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Wu JW, Liu HL. In silico investigation of the disease-associated retinoschisin C110Y and C219G mutants. J Biomol Struct Dyn 2012; 29:937-59. [PMID: 22292953 DOI: 10.1080/07391102.2012.10507420] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The juvenile X-linked retinoschisis (XLRS) is a retinal disease caused by mutations in the secretory protein, retinoschisin (RS1). Majority of the disease is resulted from single point mutations on the RS1 discoidin domain with cysteine mutations being related to some of the more severe cases of XLRS. Previous studies have indicated that two mutations (C110Y and C219G), which involve cysteines that form intramolecular disulfide bonds in the native discoidin domain, resulted in different oligomerization states of the proteins and did not correlate with the degree of protein stability as calculated by the change in folding free energy. Through homology modeling, bioinformatics predictions, molecular dynamics (MD) and docking simulations, we attempt to investigate the effects of these two mutations on the structure of the RS1 discoidin domain in relevance to the discrepancy found between structural stability and aggregation propensity. Based on our findings, this discrepancy can be explained by the ability of C110Y mutant to establish suitable modules for initiating amorphous aggregation and to expand the aggregating mass through predominantly hydrophobic interactions. The low capability of C219G mutant to oligomerize, on the other hand, may be due to its greater structural instability and lesser hydrophobic tendency, two properties that may be unsupportive of aggregation. The results, altogether, indicate that aggregation propensity in the RS1 C110Y mutant is dependent upon the formation of suitable aggregating substrates for propagation of aggregation and not directly related to or determined by overall structural instability. As for the wildtype protein, the binding specificity of the spikes for biological function and the formation of octameric structure are contributed by important loop interactions, as well as evolved structural and sequence-based properties that prevent aggregation.
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Affiliation(s)
- Josephine W Wu
- Institute of Biotechnology, National Taipei University of Technology, Taipei 10608, Taiwan
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Noh JD, Rieger H, Enderle M, Knorr K. Critical behavior of the frustrated antiferromagnetic six-state clock model on a triangular lattice. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2002; 66:026111. [PMID: 12241241 DOI: 10.1103/physreve.66.026111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2002] [Indexed: 05/23/2023]
Abstract
We study the antiferromagnetic six-state clock model with nearest neighbor interactions on a triangular lattice with extensive Monte Carlo simulations. We find clear indications of two phase transitions at two different temperatures: Below T(I) a chirality order sets in and by a thorough finite-size-scaling analysis of the specific heat and the chirality correlation length we show that this transition is in the Ising universality class (with a nonvanishing chirality order parameter below T(I)). At T(KT) (<T(I)) the spin-spin correlation length as well as the spin susceptibility diverges according to a Kosterlitz-Thouless (KT) form and spin correlations decay algebraically below T(KT). We compare our results to recent x-ray diffraction experiments on the orientational ordering of CF3Br monolayers physisorbed on graphite. We argue that the six-state clock model describes the universal feature of the phase transition in the experimental system and that the orientational ordering belongs to the KT universality class.
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Affiliation(s)
- J D Noh
- Theoretische Physik, Universität des Saarlandes, 66041 Saarbrücken, Germany
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Lee SJ, Lee JR, Kim B. Patterns of striped order in the classical lattice Coulomb gas. PHYSICAL REVIEW LETTERS 2002; 88:025701. [PMID: 11801025 DOI: 10.1103/physrevlett.88.025701] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2001] [Indexed: 05/23/2023]
Abstract
We obtain via Monte Carlo simulations the low-temperature charge configurations in the lattice Coulomb gas on a square lattice for charge filling ratio f in the range 1/3<f<1/2. We find a simple regularity in the low-temperature charge configurations which consist of a suitable periodic combination of a few basic striped patterns characterized by the existence of partially filled diagonal channels. In general, there exist two separate transitions where the lower temperature transition (T(p)) corresponds to the freezing of charges within the partially filled channels. T(p) is found to be sensitively dependent on f through the charge number density nu = p1/q1 within the channels.
