Functional properties of threefold and fourfold channels in ferritin deduced from electrostatic calculations
Takahashi T, Kuyucak S
BIOPHYSICAL JOURNAL
84 (4): 2256-2263 APR 2003
Document type: Article Language: English Cited References: 35 Times Cited: 0
Abstract:
The iron storage protein ferritin contains threefold and fourfold symmetric channels that are thought to provide pathways for the transfer of Fe2+ ions in and out of the protein. Using the known crystal structure of the ferritin protein, we perform electrostatic potential energy calculations to elucidate the functional properties of these channels. The threefold channel is shown to be responsible for the transit of Fe2+ ions. Monovalent ions can also diffuse through the threefold channel but presence of divalent ions in the pore retards this process leading to a selectivity mechanism similar to the one observed in calcium channels. The fourfold channel is found to be impermeant to all cations with the possible exception of protons. Because proton transfer is essential to maintain the electroneutrality of the protein during iron deposition, we suggest that the function of the fourfold channel is to form a "proton wire" that facilitates their transfer in and out of ferritin.
KeyWords Plus:
SITE-DIRECTED MUTAGENESIS, RECOMBINANT-HUMAN-H, BROWNIAN DYNAMICS, ION CHANNELS, HIGH-RESOLUTION, IRON UPTAKE, PERMEATION, ENERGY, CONTINUUM, PROFILES
Addresses:
Kuyucak S, Australian Natl Univ, Res Sch Phys Sci, Dept Theoret Phys, Canberra, ACT 0200, Australia
Australian Natl Univ, Res Sch Phys Sci, Dept Theoret Phys, Canberra, ACT 0200, Australia
Okazaki Natl Res Inst, Res Ctr Computat Sci, Okazaki, Aichi 4448585, Japan
Publisher:
BIOPHYSICAL SOCIETY, BETHESDA
IDS Number:
682ZZ
ISSN:
0006-3495
Comparison of all atom, continuum, and linear fitting empirical models for charge screening effect of aqueous medium surrounding a protein molecule
Takahashi T, Sugiura J, Nagayama K
JOURNAL OF CHEMICAL PHYSICS
116 (18): 8232-8237 MAY 8 2002
Document type: Article Language: English Cited References: 31 Times Cited: 0
Abstract:
To investigate the role hydration plays in the electrostatic interactions of proteins, the time-averaged electrostatic potential of the B1 domain of protein G in an aqueous solution was calculated with full atomic molecular dynamics simulations that explicitly considers every atom (i.e., an all atom model). This all atom calculated potential was compared with the potential obtained from an electrostatic continuum model calculation. In both cases, the charge-screening effect was fairly well formulated with an effective relative dielectric constant which increased linearly with increasing charge-charge distance. This simulated linear dependence agrees with the experimentally determined linear relation proposed by Pickersgill. Cut-off approximations for Coulomb interactions failed to reproduce this linear relation. Correlation between the all atom model and the continuum models was found to be better than the respective correlation calculated for linear fitting to the two models. This confirms that the continuum model is better at treating the complicated shapes of protein conformations than the simple linear fitting empirical model. We have tried a sigmoid fitting empirical model in addition to the linear one. When weights of all data were treated equally, the sigmoid model, which requires two fitting parameters, fits results of both the all atom and the continuum models less accurately than the linear model which requires only one fitting parameter. When potential values are chosen as weighting factors, the fitting error of the sigmoid model became smaller, and the slope of both linear fitting curves became smaller. This suggests the screening effect of an aqueous medium within a short range, where potential values are relatively large, is smaller than that expected from the linear fitting curve whose slope is almost 4. To investigate the linear increase of the effective relative dielectric constant, the Poisson equation of a low-dielectric sphere in a high-dielectric medium was solved and charges distributed near the molecular surface were indicated as leading to the apparent linearity. (C) 2002 American Institute of Physics.
KeyWords Plus:
DYNAMICS SIMULATIONS, SELF-CONSISTENT, STABILITY, WATER, APPROXIMATION
Addresses:
Takahashi T, Res Ctr Computat Sci, 38 Aza Nishigounaka,Myoudaiji Machi, Okazaki, Aichi 444, Japan
Res Ctr Computat Sci, Okazaki, Aichi 444, Japan
Univ Tokyo, Grad Sch Arts & Sci, Dept Life Sci, Meguro Ku, Tokyo 153, Japan
Ctr Integrat Biosci, Okazaki, Aichi 444, Japan
Publisher:
AMER INST PHYSICS, MELVILLE
IDS Number:
545BL
ISSN:
0021-9606
Record 1 of 11
Author(s): Takano M; Takahashi T; Nagayama K
Title: Helix-coil transition and 1/f fluctuation in a polypeptide
Source: PHYSICAL REVIEW LETTERS 1998, Vol 80, Iss 25, pp 5691-5694
No. cited references: 31
Publisher: AMERICAN PHYSICAL SOC
Addresses: Takano M, Univ Tokyo, Grad Sch Arts & Sci, Dept Life Sci, Meguro Ku, 3-8-1 Komaba, Tokyo 1538902, Japan
Univ Tokyo, Grad Sch Arts & Sci, Dept Life Sci, Meguro Ku, Tokyo 1538902, Japan
KeywordsPlus: MOLECULAR-DYNAMICS; PROTEIN; ENERGY; NOISE; SIMULATIONS; PRINCIPLES; SURFACES; PEPTIDES; CLUSTERS
Abstract: We report on molecular dynamics simulations of the helix-coil transition of a polypeptide. The simulated transition was two-state-like and similar to the solid-liquid-like transition that has been observed in computer simulations of an atomic cluster. At the transition temperature, the polypeptide chain fluctuated between a helical and a random-coil state, and we observed 1/f fluctuation through potential-energy fluctuations. The origin of the observed 1/f fluctuation is discussed, considering the underlying potential-energy landscape.
