-charging and the intrinsic pK values for isolated γB molecules and we calculate the probabilities of leading proton occupancy configurations, for 4<pH<8 and Debye screening lengths from 6 to 20 Å. We select the interior dielectric value to model γB titration data. At pH 7.1 and Debye length 6.0 Å, on a given γB molecule the predicted top occupancy pattern is present nearly 20% of the time, and 90% of the time one or another of the first 100 patterns will be present. Many of these occupancy patterns differ in net charge sign as well as in surface voltage profile. We illustrate how charge pattern probabilities deviate from the multinomial distribution that would result from use of effective pK values alone and estimate the extents to which γB charge pattern distributions broaden at lower pH and narrow as ionic strength is lowered. These results suggest that for accurate modeling of orientation-dependent γB-γB interactions, consideration of numerous pairs of proton occupancy patterns will be needed.
Collapse
Affiliation(s)
- Christopher W. Wahle
- School of Mathematical Sciences, Rochester Institute of Technology, Rochester, New York 14623, USA
| | - K. Michael Martini
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, New York 14623, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana-Champaign, Illinois 61801, USA
| | - Dawn M. Hollenbeck
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, New York 14623, USA
| | - Andreas Langner
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, USA
| | - David S. Ross
- School of Mathematical Sciences, Rochester Institute of Technology, Rochester, New York 14623, USA
| | - John F. Hamilton
- School of Mathematical Sciences, Rochester Institute of Technology, Rochester, New York 14623, USA
| | - George M. Thurston
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, New York 14623, USA
| |
Collapse
|
8
|
Maiangwa J, Mohamad Ali MS, Salleh AB, Rahman RNZRA, Normi YM, Mohd Shariff F, Leow TC. Lid opening and conformational stability of T1 Lipase is mediated by increasing chain length polar solvents. PeerJ 2017; 5:e3341. [PMID: 28533982 PMCID: PMC5438581 DOI: 10.7717/peerj.3341] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 04/21/2017] [Indexed: 11/20/2022] Open
Abstract
The dynamics and conformational landscape of proteins in organic solvents are events of potential interest in nonaqueous process catalysis. Conformational changes, folding transitions, and stability often correspond to structural rearrangements that alter contacts between solvent molecules and amino acid residues. However, in nonaqueous enzymology, organic solvents limit stability and further application of proteins. In the present study, molecular dynamics (MD) of a thermostable Geobacillus zalihae T1 lipase was performed in different chain length polar organic solvents (methanol, ethanol, propanol, butanol, and pentanol) and water mixture systems to a concentration of 50%. On the basis of the MD results, the structural deviations of the backbone atoms elucidated the dynamic effects of water/organic solvent mixtures on the equilibrium state of the protein simulations in decreasing solvent polarity. The results show that the solvent mixture gives rise to deviations in enzyme structure from the native one simulated in water. The drop in the flexibility in H2O, MtOH, EtOH and PrOH simulation mixtures shows that greater motions of residues were influenced in BtOH and PtOH simulation mixtures. Comparing the root mean square fluctuations value with the accessible solvent area (SASA) for every residue showed an almost correspondingly high SASA value of residues to high flexibility and low SASA value to low flexibility. The study further revealed that the organic solvents influenced the formation of more hydrogen bonds in MtOH, EtOH and PrOH and thus, it is assumed that increased intraprotein hydrogen bonding is ultimately correlated to the stability of the protein. However, the solvent accessibility analysis showed that in all solvent systems, hydrophobic residues were exposed and polar residues tended to be buried away from the solvent. Distance variation of the tetrahedral intermediate packing of the active pocket was not conserved in organic solvent systems, which could lead to weaknesses in the catalytic H-bond network and most likely a drop in catalytic activity. The conformational variation of the lid domain caused by the solvent molecules influenced its gradual opening. Formation of additional hydrogen bonds and hydrophobic interactions indicates that the contribution of the cooperative network of interactions could retain the stability of the protein in some solvent systems. Time-correlated atomic motions were used to characterize the correlations between the motions of the atoms from atomic coordinates. The resulting cross-correlation map revealed that the organic solvent mixtures performed functional, concerted, correlated motions in regions of residues of the lid domain to other residues. These observations suggest that varying lengths of polar organic solvents play a significant role in introducing dynamic conformational diversity in proteins in a decreasing order of polarity.