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Affiliation(s)
- Sung Jong Lee
- Department of Physics, The University of Suwon, Hwasung-Gun, Kyunggi-Do 445-743, Korea
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Rojas C, José JV. Critical properties of two-dimensional Josephson-junction arrays with zero-point quantum fluctuations. PHYSICAL REVIEW. B, CONDENSED MATTER 1996; 54:12361-12385. [PMID: 9985100 DOI: 10.1103/physrevb.54.12361] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Ling XS, Lezec HJ, Higgins MJ, Tsai JS, Fujita J, Numata H, Nakamura Y, Ochiai Y, Tang C, Chaikin PM, Bhattacharya S. Nature of phase transitions of superconducting wire networks in a magnetic field. PHYSICAL REVIEW LETTERS 1996; 76:2989-2992. [PMID: 10060842 DOI: 10.1103/physrevlett.76.2989] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Lee S, Lee KC. Phase transitions in the uniformly frustrated XY model with frustration parameter f=1/3 studied with use of the microcanonical Monte Carlo technique. PHYSICAL REVIEW. B, CONDENSED MATTER 1995; 52:6706-6711. [PMID: 9981899 DOI: 10.1103/physrevb.52.6706] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Kim BJ, Choi MY. Quantum fluctuations in superconducting arrays with a general capacitance matrix. PHYSICAL REVIEW. B, CONDENSED MATTER 1995; 52:3624-3631. [PMID: 9981489 DOI: 10.1103/physrevb.52.3624] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Franz M, Teitel S. Vortex-lattice melting in two-dimensional superconducting networks and films. PHYSICAL REVIEW. B, CONDENSED MATTER 1995; 51:6551-6574. [PMID: 9977191 DOI: 10.1103/physrevb.51.6551] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Lee SJ, Lee JR, Kim B. Dynamics of spin and chiral ordering in the two-dimensional fully frustrated XY model. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1995; 51:R4-R7. [PMID: 9962720 DOI: 10.1103/physreve.51.r4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Lee JR, Teitel S. Driven diffusion in the two-dimensional lattice Coulomb gas: A model for flux flow in superconducting networks. PHYSICAL REVIEW. B, CONDENSED MATTER 1994; 50:3149-3157. [PMID: 9976563 DOI: 10.1103/physrevb.50.3149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Lee S, Lee KC. Phase transitions in the fully frustrated XY model studied with use of the microcanonical Monte Carlo technique. PHYSICAL REVIEW. B, CONDENSED MATTER 1994; 49:15184-15189. [PMID: 10010625 DOI: 10.1103/physrevb.49.15184] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Ramirez-Santiago G, José JV. Critical exponents of the fully frustrated two-dimensional XY model. PHYSICAL REVIEW. B, CONDENSED MATTER 1994; 49:9567-9582. [PMID: 10009755 DOI: 10.1103/physrevb.49.9567] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Lee JR. Phase transitions in the two-dimensional classical lattice Coulomb gas of half-integer charges. PHYSICAL REVIEW. B, CONDENSED MATTER 1994; 49:3317-3321. [PMID: 10011193 DOI: 10.1103/physrevb.49.3317] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Granato E, Nightingale MP. Chiral exponents of the square-lattice frustrated XY model: A Monte Carlo transfer-matrix calculation. PHYSICAL REVIEW. B, CONDENSED MATTER 1993; 48:7438-7444. [PMID: 10006910 DOI: 10.1103/physrevb.48.7438] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Kim S, Choi MY. Arrays of resistively shunted Josephson junctions in magnetic fields. PHYSICAL REVIEW. B, CONDENSED MATTER 1993; 48:322-332. [PMID: 10006782 DOI: 10.1103/physrevb.48.322] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Lee JR, Teitel S. Phase transitions in classical two-dimensional lattice Coulomb gases. PHYSICAL REVIEW. B, CONDENSED MATTER 1992; 46:3247-3262. [PMID: 10004040 DOI: 10.1103/physrevb.46.3247] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Ramirez-Santiago G, José JV. Correlation Functions in the Fully Frustrated 2D XY Model. PHYSICAL REVIEW LETTERS 1992; 68:1224-1227. [PMID: 10046111 DOI: 10.1103/physrevlett.68.1224] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Lee J, Granato E, Kosterlitz JM. Nonuniversal critical behavior and first-order transitions in a coupled XY-Ising model. PHYSICAL REVIEW. B, CONDENSED MATTER 1991; 44:4819-4831. [PMID: 9998288 DOI: 10.1103/physrevb.44.4819] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Zhang GM, Chen H, Wu X. Critical properties of the quantum sine-Gordon equation. PHYSICAL REVIEW. B, CONDENSED MATTER 1991; 43:13566-13571. [PMID: 9997187 DOI: 10.1103/physrevb.43.13566] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Lee J, Kosterlitz JM, Granato E. Monte Carlo study of frustrated XY models on a triangular and square lattice. PHYSICAL REVIEW. B, CONDENSED MATTER 1991; 43:11531-11534. [PMID: 9996920 DOI: 10.1103/physrevb.43.11531] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Lee JR, Teitel S. Dense two-dimensional classical Coulomb gas on a triangular lattice. PHYSICAL REVIEW LETTERS 1991; 66:2100-2103. [PMID: 10043391 DOI: 10.1103/physrevlett.66.2100] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Granato E, Kosterlitz JM, Lee J, Nightingale MP. Phase transitions in coupled XY-Ising systems. PHYSICAL REVIEW LETTERS 1991; 66:1090-1093. [PMID: 10043993 DOI: 10.1103/physrevlett.66.1090] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Wilks CW, Bojko R, Chaikin PM. Field dependence of the resistive transition for a square wire network. PHYSICAL REVIEW. B, CONDENSED MATTER 1991; 43:2721-2725. [PMID: 9997566 DOI: 10.1103/physrevb.43.2721] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Li YH, Teitel S. Flux-flow resistance in frustrated Josephson-junction arrays. PHYSICAL REVIEW LETTERS 1990; 65:2595-2598. [PMID: 10042637 DOI: 10.1103/physrevlett.65.2595] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Falo F, Bishop AR, Lomdahl PS. I-V characteristics in two-dimensional frustrated Josephson-junction arrays. PHYSICAL REVIEW. B, CONDENSED MATTER 1990; 41:10983-10993. [PMID: 9993518 DOI: 10.1103/physrevb.41.10983] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Lee JR, Teitel S. New critical behavior in the dense two-dimensional classical Coulomb gas. PHYSICAL REVIEW LETTERS 1990; 64:1483-1486. [PMID: 10041409 DOI: 10.1103/physrevlett.64.1483] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Baskaran G. Novel local symmetries and chiral-symmetry-broken phases in S=(1/2 triangular-lattice Heisenberg model. PHYSICAL REVIEW LETTERS 1989; 63:2524-2527. [PMID: 10040910 DOI: 10.1103/physrevlett.63.2524] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Minnhagen P, Wallin M. Results for the phase diagram of the two-dimensional Coulomb gas. PHYSICAL REVIEW. B, CONDENSED MATTER 1989; 40:5109-5130. [PMID: 9992510 DOI: 10.1103/physrevb.40.5109] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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