Cited references: ANFINSEN CB-1973-SCIENCE-V181-P223
ANSARI A-1985-P-NATL-ACAD-SCI-USA-V82-P5000
ARECCHI FT-1987-EUROPHYS-LETT-V3-P5
BALL KD-1996-SCIENCE-V271-P963
BALLEW RM-1996-P-NATL-ACAD-SCI-USA-V93-P5759
BERRY RS-1995-J-PHYS-CHEM-US-V98-P6910
BERRY RS-1995-PHYS-REV-LETT-V74-P3951
BOCZKO EM-1995-SCIENCE-V269-P393
BRYNGELSON JD-1989-J-PHYS-CHEM-US-V93-P6902
BRYNGELSON JD-1995-PROTEINS-V21-P167
CZERMINSKI R-1990-J-CHEM-PHYS-V92-P5580
DUTTA P-1981-REV-MOD-PHYS-V53-P497
GROSBERG AY-1994-STAT-PHYSICS-MACROMO-PCH7
HOLIAN BL-1995-PHYS-REV-E-V52-P2338
LABASTIE P-1990-PHYS-REV-LETT-V63-P1567
LINDEMANN FA-1910-PHYS-Z-V11-P609
MARINARI E-1983-COMMUN-MATH-PHYS-V89
MARQUSEE S-1989-P-NATL-ACAD-SCI-USA-V86-P5286
MATSUOKA H-1992-PHYS-REV-LETT-V69-P297
MONTROLL EW-1982-P-NATL-ACAD-SCI-USA-V79-P3380
NOSE S-1984-J-CHEM-PHYS-V81-P511
OKAMOTO Y-1995-J-PHYS-CHEM-US-V99-P11276
POLAND D-1970-THEORY-HELIX-COIL-TR
SASAI M-1992-J-CHEM-PHYS-V96-P3045
SEKO C-1996-J-CHEM-PHYS-V104-P8613
SUNG SS-1996-PROTEINS-V25-P202
VEITSHANS T-1996-FOLD-DES-V2-P1
WEINER SJ-1986-J-COMPUT-CHEM-V7-P230
WEISSMAN MB-1988-REV-MOD-PHYS-V60-P537
ZHOU Y-1996-PHYS-REV-LETT-V23-P2822
ZIMM BH-1959-J-CHEM-PHYS-V31-P526
Times Cited: 7
Source item page count: 4
Publication Date: JUN 22
IDS No.: ZV521
29-char source abbrev: PHYS REV LETT
Publisher address: ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA
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Record 2 of 11
Author(s): Takahashi T; Hogyoku M; Nagayama K
Title: Inter-subunit electrostatic interactions in ferritin molecule: Comparison with inter-molecular interactions in crystals
Source: JOURNAL OF CRYSTAL GROWTH 1996, Vol 168, Iss 1-4, pp 130-137
No. cited references: 30
Publisher: ELSEVIER SCIENCE BV
Addresses: Takahashi T, UNIV TOKYO,COLL ARTS & SCI,DEPT PURE & APPL SCI,MEGURO KU,3-8-1 KOMABA,TOKYO 153,JAPAN
JRDC,TSUKUBA RES CONSORTIUM,NAGAYAMA PROJECT,TSUKUBA,IBARAKI 30026,JAPAN
KeywordsPlus: SOLVENT ACCESSIBLE SURFACE; OLIGOMERIC PROTEINS; TRYPSIN-INHIBITOR; STABILITY; AREA; RIBONUCLEASE; REFINEMENT; PARAMETERS; HYDRATION; LYSOZYME
Abstract: We evaluated the contribution of electrostatic interactions to the stability of macromolecular assembly in a horse L ferritin molecule composed of 24 subunits and the three-dimensional crystal of the ferritin molecules with numerical calculation of Poisson-Boltzmann equation based on dielectric model. The calculation showed that the electrostatic energy both favors the assembly of the 24 subunits and the crystalline assembly of the ferritin molecules (i.e., 24-mers), Short-range interactions less than 5 Angstrom such as salt bridges and hydrogen bonds were important for both the subunit assembly and the crystalline assembly. To elucidate the strong stabilization by electrostatic interactions in both the ferritin 24-mer and its crystal, we analyzed the contribution of individual atoms. It revealed that the stabilization was arising from buried salt bridges or hydrogen bonds, which yielded more than 5 kcal/mol in some interactions. These large electrostatic stabilization and also the unexpected small ionic strength dependence was different from those of bovine pancreatic trypsin inhibitor (BPTI) orthorhombic and pig-insulin cubic crystals previously calculated, We also evaluated changes of the accessible surface area (ASA) and hydration free energy in accordance with the process of the subunit assembly, The change of hydration free energy, which was very large (i.e. similar to + 100 kcal/mol/subunit) and unfavorable for the assembly, was proportional to the electrostatic hydration energy (i.e. Born energy change in hydration process). Hydrophobic groups were likely to appear more frequently than hydrophilic groups at the subunit interfaces. These results suggest that the molecular structure of the ferritin 24-mer and the crystal structure of the 24-mers were both stabilized by local electrostatic interactions, in particular. We view protein crystals as an extension of the protein oligomer to an infinite number of subunits association.