Collapse
Affiliation(s)
- Jonathan Maiangwa
- Department of Cell and Molecular Biology/Enzyme Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Serlangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Department of Biochemistry/Enzyme Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Abu Bakar Salleh
- Department of Biochemistry/Enzyme Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Department of Microbiology/Enzyme Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Yahaya M Normi
- Department of Cell and Molecular Biology/Enzyme Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Serlangor, Malaysia
| | - Fairolniza Mohd Shariff
- Department of Microbiology/Enzyme Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Department of Cell and Molecular Biology/Enzyme and Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science/Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| |
Collapse
|
9
|
Martins ACV, de-Lima-Neto P, Caetano EWS, Freire VN. An improved quantum biochemistry description of the glutamate–GluA2 receptor binding within an inhomogeneous dielectric function framework. NEW J CHEM 2017. [DOI: 10.1039/c6nj03939a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A new methodology to define the inhomogeneous dielectric constant of protein residues, to apply to the calculation of protein–ligand properties such as the electrostatic interaction.
Collapse
Affiliation(s)
- A. C. V. Martins
- Department of Analytical Chemistry and Physical-Chemistry
- Federal University of Ceara
- 60455-760 Fortaleza
- Brazil
| | - P. de-Lima-Neto
- Department of Analytical Chemistry and Physical-Chemistry
- Federal University of Ceara
- 60455-760 Fortaleza
- Brazil
| | - E. W. S. Caetano
- Federal Institute of Education
- Science and Technology of Ceara
- 60040-531 Fortaleza
- Brazil
| | - V. N. Freire
- Department of Physics
- Federal University of Ceara
- 60455-760 Fortaleza
- Brazil
| |
Collapse
|
10
|
Chen Z, Wang G, Xu Z, Wang J, Yu Y, Cai T, Shao Q, Shi J, Zhu W. How Do Distance and Solvent Affect Halogen Bonding Involving Negatively Charged Donors? J Phys Chem B 2016; 120:8784-93. [DOI: 10.1021/acs.jpcb.6b05027] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhaoqiang Chen
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Guimin Wang
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Zhijian Xu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Jinan Wang
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Yuqi Yu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Tingting Cai
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Qiang Shao
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Jiye Shi
- UCB Biopharma SPRL, Chemin
du Foriest, Braine-l’Alleud B-1420, Belgium
| | - Weiliang Zhu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| |
Collapse
|
11
|
Sousa BL, Barroso-Neto IL, Oliveira EF, Fonseca E, Lima-Neto P, Ladeira LO, Freire VN. Explaining RANKL inhibition by OPG through quantum biochemistry computations and insights into peptide-design for the treatment of osteoporosis. RSC Adv 2016. [DOI: 10.1039/c6ra16712h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Quantum biochemistry computations are applied to precisely describe important protein–protein interactions, providing a basis for the design of inhibitory peptides against osteoporosis.
