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Membrane-mediated protein-protein interaction: A Monte Carlo study 膜介导的蛋白-蛋白相互作用:蒙特卡洛研究
arXiv: Biological Physics Pub Date : 2011-09-30 DOI: 10.2174/157341311797483655
J. Neder, B. West, P. Nielaba, F. Schmid
{"title":"Membrane-mediated protein-protein interaction: A Monte Carlo study","authors":"J. Neder, B. West, P. Nielaba, F. Schmid","doi":"10.2174/157341311797483655","DOIUrl":"https://doi.org/10.2174/157341311797483655","url":null,"abstract":"We investigate membrane-mediated interactions between transmembrane proteins using coarse-grained models. We compare the effective potential of mean force (PMF) between two proteins, which are always aligned parallel to the z-axis of the simulation box, with those PMFs obtained for proteins with fluctuating orientations. The PMFs are dominated by an oscillatory packing-driven contribution and a smooth attractive hydrophobic mismatch contribution, which vanishes if the hydrophobic length of the protein matches the thickness of the membrane. If protein orientations are allowed to fluctuate, the oscillations are greatly reduced compared to proteins with fixed orientation. Furthermore, the hydrophobic mismatch interaction has a smaller range. Finally, we compare the two-dimensional thickness profiles around two proteins with the predictions from the elastic theory of two coupled monolayers, and find them to be in very good agreement.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134064634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 10
Efficient energy transfer in light-harvesting systems, III: The influence of the eighth bacteriochlorophyll on the dynamics and efficiency in FMO 光收集系统的有效能量传递，III:第八细菌叶绿素对FMO动力学和效率的影响
arXiv: Biological Physics Pub Date : 2011-09-14 DOI: 10.1021/JZ201259V
Jeremy M Moix, Jianlan Wu, P. Huo, D. Coker, Jianshu Cao
{"title":"Efficient energy transfer in light-harvesting systems, III: The influence of the eighth bacteriochlorophyll on the dynamics and efficiency in FMO","authors":"Jeremy M Moix, Jianlan Wu, P. Huo, D. Coker, Jianshu Cao","doi":"10.1021/JZ201259V","DOIUrl":"https://doi.org/10.1021/JZ201259V","url":null,"abstract":"The most recent crystal structure of the Fenna-Matthews-Olson (FMO) protein complex indicates that each subunit contains an additional eighth chromophore. It has been proposed that this extra site functions as a link between the chlorosome antenna complex and the remaining seven chromophores in FMO [Schmidt am Busch et al, J. Phys. Chem. Lett., {bf 2}, 93 (2011)]. Here, we investigate the implications of this scenario through numerical calculations with the generalized Bloch-Redfield (GBR) equation and the non-interacting blip approximation (NIBA). Three key insights into the population dynamics and energy transfer efficiency in FMO are provided. First, it is shown that the oscillations that are often observed in the population relaxation of the dimer composed of sites one and two may be completely suppressed in the eight site model. The presence of the coherent oscillations is shown to depend upon the particular initial preparation of the dimer state. Secondly it is demonstrated that while the presence of the eighth chromophore does not cause a dramatic change in the energy transfer efficiency, it does however lead to a dominant energy transfer pathway which can be characterized by an effective three site system arranged in an equally spaced downhill configuration. Such a configuration leads to an optimal value of the site energy of the eighth chromophore which is shown to be near to its suggested value. Finally we confirm that the energy transfer process in the eight site FMO complex remains efficient and robust. The optimal values of the bath parameters are computed and shown to be closer to the experimentally fitted values than those calculated previously for the seven site system.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128627045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 127
Multimodal transition and excitability of a neural oscillator 神经振荡器的多模态跃迁和兴奋性
arXiv: Biological Physics Pub Date : 2011-09-13 DOI: 10.12693/APhysPolA.122.776
L. Borkowski
{"title":"Multimodal transition and excitability of a neural oscillator","authors":"L. Borkowski","doi":"10.12693/APhysPolA.122.776","DOIUrl":"https://doi.org/10.12693/APhysPolA.122.776","url":null,"abstract":"We analyze the response of the Morris-Lecar model to a periodic train of short current pulses in the period-amplitude plane. For a wide parameter range encompassing both class 2 and class 3 behavior in Hodgkin's classification there is a multimodal transition between the set of odd modes and the set of all modes. It is located between the 2:1 and 3:1 locked-in regions. It is the same dynamic instability as the one discovered earlier in the Hodgkin-Huxley model and observed experimentally in squid giant axons. It appears simultaneously with the bistability of the states 2:1 and 3:1 in the perithreshold regime. These results imply that the multimodal transition may be a universal property of resonant neurons.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"28 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133850761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