Cited references: INT-TABLES-CRYSTALLO
BORN M-1920-Z-PHYS-V1-P45
BRUNGER AT-1989-ACTA-CRYSTALLOGR-A-V45-P50
BRYANT SH-1989-PROTEINS-V6-P418
CRICHTON RR-1973-BIOCHEM-J-V133-P289
CROSIO MP-1992-J-MOL-BIOL-V228-P243
HENDSCH ZS-1994-PROTEIN-SCI-V3-P211
IRISA M-1995-MOL-PHYS-V85-P1227
ISLAM SA-1990-PROTEINS-V8-P1
ISRAELACHVILI JN-1989-INTERMOLECULAR-SURFA
JANIN J-1988-J-MOL-BIOL-V204-P155
JANIN J-1976-J-MOL-BIOL-V100-P197
KUROKI R-1989-P-NATL-ACAD-SCI-USA-V86-P6903
LAWSON DM-1991-NATURE-V349-P541
MACKERELL AD-1995-J-MOL-BIOL-V247-P774
MILLER S-1987-NATURE-V328-P834
NAKAMURA H-1987-J-PHYS-SOC-JPN-V56-P1609
NEMETHY G-1983-J-PHYS-CHEM-US-V87-P1883
OOBATAKE M-1993-PROG-BIOPHYS-MOL-BIO-V59-P237
OOI T-1987-P-NATL-ACAD-SCI-USA-V84-P3086
OOTAKI H-1987-CHEM-SOLUTIONS-P224
RICHMOND TJ-1984-J-MOL-BIOL-V178-P63
SHRAKE A-1973-J-MOL-BIOL-V79-P351
TAKAHASHI T-1992-BIOPOLYMERS-V32-P897
TAKAHASHI T-1993-J-MOL-BIOL-V234-P421
TAKEDA S-1995-PROTEINS-V23-P548
WARWICKER J-1982-J-MOL-BIOL-V157-P671
WLODAWER A-1984-J-MOL-BIOL-V180-P301
XIAO B-1992-J-CRYST-GROWTH-V122-P144
YOUNG L-1994-PROTEIN-SCI-V3-P717
Times Cited: 2
Source item page count: 8
Publication Date: OCT
IDS No.: VQ249
29-char source abbrev: J CRYST GROWTH
Publisher address: PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS
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Record 3 of 11
Author(s): Takahashi T; Dimitrov AS; Nagayama K
Title: Two-dimensional patterns of magnetic particles at air-water or glass-water interfaces induced by an external magnetic field: Theory and simulation of the formation process
Source: JOURNAL OF PHYSICAL CHEMISTRY 1996, Vol 100, Iss 8, pp 3157-3162
No. cited references: 12
Publisher: AMER CHEMICAL SOC
Addresses: TSUKUBA RES CONSORTIUM,JRDC,ERATO,NAGAYAMA PROT ARRAY PROJECT,TSUKUBA,IBARAKI 30026,JAPAN
Abstract: We describe theoretically the formation process of two-dimensional patterns of magnetic particles at an interface under the action of an external magnetic field. First, we developed a theoretical model for the forces acting on the particles, which are the magnetic attraction toward the axis of symmetry, magnetic repulsion due to the induced dipoles, electrostatic repulsion due to the surface net charge and electric dipoles of the particles, and lateral capillary forces in the case of a liquid interface. Then, we developed a Brownian dynamics algorithm and simulated the pattern formation. Our simulations reproduced the hexagonally aligned two-dimensional patterns, which were experimentally observed and reported in the complementary experimental work, that is, they reproduced the distance between the particles and the time of pattern formation. Irregular patterns such as square and pentagonal ones that were experimentally observed were also simulated, We calculated that when the distance between particles is larger than 20 mu m (i.e., in case or a weak magnetic field), the magnetic force is sufficient to explain the pattern formation. But, when the distance is smaller than 20 mu m, the electrostatic repulsive force may play an essential role in determining the interparticle distance. Our calculations showed that the lateral capillary forces and the electrostatic dipolar repulsive forces were negligible for the pattern formation process. Finally, our method for simulating the pattern formation may be applied for understanding these processes and predicting the patterns that might be formed at liquid or solid interfaces.