Collapse
Affiliation(s)
- Bruno L. Sousa
- Departamento de Física
- Universidade Federal do Ceará
- Fortaleza
- Brazil
| | - Ito L. Barroso-Neto
- Departamento de Química Analítica e Físico-Química
- Universidade Federal do Ceará
- Fortaleza
- Brazil
| | | | - Emerson Fonseca
- Departamento de Física
- Universidade Federal de Minas Gerais
- Belo Horizonte
- Brazil
| | - Pedro Lima-Neto
- Departamento de Química Analítica e Físico-Química
- Universidade Federal do Ceará
- Fortaleza
- Brazil
| | - Luiz O. Ladeira
- Departamento de Física
- Universidade Federal de Minas Gerais
- Belo Horizonte
- Brazil
| | - Valder N. Freire
- Departamento de Física
- Universidade Federal do Ceará
- Fortaleza
- Brazil
| |
Collapse
|
12
|
Yang Y, Xu Z, Zhang Z, Yang Z, Liu Y, Wang J, Cai T, Li S, Chen K, Shi J, Zhu W. Like-Charge Guanidinium Pairing between Ligand and Receptor: An Unusual Interaction for Drug Discovery and Design? J Phys Chem B 2015; 119:11988-97. [DOI: 10.1021/acs.jpcb.5b04130] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yang Yang
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhijian Xu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- State
Key Laboratory of Medicinal Chemical Biology, Nankai University, 94
Weijin Road, Nankai District, Tianjin300071, China
| | - Zhengyan Zhang
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- College
of Chemistry, Chemical Engineering and Materials Science of Soochow
University, Soochow University, Suzhou, Jiangsu 215123, China
| | - Zhuo Yang
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yingtao Liu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jinan Wang
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tingting Cai
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shujin Li
- College
of Chemistry, Chemical Engineering and Materials Science of Soochow
University, Soochow University, Suzhou, Jiangsu 215123, China
| | - Kaixian Chen
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jiye Shi
- Informatics
Department, UCB Pharma, 216 Bath Road, Slough SL1 4EN, United Kingdom
| | - Weiliang Zhu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| |
Collapse
|
13
|
Song X, Wang Y, Zhang S, Yan S, Li T, Yao L. Characterization of the Dielectric Constant in the Trichoderma reesei Cel7B Active Site. J Chem Inf Model 2015; 55:1369-76. [PMID: 26114648 DOI: 10.1021/acs.jcim.5b00155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An attempt is made to evaluate the dielectric constant of the Trichoderma reesei Cel7B active site. Through kinetic measurements, the pKa value of the catalytic acid E201 is determined. Mutations (away from E201) with net charge changes are introduced to perturb the E201 pKa. It is shown that the mutation with a +1 charge change (including G225R, G230R, and A335R) decreases the pKa of E201, whereas the mutation with a -1 charge change (including Q149E, A222D, G225D, and G230D) increases the pKa. This effect is consistent with the electrostatic interaction between the changed charge and the E201 side chain. The fitting of the experimental data yields an apparent dielectric constant of 25-80. Molecular dynamics simulations with explicit water molecules indicate that the high solvent accessibility of the active site contributes largely to the high dielectric constant. ONIOM calculations show that high dielectric constant benefits the catalysis through decreasing the energy of the transition state relative to that of the enzyme substrate complex.
Collapse
Affiliation(s)
- Xiangfei Song
- †Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266061, China
| | - Yefei Wang
- †Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266061, China
| | - Shujun Zhang
- †Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266061, China
| | - Shihai Yan
- ‡College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, Shandong, 266109, China
| | - Tong Li
- †Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266061, China
| | - Lishan Yao
- †Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266061, China
| |
Collapse
|
14
|
Yang Z, Xu Z, Liu Y, Wang J, Shi J, Chen K, Zhu W. Unstable, metastable, or stable halogen bonding interaction involving negatively charged donors? A statistical and computational chemistry study. J Phys Chem B 2014; 118:14223-33. [PMID: 25390886 DOI: 10.1021/jp506291v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The noncovalent halogen bonding could be attributed to the attraction between the positively charged σ-hole and a nucleophile. Quantum mechanics (QM) calculation indicated that the negatively charged organohalogens have no positively charged σ-hole on their molecular surface, leading to a postulation of repulsion between negatively charged organohalogens and nucleophiles in vacuum. However, PDB survey revealed that 24% of the ligands with halogen bonding geometry could be negatively charged. Moreover, 36% of ionizable drugs in CMC (Comprehensive Medicinal Chemistry) are possibly negatively charged at pH 7.0. QM energy scan showed that the negatively charged halogen bonding is probably metastable in vacuum. However, the QM calculated bonding energy turned negative in various solvents, suggesting that halogen bonding with negatively charged donors should be stable in reality. Indeed, QM/MM calculation on three crystal structures with negatively charged ligands revealed that the negatively charged halogen bonding was stable. Hence, we concluded that halogen bonding with negatively charged donors is unstable or metastable in vacuum but stable in protein environment, and possesses similar geometric and energetic characteristics as conventional halogen bonding. Therefore, negatively charged organohalogens are still effective halogen bonding donors for medicinal chemistry and other applications.