Equilibrium insertion of nanoscale objects into phospholipid bilayers 纳米级物体在磷脂双层中的平衡插入
arXiv: Biological Physics Pub Date : 2011-08-30 DOI: 10.2174/157341311797483871
S. Pogodin, V. Baulin
{"title":"Equilibrium insertion of nanoscale objects into phospholipid bilayers","authors":"S. Pogodin, V. Baulin","doi":"10.2174/157341311797483871","DOIUrl":"https://doi.org/10.2174/157341311797483871","url":null,"abstract":"Certain membrane proteins, peptides, nanoparticles and nanotubes have rigid structure and fixed shape. They are often viewed as spheres and cylinders with certain surface properties. Single Chain Mean Field theory is used to model the equilibrium insertion of nanoscale spheres and rods into the phospholipid bilayer. The equilibrium structures and the resulting free energies of the nano-objects in the bilayer allow to distinguish different orientations in the bilayer and estimate the energy barrier of insertion.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"49 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131121006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 15
Computational Studies of the Structural Stability of Rabbit Prion Protein Compared to Human and Mouse Prion Proteins 兔朊蛋白与人、鼠朊蛋白结构稳定性的计算研究
arXiv: Biological Physics Pub Date : 2011-07-25 DOI: 10.5772/28858
Jiapu Zhang
{"title":"Computational Studies of the Structural Stability of Rabbit Prion Protein Compared to Human and Mouse Prion Proteins","authors":"Jiapu Zhang","doi":"10.5772/28858","DOIUrl":"https://doi.org/10.5772/28858","url":null,"abstract":"Prion diseases are invariably fatal and highly infectious neurodegenerative diseases affecting humans and animals. The neurodegenerative diseases such as Creutzfeldt-Jakob disease, variant Creutzfeldt-Jakob diseases, Gerstmann-Str$ddot{a}$ussler-Scheinker syndrome, Fatal Familial Insomnia, Kuru in humans, scrapie in sheep, bovine spongiform encephalopathy (or 'mad-cow' disease) and chronic wasting disease in cattle belong to prion diseases. By now there have not been some effective therapeutic approaches to treat all these prion diseases. Dogs, rabbits and horses were reported to be resistant to prion diseases. By the end of year 2010 all the NMR structures of dog, rabbit and horse prion proteins (X-ray for rabbits too) had been finished to release into protein data bank. Thus, at this moment it is very worth studying the NMR and X-ray molecular structures of horse, dog and rabbit prion proteins to obtain insights into their immunity prion diseases. \u0000The author found that dog and horse prion proteins have stable molecular dynamical structures whether under neutral or low pH environments, but rabbit prion protein has stable molecular dynamical structures only under neutral pH environment. Under low pH environment, the stable $alpha$-helical molecular structures of rabbit prion protein collapse into $beta$-sheet structures. This article focuses the studies on rabbit prion protein (within its C-terminal NMR, Homology and X-ray molecular structured region RaPrP$^text{C}$ (120-230)), compared with human and mouse prion proteins (HuPrP$^text{C}$ (125-228) and MoPrP$^text{C}$ (124-226) respectively). The author finds that some salt bridges contribute to the structural stability of rabbit prion protein under neutral pH environment.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"50 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131544435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Response of the Hodgkin-Huxley neuron to a periodic sequence of biphasic pulses 霍奇金-赫胥黎神经元对周期性双相脉冲序列的响应
arXiv: Biological Physics Pub Date : 2011-05-26 DOI: 10.12693/APHYSPOLA.125.145
L. Borkowski