Cited references: ARMSTRONG AJ-1989-J-PHYS-CONDENS-MAT-V1-P1707
BERENDSEN HJC-1984-J-CHEM-PHYS-V81-P3684
CHANTRELL RW-1980-J-PHYS-D-V13-PL119
DAVIES P-1986-J-PHYS-D-APPL-PHYS-V19-P469
DIMITROV AS-1996-J-PHYS-CHEM-US-V100-P3163
HURD AJ-1985-J-PHYS-A-V18-P1055
KRALCHEVSKY PA-1994-LANGMUIR-V10-P23
MCCARTNEY LN-1969-J-COLLOID-INTERF-SCI-V30-P345
MEAKIN P-1993-ADV-PHYS-V42-P1
PIERANSKI P-1980-PHYS-REV-LETT-V45-P569
SMIT J-1959-PHILIPS-TECH-LIB
STILLINGER FH-1961-J-CHEM-PHYS-V35-P1584
Times Cited: 2
Source item page count: 6
Publication Date: FEB 22
IDS No.: TX257
29-char source abbrev: J PHYS CHEM
Publisher address: 1155 16TH ST, NW, WASHINGTON, DC 20036
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Record 4 of 11
Author(s): Dimitrov AS; Takahashi T; Furusawa K; Nagayama K
Title: Two-dimensional patterns of magnetic particles at air-water or glass-water interfaces induced by an external magnetic field: Experimental observation and dependencies
Source: JOURNAL OF PHYSICAL CHEMISTRY 1996, Vol 100, Iss 8, pp 3163-3168
No. cited references: 17
Publisher: AMER CHEMICAL SOC
Addresses: Dimitrov AS, LOREAL,TSUKUBA CTR,TSUKUBA RES BLDG,5-5 TOKODAI,TSUKUBA,IBARAKI 30026,JAPAN
TSUKUBA RES CONSORTIUM,JDRC,ERATO,NAGAYAMA PROT ARRAY PROJECT,TSUKUBA,IBARAKI 30026,JAPAN
KeywordsPlus: NATURAL LITHOGRAPHY; SURFACE
Abstract: We report a formation of hexagonally aligned patterns of paramagnetic polystyrene particles attached at air-water or glass-water interfaces. Contrary to the closely packed 2D particle arrays reported up to now, the patterns described here showed interparticle distances from 6 to 10 particle diameters. The particles were gathered due to the gradient in the external magnetic field, which was applied across the interface. The source of the magnetic field was a permanent magnetic dipole. The created magnetic field attracted the particles toward the interface and the magnetic dipole axis of symmetry. The external field induced magnetic dipole moments in the particles and they repulsed each other due to the dipole-dipole magnetic interactions. The particles were negatively charged and they repulsed each other also electrostatically, which was proven by adding electrolyte in the water subphase. Finally, we suggest that the interparticle distances were determined by the action among three forces: magnetic attraction toward the axis of symmetry, dipole-dipole magnetic repulsion, and electrostatic repulsion. This statement is clarified in the complementary theoretical paper.
Cited references: ALFREY T-1954-J-OPT-SOC-AM-V44-P603
BURCH JM-1953-NATURE-V171-P889
DECKMAN HW-1982-APPL-PHYS-LETT-V41-P377
DECKMAN HW-1983-J-VAC-SCI-TECHNOL-B-V1-P1109
DIMITROV AS-IN-PRESS-LANGMUIR
HAHN RE-1978-PHYSICS-THIN-FILMS
HAYASHI S-1991-J-COLLOID-INTERF-SCI-V144-P538
HOOKE R-1961-J-ASSOC-COMPUT-MACH-V8-P212
HWANG YH-1994-PHYS-REV-E-V49-P3102
LORRAIN P-1970-ELECTROMAGNETIC-FIEL
PERRIN J-1909-ANN-CHIM-PHYS-V18-P5
PIERANSKI P-1980-PHYS-REV-LETT-V45-P569
SKJELTORP AT-1983-PHYS-REV-LETT-V51-P2306
TAKAHASHI T-1996-J-PHYS-CHEM-US-V100-P3157
WEITZ DA-1980-PHYS-REV-LETT-V45-P355
YABLONOVITCH E-1982-IEEE-T-ELECTRON-DEV-V29-P300
YOLDAS BE-1984-APPL-OPTICS-V23-P1418
Times Cited: 3
Source item page count: 6
Publication Date: FEB 22
IDS No.: TX257
29-char source abbrev: J PHYS CHEM
Publisher address: 1155 16TH ST, NW, WASHINGTON, DC 20036
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Record 5 of 11
Author(s): Takeda S; Yoshimura H; Endo S; Takahashi T; Nagayama K
Title: Control of crystal forms of apoferritin by site-directed mutagenesis
Source: PROTEINS-STRUCTURE FUNCTION AND GENETICS 1995, Vol 23, Iss 4, pp 548-556
No. cited references: 21
Publisher: WILEY-LISS
Addresses: JRDC,ERATO,NAGAYAMA PROT ARRAY PROJECT,TSUKUBA,IBARAKI 30026,JAPAN
Author Keywords: electron crystallography; molecular interaction; surface potential; protein crystallization; two-dimensional crystal
KeywordsPlus: ESCHERICHIA-COLI; ELECTRON-MICROSCOPY; FERRITIN; CRYSTALLIZATION; EXPRESSION; PROTEINS; CLONING; CHAIN
Abstract: Surface charges of protein molecules are not only important to biological functions but also crucial to the molecular assembly responsible for crystallization. Appropriate alteration in the surface charge distribution of a protein molecule induces new molecular alignment in the proper direction in the crystal and, hence, controls the crystal form, Apoferritin molecules are known to crystallize in two- and three-dimensional forms in the presence of cadmium ions, which bridge neighboring protein molecules, Here we report a controlled transformation of the apoferritin 2-D crystal by site-directed mutagenesis, In mutant apoferritin, two amino acid residues binding a cadmium-ion through their negative charge, were replaced by one type of nonionic amino acid residues, The amino acid residues, Asp-84 and Gln-86 in the sequence of recombinant (i.e., wild-type) horse L-apoferritin, were replaced by Ser, The wild-type apoferritin yielded a hexagonal lattice 2-D crystal in the presence of cadmium ions, In contrast, the mutant apoferritin yielded two types of oblique crystals independent of the presence of cadmium ions, Image reconstruction of electron micrographs of the mutant crystals made clear that the mutant apoferritin molecules oriented themselves with the 2-fold symmetry axis perpendicular to the crystal plane in both crystals, while the wild-type apoferritin molecules oriented themselves with the 3-fold symmetry axis perpendicular to the crystal plane. The changes of crystal forms and molecular orientation in the 2-D crystals were well explained by a change of the electrostatic interactions induced by the mutagenesis. (C) 1995 Wiley-Liss, Inc.