Collapse
Affiliation(s)
- Zhuo Yang
- Drug Discovery and Design Center, Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai, 201203, China
| | | | | | | | | | | | | |
Collapse
|
15
|
Wilson PB, Weaver PJ, Greig IR, Williams IH. Solvent effects on isotope effects: methyl cation as a model system. J Phys Chem B 2014; 119:802-9. [PMID: 25010417 DOI: 10.1021/jp505344a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The isotopic sensitivity (CH3(+) vs CD3(+)) of the equilibrium between the methyl cation in vacuum and in solution has been investigated. Two alternative options for describing the shape of the solute cavity within the widely used polarized continuum model for implicit solvation were compared; the UFF and UA0 methods give equilibrium isotope effects (EIEs) that vary as a function of the dielectric constant in opposite directions. The same isotope effect was also obtained as the average over 40 structures from a hybrid quantum mechanical/molecular mechanical molecular dynamics simulation for the methyl cation explicitly solvated by many water molecules; the inverse value of the EIE agrees with UFF but not UA0. The opposing trends may be satisfactorily explained in terms of the different degrees of exposure of the atomic charges to the dielectric continuum in cavities of different shapes.
Collapse
Affiliation(s)
- Philippe B Wilson
- Department of Chemistry, University of Bath , Bath BA2 7AY, United Kingdom
| | | | | | | |
Collapse
|
16
|
Martin C, Cohen B, Gaamoussi I, Ijjaali M, Douhal A. Ultrafast Dynamics of C30 in Solution and within CDs and HSA Protein. J Phys Chem B 2014; 118:5760-71. [DOI: 10.1021/jp5026575] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Cristina Martin
- Departamento
de Química Física, Facultad de Ciencias Ambientales
y Bioquímica, and INAMOL, Universidad de Castilla-La Mancha, Avenida Carlos III, S/N, 45071 Toledo, Spain
| | - Boiko Cohen
- Departamento
de Química Física, Facultad de Ciencias Ambientales
y Bioquímica, and INAMOL, Universidad de Castilla-La Mancha, Avenida Carlos III, S/N, 45071 Toledo, Spain
| | - Issam Gaamoussi
- Departamento
de Química Física, Facultad de Ciencias Ambientales
y Bioquímica, and INAMOL, Universidad de Castilla-La Mancha, Avenida Carlos III, S/N, 45071 Toledo, Spain
- Laboratorie
de Chimie de la Matière Condensée, Faculté des
Sciences et Techniques, University of Sidi Mohamed Ben Abdellah, Fez, Morocco 2202
| | - Mustapha Ijjaali
- Laboratorie
de Chimie de la Matière Condensée, Faculté des
Sciences et Techniques, University of Sidi Mohamed Ben Abdellah, Fez, Morocco 2202
| | - Abderrazzak Douhal
- Departamento
de Química Física, Facultad de Ciencias Ambientales
y Bioquímica, and INAMOL, Universidad de Castilla-La Mancha, Avenida Carlos III, S/N, 45071 Toledo, Spain
| |
Collapse
|
17
|
Bossa GV, Fahr A, Pereira de Souza T. Study of pK values and effective dielectric constants of ionizable residues in pentapeptides and in staphylococcal nuclease (SNase) using a mean-field approach. J Phys Chem B 2014; 118:4053-61. [PMID: 24708515 DOI: 10.1021/jp411331p] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The determination of pK values of amino acid residues as a function of temperature and ionic concentration is crucial to understanding the dynamics of various biological processes such as adsorption of peptides and their interactions with active sites of enzymes. In this study we developed a mean-field model to calculate the position-dependent dielectric constants of ionizable groups and the mean electrostatic potential on the surface. Such