{"title":"Response of the Hodgkin-Huxley neuron to a periodic sequence of biphasic pulses","authors":"L. Borkowski","doi":"10.12693/APHYSPOLA.125.145","DOIUrl":"https://doi.org/10.12693/APHYSPOLA.125.145","url":null,"abstract":"We study the response of the Hodgkin-Huxley neuron stimulated periodically by biphasic rectangular current pulses. The optimal response for charge-balanced input is obtained for cathodic-first pulses with an inter-phase gap (IPG) approximately equal 5 ms. For short pulses the topology of the global bifurcation diagram in the period-amplitude plane is approximately invariant with respect to the pulse polarity and shape details. If stimuli are delivered at neuron's resonant frequencies the firing rate is a continuous function of pulse amplitude. At nonresonant frequencies the quiescent state and the firing state coexist over a range of amplitude values and the transition to excitability is a discontinuous one. There is a multimodal odd-all transition between the 2:1 and 3:1 locked-in states. A strong antiresonant effect is found between the states 3:1 and 4:1, where the modes (2+3n):1, $n=0,1,2,...$, are entirely absent. At high frequencies the excitation threshold is a nonmonotonic function of the stimulus and the perithreshold region is bistable, with the quiescent state coexisting with either a regular or chaotic firing.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"103 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115555765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
X-ray phase contrast imaging of biological specimens with tabletop synchrotron radiation 台式同步辐射生物标本的x射线相衬成像
arXiv: Biological Physics Pub Date : 2011-05-12 DOI: 10.1038/NPRE.2011.5946.1
S. Kneip, C. McGuffey, F. Dollar, M. Bloom, V. Chvykov, G. Kalintchenko, K. Krushelnick, A. Maksimchuk, S. Mangles, T. Matsuoka, Z. Najmudin, C. Palmer, J. Schreiber, W. Schumaker, A. Thomas, V. Yanovsky
{"title":"X-ray phase contrast imaging of biological specimens with tabletop synchrotron radiation","authors":"S. Kneip, C. McGuffey, F. Dollar, M. Bloom, V. Chvykov, G. Kalintchenko, K. Krushelnick, A. Maksimchuk, S. Mangles, T. Matsuoka, Z. Najmudin, C. Palmer, J. Schreiber, W. Schumaker, A. Thomas, V. Yanovsky","doi":"10.1038/NPRE.2011.5946.1","DOIUrl":"https://doi.org/10.1038/NPRE.2011.5946.1","url":null,"abstract":"","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"61 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130320119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
A low-Reynolds-number treadmilling swimmer near a semi-infinite wall 一个低雷诺数的跑步者靠近半无限的墙
arXiv: Biological Physics Pub Date : 2011-04-01 DOI: 10.1007/978-1-4614-3997-4_15
K. Obuse, Jean-Luc Thiffeault
{"title":"A low-Reynolds-number treadmilling swimmer near a semi-infinite wall","authors":"K. Obuse, Jean-Luc Thiffeault","doi":"10.1007/978-1-4614-3997-4_15","DOIUrl":"https://doi.org/10.1007/978-1-4614-3997-4_15","url":null,"abstract":"","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"438 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134484605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
High temperature unfolding simulations of a single stranded DNA i-motif 单链DNA i基序的高温展开模拟
arXiv: Biological Physics Pub Date : 2011-03-30 DOI: 10.2174/1877946811202010115
Jens Smiatek, Dongsheng Liu, A. Heuer
{"title":"High temperature unfolding simulations of a single stranded DNA i-motif","authors":"Jens Smiatek, Dongsheng Liu, A. Heuer","doi":"10.2174/1877946811202010115","DOIUrl":"https://doi.org/10.2174/1877946811202010115","url":null,"abstract":"We present the results of high temperature 500 K Molecular Dynamics simulations of the DNA i-motif. The essential dynamics and the main unfolding pathways are compared to a biased metadynamics simulation at 300 K. Our results indicate a remarkable agreement of the concerted motion at both temperatures. The transition can be described by a few number of eigenvectors indicating a simple unfolding process. Two main mechanisms for the unfolding pathway at 500 K can be detected which are in good agreement to the results of the biased simulation at 300 K.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127970669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
SIR epidemics in monogamous populations with recombination SIR在一夫一妻制重组人群中的流行
arXiv: Biological Physics Pub Date : 2011-03-25 DOI: 10.4279/PIP.030001
D. Zanette
{"title":"SIR epidemics in monogamous populations with recombination","authors":"D. Zanette","doi":"10.4279/PIP.030001","DOIUrl":"https://doi.org/10.4279/PIP.030001","url":null,"abstract":"We study the propagation of an SIR (susceptible-infectious-recovered) disease over an agent population which, at any instant, is fully divided into couples of agents. Couples are occasionally allowed to exchange their members. This process of couple recombination can compensate the instantaneous disconnection of the interaction pattern and thus allow for the propagation of the infection. We study the incidence of the disease as a function of its infectivity and of the recombination rate of couples, thus characterizing the interplay between the epidemic dynamics and the evolution of the population's interaction pattern.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127629013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
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