Cited references: AMOS LA-1982-PROG-BIOPHYS-MOL-BIO-V39-P183
ANDREWS SC-1992-J-INORG-BIOCHEM-V47-P161
AROSIO P-1983-BIOCHIM-BIOPHYS-ACTA-V744-P230
BANYARD SH-1978-NATURE-V271-P382
ITO W-1991-GENE-V102-P67
LAEMMLI UK-1970-NATURE-V227-P680
LAWSON DM-1991-NATURE-V349-P541
MASLEN EN-1992-INT-TABLES-CRYSTALLO-C-P476
MASSOVER WH-1990-12TH-P-INT-C-EL-MICR-V1-P288
MASSOVER WH-1993-MICRON-V24-P389
NAKAMURA H-1987-J-PHYS-SOC-JPN-V56-P1609
REICHELT R-1977-MICRON-V8-P29
SMITH JMA-1989-J-MOL-BIOL-V205-P465
TAKAHASHI T-1992-BIOPOLYMERS-V32-P897
TAKAHASHI T-1993-J-MOL-BIOL-V234-P421
TAKEDA S-1993-BIOCHIM-BIOPHYS-ACTA-V1174-P218
THEIL EC-1987-ANNU-REV-BIOCHEM-V56-P289
THOMAS CD-1988-BIOCHEM-SOC-T-V16-P838
TRIKHA J-1994-PROTEINS-V18-P107
YOSHIMURA H-1994-LANGMUIR-V10-P3290
YOSHIMURA H-1990-ULTRAMICROSCOPY-V32-P265
Times Cited: 16
Source item page count: 9
Publication Date: DEC
IDS No.: TL844
29-char source abbrev: PROTEIN-STRUCT FUNCT GENET
Publisher address: DIV JOHN WILEY & SONS INC 605 THIRD AVE, NEW YORK, NY 10158-0012
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Record 6 of 11
Author(s): IRISA M; TAKAHASHI T; HIRATA F; YANAGIDA T
Title: SOLVATION FREE-ENERGY OF PROTEIN REPRODUCED BY THE COMBINATION OF THE EXTENDED SCALED PARTICLE THEORY AND THE POISSON-BOLTZMANN EQUATION
Source: JOURNAL OF MOLECULAR LIQUIDS 1995, Vol 65-6, pp 381-384
No. cited references: 12
Publisher: ELSEVIER SCIENCE BV
Addresses: IRISA M, JRDC,ERATO,YANAGIDA BIOMOTRON PROJECT,SENBA HIGASHI,MINO,OSAKA 562,JAPAN
JRDC,ERATO,NAGAYAMA PROT ARRAY PROJECT,TSUKUBA,IBARAKI 30026,JAPAN
KYOTO UNIV,FAC SCI,DEPT CHEM,KYOTO 606,JAPAN
Abstract: A hybrid approach of the extended scaled particle theory (SPT) and the Poisson-Boltzmann (PB) equation for the solvation free energy of non-polar and polar solutes has been proposed by us. This new method is applied for the hydration free energy of the protein, avian pancreatic polypeptide (36 residues). The contributions form the cavity formation and the attractive interaction between the solute and the solvent to the solvation free energy compensate each other. The electrostatic contribution is much larger than other terms in this hydration free energy, because hydrophilic residues are ionized in water. This work is the first step toward further applications of our new method to free energy difference calculation appeared in the stability analysis of protein.
Cited references: BLUNDELL TL-1981-P-NATL-ACAD-SCI-USA-V78-P4175
BOUBLIK T-1974-MOL-PHYS-V27-P1415
IRISA M-1993-CHEM-PHYS-LETT-V207-P430
IRISA M-UNPUB
IRISA M-UNPUB
JORGENSEN WL-1988-J-AM-CHEM-SOC-V110-P1657
NAKAMURA H-1987-J-PHYS-SOC-JPN-V56-P1609
PIEROTTI RA-1965-CHEM-REV-V76-P717
PIEROTTI RA-1965-J-PHYS-CHEM-US-V69-P281
PIEROTTI RA-1963-J-PHYS-CHEM-US-V67-P1840
STILL WC-1990-J-AM-CHEM-SOC-V112-P6127
TAKAHASHI T-1992-BIOPOLYMERS-V32-P897
Times Cited: 2
Source item page count: 4
Publication Date: NOV
IDS No.: TK241
29-char source abbrev: J MOL LIQ
Publisher address: PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS
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Record 7 of 11
Author(s): IRISA M; TAKAHASHI T; NAGAYAMA K; HIRATA F
Title: SOLVATION FREE-ENERGIES OF NONPOLAR AND POLAR SOLUTES REPRODUCED BY A COMBINATION OF EXTENDED SCALED PARTICLE THEORY AND THE POISSON-BOLTZMANN EQUATION
Source: MOLECULAR PHYSICS 1995, Vol 85, Iss 6, pp 1227-1238
No. cited references: 29
Publisher: TAYLOR & FRANCIS LTD LONDON
Addresses: IRISA M, JRDC,ERATO,YANAGIDA BIOMOTRON PROJECT,2-4-14 SENBA HIGASHI,MINO,OSAKA 565,JAPAN
JRDC,ERATO,NAGAYAMA PROT ARRAY PROJECT,TSUKUBA,IBARAKI 30026,JAPAN
KYOTO UNIV,FAC SCI,DEPT CHEM,SAKYO KU,KYOTO 606,JAPAN
KeywordsPlus: SURFACE-AREA; PROTEIN; SOLVENT; WATER; DYNAMICS; SPHERES; FLUIDS; VOLUME
Abstract: A hybrid approach using extended scaled particle theory and the Poisson-Boltzmann (PB) equation is proposed for calculating the solvation free energy of a solute with partial charges in dilute aqueous solution. The applicability of this method is demonstrated by taking a series of the normal alcohols and normal alkanes. The solvation free energy of normal alkanes, which has been studied prevously based on a rather crude model, is recalculated using a more elaborate model. The electrostatic contribution to the free energy for the polar solute is calculated by the PB equation. In order to take into account the complicated boundary condition associated with the shape of molecular surface, the PB equation is solved numerically using a finite difference method. A superposition of hydrophobic and electrostatic contributions to the solvation free energy gives reasonable agreement with corresponding experimental data for the polar solute. The possibility of further applications of the method is discussed.