potential, which takes into account the contributions exerted by neighboring groups and ions in solution, is responsible for the fine-tuning of the pK value of each residue. The proposed model was applied to the amino acids Asp, Glu, Lys, His, Tyr, and Cys, and since the results were consistent with experimentally obtained values, the model was extended and applied to computation of pK values of Gly and Ala pentapeptides and of ionizable residues of the enzyme staphylococcal nuclease (SNase). In this latter case, we used an approach similar to a first-neighbors approximation, and the results turned out to be in good agreement with previously reported data when considering only the interactions of charged groups located at distances of maximally 20 Å. These considerations and the little computational cost involved turn the suggested approach into a promising tool for the modeling of force fields in computational simulations.
Collapse
Affiliation(s)
- Guilherme Volpe Bossa
- Instituto de Biociencias, Letras e Ciencias Exatas, Sao Paulo State University , Sao Jose do Rio Preto, 15054-000, Brazil
| | | | | |
Collapse
|
18
|
Zanatta G, Gottfried C, Silva AM, Caetano EWS, Sales FAM, Freire VN. L-Asparagine crystals with wide gap semiconductor features: optical absorption measurements and density functional theory computations. J Chem Phys 2014; 140:124511. [PMID: 24697463 DOI: 10.1063/1.4869179] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Results of optical absorption measurements are presented together with calculated structural, electronic, and optical properties for the anhydrous monoclinic L-asparagine crystal. Density functional theory (DFT) within the generalized gradient approximation (GGA) including dispersion effects (TS, Grimme) was employed to perform the calculations. The optical absorption measurements revealed that the anhydrous monoclinic L-asparagine crystal is a wide band gap material with 4.95 eV main gap energy. DFT-GGA+TS simulations, on the other hand, produced structural parameters in very good agreement with X-ray data. The lattice parameter differences Δa, Δb, Δc between theory and experiment were as small as 0.020, 0.051, and 0.022 Å, respectively. The calculated band gap energy is smaller than the experimental data by about 15%, with a 4.23 eV indirect band gap corresponding to Z → Γ and Z → β transitions. Three other indirect band gaps of 4.30 eV, 4.32 eV, and 4.36 eV are assigned to α3 → Γ, α1 → Γ, and α2 → Γ transitions, respectively. Δ-sol computations, on the other hand, predict a main band gap of 5.00 eV, just 50 meV above the experimental value. Electronic wavefunctions mainly originating from O 2p-carboxyl, C 2p-side chain, and C 2p-carboxyl orbitals contribute most significantly to the highest valence and lowest conduction energy bands, respectively. By varying the lattice parameters from their converged equilibrium values, we show that the unit cell is less stiff along the b direction than for the a and c directions. Effective mass calculations suggest that hole transport behavior is more anisotropic than electron transport, but the mass values allow for some charge mobility except along a direction perpendicular to the molecular layers of L-asparagine which form the crystal, so anhydrous monoclinic L-asparagine crystals could behave as wide gap semiconductors. Finally, the calculations point to a high degree of optical anisotropy for the absorption and complex dielectric function, with more structured curves for incident light polarized along the 100 and 101 directions.
Collapse
Affiliation(s)
- G Zanatta
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul, 90035-003 Porto Alegre-RS, Brazil
| | - C Gottfried
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul, 90035-003 Porto Alegre-RS, Brazil
| | - A M Silva
- Universidade Estadual do Piauí, 64260-000 Piripiri-Pi, Brazil
| | - E W S Caetano
- Instituto de Educação, Ciência e Tecnologia do Ceará, 60040-531 Fortaleza-CE, Brazil
| | - F A M Sales
- Departamento de Física, Universidade Federal do Ceará, Caixa Postal 6030, 60455-760 Fortaleza-CE, Brazil
| | - V N Freire
- Departamento de Física, Universidade Federal do Ceará, Caixa Postal 6030, 60455-760 Fortaleza-CE, Brazil
| |
Collapse
|
19
|
Vonderach M, Winghart MO, MacAleese L, Chirot F, Antoine R, Dugourd P, Weis P, Hampe O, Kappes MM. Conformer-selective photoelectron spectroscopy of α-lactalbumin derived multianions in the gas phase. Phys Chem Chem Phys 2014; 16:3007-13. [DOI: 10.1039/c3cp54596b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
20
|
Foderà V, Zaccone A, Lattuada M, Donald AM. Electrostatics controls the formation of amyloid superstructures in protein aggregation. PHYSICAL REVIEW LETTERS 2013; 111:108105. [PMID: 25166715 DOI: 10.1103/physrevlett.111.108105] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Indexed: 05/23/2023]
Abstract
The possibility for proteins to aggregate in different superstructures, i.e. large-scale polymorphism, has been widely observed, but an understanding of the physicochemical mechanisms behind it is still out of reach. Here we present a theoretical model for the description of a generic aggregate formed from an ensemble of charged proteins. The model predicts the formation of multifractal structures with the geometry of the growth determined by the electrostatic interactions between single proteins. The model predictions are successfully verified in comparison with experimental curves for aggregate growth allowing us to reveal the mechanism of formation of such complex structures. The model is general and is able to predict aggregate morphologies occurring both in vivo and in vitro. Our findings provide a framework where the physical interactions between single proteins, the aggregate morphology, and the growth kinetics are connected into a single model in agreement with the experimental data.
Collapse
Affiliation(s)
- Vito Foderà
- Sector of Biological and Soft Systems, Department of Physics, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Alessio Zaccone
- Sector of Biological and Soft Systems, Department of Physics, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom and Theory of Condensed Matter, Department of Physics, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Marco Lattuada
- ETH Institute for Chemical and Bioengineering, HCI F135, Wolfgang Pauli Strasse 10, 8093 Zurich, Switzerland
| | - Athene M Donald
- Sector of Biological and Soft Systems, Department of Physics, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| |
Collapse
|
21
|
Rocklin GJ, Mobley DL, Dill KA. Calculating the sensitivity and robustness of binding free energy calculations to force field parameters. J Chem Theory Comput 2013; 9:3072-3083. [PMID: 24015114 PMCID: PMC3763860 DOI: 10.1021/ct400315q] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Binding free energy calculations offer a thermodynamically rigorous method to compute protein-ligand binding, and they depend on empirical force fields with hundreds of parameters. We examined the sensitivity of computed binding free energies to the ligand's electrostatic and van der Waals parameters. Dielectric screening and cancellation of effects between ligand-protein and ligand-solvent interactions reduce the parameter sensitivity of binding affinity by 65%, compared with interaction strengths computed in the gas-phase. However, multiple changes to parameters combine additively on average, which can lead to large changes in overall affinity from many small changes to parameters. Using these results, we estimate that random, uncorrelated errors in force field nonbonded parameters must be smaller than 0.02 e per charge, 0.06 Å per radius, and 0.01 kcal/mol per well depth in order to obtain 68% (one standard deviation) confidence that a computed affinity for a moderately-sized lead compound will fall within 1 kcal/mol of the true affinity, if these are the only sources of error considered.