Cited references: 1991-CHEM-PHYS-V158-P3
BOUBLIK T-1983-ADV-CHEM-SER-V204-P173
BOUBLIK T-1981-MOL-PHYS-V44-P1369
BOUBLIK T-1974-MOL-PHYS-V27-P1415
DODD LR-1991-MOL-PHYS-V72-P1313
FLORY PJ-1941-J-CHEM-PHYS-V9-P660
GIBBONS RM-1969-MOL-PHYS-V17-P81
HUGGINS ML-1941-J-CHEM-PHYS-V9-P440
IRISA M-1993-CHEM-PHYS-LETT-V207-P430
IRISA M-1995-UNPUB-J-COMPUT-PHYS
JORGENSEN WL-1981-J-AM-CHEM-SOC-V103-P335
KITAO A-1991-CHEM-PHYS-V158-P447
NAKAMURA H-1988-J-PHYS-SOC-JPN-V57-P3702
OOI T-1988-J-BIOCH-V103-P114
OOI T-1987-P-NATL-ACAD-SCI-USA-V84-P3086
PIEROTTI RA-1965-CHEM-REV-V76-P717
PIEROTTI RA-1965-J-PHYS-CHEM-US-V69-P281
PIEROTTI RA-1963-J-PHYS-CHEM-US-V67-P1840
REISS H-1959-J-CHEM-PHYS-V31-P369
RICHARDS FM-1977-ANNU-REV-BIOPHYS-BIO-V6-P151
RICHMOND TJ-1984-J-MOL-BIOL-V178-P63
ROGERS NK-1986-PROG-BIOPHYS-MOL-BIO-V48-P37
SHARP KA-1991-BIOCHEMISTRY-US-V30-P9686
SHARP KA-1991-SCIENCE-V252-P106
SODA K-1993-J-PHYS-SOC-JPN-V62-P1782
STILL WC-1990-J-AM-CHEM-SOC-V112-P6127
TAKAHASHI T-1992-BIOPOLYMERS-V32-P897
TANFORD C-1957-J-AM-CHEM-SOC-V79-P5333
WARWICKER J-1982-J-MOL-BIOL-V157-P671
Times Cited: 8
Source item page count: 12
Publication Date: AUG 20
IDS No.: RV614
29-char source abbrev: MOL PHYS
Publisher address: ONE GUNDPOWDER SQUARE, LONDON, ENGLAND EC4A 3DE
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Record 8 of 11
Author(s): HIGO J; YAMAKI M; HOGYOKU M; TAKAHASHI T; ENDO S; NAGAYAMA K
Title: STABILITY OF 2-DIMENSIONAL CRYSTALLINE AGGREGATES OF A PROTEIN STUDIED BY MOLECULAR-DYNAMICS
Source: JOURNAL OF COMPUTATIONAL CHEMISTRY 1994, Vol 15, Iss 11, pp 1278-1290
No. cited references: 25
Publisher: JOHN WILEY & SONS INC
Addresses: ERATO,JRDC,NAGAYAMA PROT ARRAY PROJECT,TSUKUBA,IBARAKI 30026,JAPAN
KeywordsPlus: SURFACE-INDUCED AGGREGATION; LIGHT-SCATTERING; ELECTRON CRYSTALLOGRAPHY; 3-DIMENSIONAL STRUCTURE; LYSOZYME; GROWTH; RESOLUTION; FERRITIN; KINETICS; MEMBRANE
Abstract: Two-dimensional protein (ferritin) aggregates with a square lattice symmetry, which were formed within a thin liquid layer on a mercury surface, were studied by molecular dynamics (MD) simulation. For the simulation, the ferritin molecule was modeled by an assembly of 49 spheres, and the intermolecular interactions were given by simple formulae. During the simulation, molecules were confined within a layer, which corresponds to the thin liquid layer. An annealing MD simulation was done starting from a random molecular configuration within the layer, and aggregates with the square lattice symmetry were also obtained. To study the stability of aggregates, dissociation processes of the aggregates were analyzed using MD simulations at room temperature. Interactions between the nearest-neighbor molecules were regarded as bonds. Mean bond energies and correlation coefficients between the bond energies were calculated from the MD trajectories. A decay profile according to the dissociation was obtained, yielding a dissociation rate constant. Buried bonds were stronger than peripheral bonds. The larger the aggregate size, the stronger the bond for each of the buried and peripheral bonds. A simple theoretical account, which is applicable to a general bonded network, was introduced to analyze the dynamics of the aggregates. (C) 1994 by John Wiley & Sons, Inc.