Collapse
Affiliation(s)
- Gabriel J Rocklin
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4 St, San Francisco California 94143-2550, USA ; Biophysics Graduate Program, University of California San Francisco, 1700 4 St, San Francisco California 94143-2550, USA
| | | | | |
Collapse
|
22
|
Zhang Z, Xu Z, Yang Z, Liu Y, Wang J, Shao Q, Li S, Lu Y, Zhu W. The stabilization effect of dielectric constant and acidic amino acids on arginine-arginine (Arg-Arg) pairings: database survey and computational studies. J Phys Chem B 2013; 117:4827-35. [PMID: 23581492 DOI: 10.1021/jp4001658] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Database survey in this study revealed that about one-third of the protein structures deposited in the Protein Data Bank (PDB) contain arginine-arginine (Arg-Arg) pairing with a carbon···carbon (CZ···CZ) interaction distance less than 5 Å. All the Arg-Arg pairings were found to bury in a polar environment composed of acidic residues, water molecules, and strong polarizable or negatively charged moieties from binding site or bound ligand. Most of the Arg-Arg pairings are solvent exposed and 68.3% Arg-Arg pairings are stabilized by acidic residues, forming Arg-Arg-Asp/Glu clusters. Density functional theory (DFT) was then employed to study the effect of environment on the pairing structures. It was revealed that Arg-Arg pairings become thermodynamically stable (about -1 kcal/mol) as the dielectric constant increases to 46.8 (DMSO), in good agreement with the results of the PDB survey. DFT calculations also demonstrated that perpendicular Arg-Arg pairing structures are favorable in low dielectric constant environment, while in high dielectric constant environment parallel structures are favorable. Additionally, the acidic residues can stabilize the Arg-Arg pairing structures to a large degree. Energy decomposition analysis of Arg-Arg pairings and Arg-Arg-Asp/Glu clusters showed that both solvation and electrostatic energies contribute significantly to their stability. The results reported herein should be very helpful for understanding Arg-Arg pairing and its application in drug design.
Collapse
Affiliation(s)
- Zhengyan Zhang
- College of Chemistry, Chemical Engineering and Materials Science of Soochow University, Soochow University, Suzhou, Jiangsu, 215123, China
| | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Chan HY, Lankevich V, Vekilov PG, Lubchenko V. Anisotropy of the Coulomb interaction between folded proteins: consequences for mesoscopic aggregation of lysozyme. Biophys J 2012; 102:1934-43. [PMID: 22768950 DOI: 10.1016/j.bpj.2012.03.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 02/16/2012] [Accepted: 03/02/2012] [Indexed: 10/28/2022] Open
Abstract
Toward quantitative description of protein aggregation, we develop a computationally efficient method to evaluate the potential of mean force between two folded protein molecules that allows for complete sampling of their mutual orientation. Our model is valid at moderate ionic strengths and accounts for the actual charge distribution on the surface of the molecules, the dielectric discontinuity at the protein-solvent interface, and the possibility of protonation or deprotonation of surface residues induced by the electric field due to the other protein molecule. We apply the model to the protein lysozyme, whose solutions exhibit both mesoscopic clusters of protein-rich liquid and liquid-liquid separation; the former requires that protein form complexes with typical lifetimes of approximately milliseconds. We find the electrostatic repulsion is typically lower than the prediction of the Derjaguin-Landau-Verwey-Overbeek theory. The Coulomb interaction in the lowest-energy docking configuration is nonrepulsive, despite the high positive charge on the molecules. Typical docking configurations barely involve protonation or deprotonation of surface residues. The obtained potential of mean force between folded lysozyme molecules is consistent with the location of the liquid-liquid coexistence, but produces dimers that are too short-lived for clusters to exist, suggesting lysozyme undergoes conformational changes during cluster formation.
Collapse
Affiliation(s)
- Ho Yin Chan
- Department of Physics, University of Houston, Houston, Texas, USA
| | | | | | | |
Collapse
|
24
|
Interaction of organic solvents with protein structures at protein-solvent interface. J Mol Model 2012; 19:4701-11. [DOI: 10.1007/s00894-012-1507-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2011] [Accepted: 06/13/2012] [Indexed: 10/28/2022]
|
25
|
Cohen B, Martin Álvarez C, Alarcos Carmona N, Organero JA, Douhal A. Proton-Transfer Reaction Dynamics within the Human Serum Albumin Protein. J Phys Chem B 2011; 115:7637-47. [DOI: 10.1021/jp200294q] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Boiko Cohen
- Departamento de Química Física, Facultad de Ciencias Ambientales y Bioquímica, and INAMOL, Universidad de Castilla-La Mancha, Avenida Carlos III, S/N, 45071 Toledo, Spain
| | - Cristina Martin Álvarez
- Departamento de Química Física, Facultad de Ciencias Ambientales y Bioquímica, and INAMOL, Universidad de Castilla-La Mancha, Avenida Carlos III, S/N, 45071 Toledo, Spain
| | - Noemí Alarcos Carmona
- Departamento de Química Física, Facultad de Ciencias Ambientales y Bioquímica, and INAMOL, Universidad de Castilla-La Mancha, Avenida Carlos III, S/N, 45071 Toledo, Spain
| | - Juan Angel Organero
- Departamento de Química Física, Facultad de Ciencias Ambientales y Bioquímica, and INAMOL, Universidad de Castilla-La Mancha, Avenida Carlos III, S/N, 45071 Toledo, Spain
| | - Abderrazzak Douhal
- Departamento de Química Física, Facultad de Ciencias Ambientales y Bioquímica, and INAMOL, Universidad de Castilla-La Mancha, Avenida Carlos III, S/N, 45071 Toledo, Spain
| |
Collapse
|
26
|
The dynamics of Ca2+ ions within the solvation shell of calbindin D9k. PLoS One 2011; 6:e14718. [PMID: 21364983 PMCID: PMC3043054 DOI: 10.1371/journal.pone.0014718] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 01/28/2011] [Indexed: 11/25/2022] Open
Abstract
The encounter of a Ca2+ ion with a protein and its subsequent
binding to specific binding sites is an intricate process that cannot be fully
elucidated from experimental observations. We have applied Molecular Dynamics to
study this process with atomistic details, using Calbindin D9k (CaB) as a model
protein. The simulations show that in most of the time the Ca2+
ion spends within the Debye radius of CaB, it is being detained at the 1st and
2nd solvation shells. While being detained near the protein, the diffusion
coefficient of the ion is significantly reduced. However, due to the relatively
long period of detainment, the ion can scan an appreciable surface of the
protein. The enhanced propagation of the ion on the surface has a functional
role: significantly increasing the ability of the ion to scan the protein's
surface before being dispersed to the bulk. The contribution of this mechanism
to Ca2+ binding becomes significant at low ion concentrations,
where the intervals between successive encounters with the protein are getting
longer. The efficiency of the surface diffusion is affected by the distribution
of charges on the protein's surface. Comparison of the Ca2+
binding dynamics in CaB and its E60D mutant reveals that in the wild type (WT)
protein the carboxylate of E60 function as a preferred landing-site for the
Ca2+ arriving from the bulk, followed by delivering it to
the final binding site. Replacement of the glutamate by aspartate significantly
reduced the ability to transfer Ca2+ ions from D60 to the final
binding site, explaining the observed decrement in the affinity of the mutated
protein to Ca2+.
Collapse
|
27
|
Guest WC, Cashman NR, Plotkin SS. A theory for the anisotropic and inhomogeneous dielectric properties of proteins. Phys Chem Chem Phys 2011; 13:6286-95. [DOI: 10.1039/c0cp02061c] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
28
|
Danielewicz-Ferchmin I, Banachowicz EM, Ferchmin AR. Role of electromechanical and mechanoelectric effects in protein hydration under hydrostatic pressure. Phys Chem Chem Phys 2011; 13:17722-8. [DOI: 10.1039/c1cp21819k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|