Cited references: ATAKA M-1990-BIOPHYS-J-V58-P807
ATAKA M-1986-BIOPOLYMERS-V25-P337
ATAKA M-1992-J-CRYST-GROWTH-V122-P60
ATAKA M-1988-J-CRYST-GROWTH-V90-P86
AZUMA T-1989-J-CRYST-GROWTH-V98-P371
BAUMEISTER W-1982-ULTRAMICROSCOPY-V9-P151
BERENDSEN HJC-1983-MOL-LIQUIDS-DYNAMICS-P475
ELGERSMA AV-1992-J-CRYST-GROWTH-V122-P31
GEORGALIS Y-1992-J-CRYST-GROWTH-V118-P360
GLAESER RM-1985-ANNU-REV-PHYS-CHEM-V36-P243
HENDERSON R-1990-J-MOL-BIOL-V213-P899
HENDERSON R-1986-ULTRAMICROSCOPY-V19-P147
ISHII N-1993-J-BIOCHEM-TOKYO-V113-P245
KAM Z-1978-J-MOL-BIOL-V123-P539
KUHLBRANDT W-1991-NATURE-V350-P130
LAWSON DM-1991-NATURE-V349-P541
LEWIS B-1980-CRYST-GROWTH-P23
MIKOL V-1990-J-MOL-BIOL-V213-P187
NYGREN H-1990-BIOPHYS-CHEM-V38-P67
SKOURI M-1991-FEBS-LETT-V295-P84
SKOURI M-1992-J-CRYST-GROWTH-V122-P14
STENBERG M-1991-BIOPHYS-CHEM-V41-P131
WEISSBUCH I-1991-SCIENCE-V253-P637
YOSHIMURA H-1989-J-BIOCHEM-TOKYO-V106-P958
YOSHIMURA H-1990-ULTRAMICROSCOPY-V32-P265
Times Cited: 1
Source item page count: 13
Publication Date: NOV
IDS No.: PL532
29-char source abbrev: J COMPUT CHEM
Publisher address: 605 THIRD AVE, NEW YORK, NY 10158-0012
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Record 9 of 11
Author(s): TAKAHASHI T; ENDO S; NAGAYAMA K
Title: STABILIZATION OF PROTEIN CRYSTALS BY ELECTROSTATIC INTERACTIONS AS REVEALED BY A NUMERICAL APPROACH
Source: JOURNAL OF MOLECULAR BIOLOGY 1993, Vol 234, Iss 2, pp 421-432
No. cited references: 26
Publisher: ACADEMIC PRESS LTD
Addresses: ERATO,JRDC,NAGAYAMA PROT ARRAY PROJECT,5-9-1 TOKODAI,TSUKUBA 30026,JAPAN
Author Keywords: ELECTROSTATIC ENERGY; PROTEIN CRYSTAL; DIELECTRIC MODEL; PERIODIC BOUNDARY; IONIC SHIELDING
KeywordsPlus: X-RAY REFINEMENT; ACTIVE-SITE; JOINT NEUTRON; POTENTIALS; INSULIN; SYSTEMS
Cited references: ALKORTA I-1993-J-COMPUT-CHEM-V5-P620
AVBELJ F-1990-BIOCHEMISTRY-US-V29-P8658
BERNSTEIN FC-1977-J-MOL-BIOL-V112-P535
BORN M-1920-Z-PHYS-V1-P45
DERJAGUIN BV-1989-THEORY-STABILITY-COL
DODSON EJ-1978-J-MOL-BIOL-V125-P387
DUQUERROY S-1991-CIBA-F-SYMP-V161-P237
FERSHT AR-1985-NATURE-V314-P235
GILSON MK-1987-NATURE-V330-P84
ISRAELACHVILI JN-1989-INTERMOLECULAR-SURFA
KARASAWA N-1989-J-PHYS-CHEM-US-V93-P7320
KIRKWOOD JG-1934-J-CHEM-PHYS-V2-P351
LIDE DR-1991-HDB-CHEM-PHYSICS-V8-P49
NAKAMURA H-1987-J-PHYS-SOC-JPN-V56-P1609
POTTEL R-1973-WATER-COMPREHENSIVE-V3-P401
SHARP KA-1990-ANNU-REV-BIOPHYS-BIO-V19-P301
SHERIDAN RP-1981-J-AM-CHEM-SOC-V103-P1544
STERNBERG MJE-1987-NATURE-V330-P86
TAKAHASHI T-1992-BIOPOLYMERS-V32-P897
TAMAMUSHI R-1967-ELECTROCHEMISTRY-P32
VERWEY EJW-1949-THEORY-STABILITY-LYO
WARSHEL A-1984-Q-REV-BIOPHYS-V17-P283
WARWICKER J-1989-J-MOL-BIOL-V206-P381
WARWICKER J-1982-J-MOL-BIOL-V157-P671
WLODAWER A-1989-ACTA-CRYSTALLOGR-B-V45-P99
WLODAWER A-1984-J-MOL-BIOL-V180-P301
Times Cited: 12
Source item page count: 12
Publication Date: NOV 20
IDS No.: MG892
29-char source abbrev: J MOL BIOL
Publisher address: 24-28 OVAL RD, LONDON, ENGLAND NW1 7DX
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Record 10 of 11
Author(s): TAKAHASHI T; NAKAMURA H; WADA A
Title: ELECTROSTATIC FORCES IN 2 LYSOZYMES - CALCULATIONS AND MEASUREMENTS OF HISTIDINE PKA VALUES
Source: BIOPOLYMERS 1992, Vol 32, Iss 8, pp 897-909
No. cited references: 34
Publisher: JOHN WILEY & SONS INC
Addresses: UNIV TOKYO,FAC SCI,DEPT PHYS,BUNKYO KU,TOKYO 113,JAPAN
PROT ENGN RES INST,SUITA,OSAKA 565,JAPAN
KeywordsPlus: PROTEIN-SOLVENT SYSTEMS; ALPHA-HELIX DIPOLES; NUMERICAL-CALCULATIONS; ACTIVE-SITE; ENERGETICS; POTENTIALS; REFINEMENT; CHARGE; MODEL
Abstract: In order to examine the electrostatic forces in globular proteins, pK(a) values and their ionic strength dependence of His residues of hen egg white lysozyme (HEWL) and human lysozyme (HUML) were measured, and they were compared with those calculated numerically. pK(a) values of His residues in HEWL, HUML, and short oligopeptides were determined from chemical shift changes of His side chains by H-1-nmr measurements. The associated changes in pK(a) values in HEWL and HUML were calculated by solving the Poisson-Boltzmann equations numerically for macroscopic dielectric models. The calculated pK(a) changes and their ionic strength dependence agreed fairly well with the observed ones.
The contribution from each residue and each alpha-helix dipole to the pK(a) values and their ionic strength dependence was analyzed using Green's reciprocity theorem. The results indicate that (1) the pK(a) of His residues are largely affected by surrounding ionized and polar groups; (2) the ionic strength dependence of the pK(a) values is determined by the overall charge distributions and their accessibilities to solvent; and (3) alpha-helix dipoles make a significant contribution to the pK(a), when the His residue is close to the helix terminus and not fully exposed to the solvent.
Cited references: AQVIST J-1991-P-NATL-ACAD-SCI-USA-V88-P2026
ARTYMIUK PJ-1981-J-MOL-BIOL-V152-P737
CAMPBELL ID-1975-P-ROY-SOC-A-V345-P41
COHEN JS-1969-NATURE-V223-P43
DIAMOND R-1974-J-MOL-BIOL-V82-P371
FERSHT A-1985-ENZYME-STRUCTURE-MEC
GILSON MK-1987-NATURE-V330-P84
GILSON MK-1988-PROTEINS-V3-P32
HOL WGJ-1978-NATURE-V273-P443
HOL WGJ-1985-PROG-BIOPHYS-MOL-BIO-V45-P149
KABSCH W-1983-BIOPOLYMERS-V22-P2577
KIRKWOOD JG-1934-J-CHEM-PHYS-V2-P351
NAKAMURA H-1988-J-PHYS-SOC-JPN-V57-P3702
NAKAMURA H-1987-J-PHYS-SOC-JPN-V56-P1609
NAKAMURA H-1989-PROTEIN-ENG-V2-P177
NEUBERGER A-1936-BIOCHEM-J-V30-P2085
NICHOLSON H-1988-NATURE-V336-P651
PARSONS SM-1972-BIOCHEM-V11-P1623
POTTEL R-1973-WATER-COMPREHENSIVE-V3-P401
ROGERS NK-1986-PROG-BIOPHYS-MOL-BIO-V48-P37
RUSSELL AJ-1987-NATURE-V328-P496
RUSSELL ST-1985-J-MOL-BIOL-V185-P389
SAKAMOTO T-1989-J-PHYS-CHEM-US-V93-P357
SCHERIDAN RP-1981-J-AM-CHEM-SOC-V103-P1544
SERRANO L-1989-NATURE-V342-P296
SHOEMAKER KR-1987-NATURE-V326-P563
SOMMAN K-1989-BIOCHEMISTRY-US-V28-P9918
SOPHIANOPOULOS AJ-1969-J-BIOL-CHEM-V244-P3188
SOPHIANOPOULOS AJ-1964-J-BIOL-CHEM-V239-P2516
STERNBERG MJE-1987-NATURE-V330-P86
WADA A-1976-ADV-BIOPHYS-V9-P1
WARSHEL A-1985-CHEM-PHYS-LETT-V121-P124
WARSHEL A-1984-Q-REV-BIOPHYS-V17-P283
WARWICKER J-1982-J-MOL-BIOL-V157-P671
Times Cited: 41
Source item page count: 13
Publication Date: AUG
IDS No.: JD771
29-char source abbrev: BIOPOLYMERS
Publisher address: 605 THIRD AVE, NEW YORK, NY 10158-0012
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Record 11 of 11
Author(s): NAKAMURA H; SAKAMOTO T; TAKAHASHI T; WADA A
Title: THEORETICAL-STUDY OF DIELECTRIC-CONSTANT OF PROTEIN
Source: JOURNAL OF MOLECULAR GRAPHICS 1988, Vol 6, Iss 4, pp 208-208
No. cited references: 1
Publisher: BUTTERWORTH-HEINEMANN
Addresses: PROT ENGN RES INST,OTA KU,TOKYO 144,JAPAN
UNIV TOKYO,FAC SCI,DEPT PHYS,BUNKYO KU,TOKYO 113,JAPAN
Cited references: NAKAMURA H-1987-J-PHYS-SOC-JPN-V56-P1609
Times Cited: 0
Source item page count: 1
Publication Date: DEC
IDS No.: R3809
29-char source abbrev: J MOL GRAPHICS
Publisher address: 225 WILDWOOD AVE #UNITB PO BOX 4500, WOBURN, MA 01801-2084
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