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Understanding actin organization in cell structure through lattice based Monte Carlo simulations. 通过基于晶格的蒙特卡罗模拟了解细胞结构中的肌动蛋白组织。
Mechanics & chemistry of biosystems : MCB Pub Date : 2004-06-01
Kathleen Puskar, Leonard Apeltsin, Shlomo Ta'asan, Russell Schwartz, Philip R LeDuc
{"title":"Understanding actin organization in cell structure through lattice based Monte Carlo simulations.","authors":"Kathleen Puskar,&nbsp;Leonard Apeltsin,&nbsp;Shlomo Ta'asan,&nbsp;Russell Schwartz,&nbsp;Philip R LeDuc","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Understanding the connection between mechanics and cell structure requires the exploration of the key molecular constituents responsible for cell shape and motility. One of these molecular bridges is the cytoskeleton, which is involved with intracellular organization and mechanotransduction. In order to examine the structure in cells, we have developed a computational technique that is able to probe the self-assembly of actin filaments through a lattice based Monte Carlo method. We have modeled the polymerization of these filaments based upon the interactions of globular actin through a probabilistic model encompassing both inert and active proteins. The results show similar response to classic ordinary differential equations at low molecular concentrations, but a bi-phasic divergence at realistic concentrations for living mammalian cells. Further, by introducing localized mobility parameters, we are able to simulate molecular gradients that are observed in nonhomogeneous protein distributions in vivo. The method and results have potential applications in cell and molecular biology as well as self-assembly for organic and inorganic systems.</p>","PeriodicalId":87411,"journal":{"name":"Mechanics & chemistry of biosystems : MCB","volume":"1 2","pages":"123-31"},"PeriodicalIF":0.0,"publicationDate":"2004-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26097510","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
Forced dissociation of the strand dimer interface between C-cadherin ectodomains. c -钙粘蛋白外结构域间链二聚体界面的强制解离。
Mechanics & chemistry of biosystems : MCB Pub Date : 2004-06-01 DOI: 10.3970/MCB.2004.001.101
M. Bayas, K. Schulten, D. Leckband
{"title":"Forced dissociation of the strand dimer interface between C-cadherin ectodomains.","authors":"M. Bayas, K. Schulten, D. Leckband","doi":"10.3970/MCB.2004.001.101","DOIUrl":"https://doi.org/10.3970/MCB.2004.001.101","url":null,"abstract":"The force-induced dissociation of the strand dimer interface in C-cadherin has been studied using steered molecular dynamics simulations. The dissociation occurred, without domain unraveling, after the extraction of the conserved trypthophans (Trp2) from their respective hydrophobic pockets. The simulations revealed two stable positions for the Trp2 side chain inside the pocket. The most internal stable position involved a hydrogen bond between the ring Nepsilon of Trp2 and the backbone carbonyl of Glu90. In the second stable position, the aromatic ring is located at the pocket entrance. After extracting the two tryptophans from their pockets, the complex exists in an intermediate bound state that involves a close packing of the tryptophans with residues Asp1 and Asp27 from both domains. Dissociation occurred after this residue association was broken. Simulations carried out with a complex formed between W2A mutants showed that the mutant complex dissociates more easily than the wild type complex does. These results correlate closely with the role of the conserved tryptophans suggested previously by site directed mutagenesis.","PeriodicalId":87411,"journal":{"name":"Mechanics & chemistry of biosystems : MCB","volume":"1 2 1","pages":"101-11"},"PeriodicalIF":0.0,"publicationDate":"2004-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70238885","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: 25
A simple phenomenological theory of tissue growth. 组织生长的简单现象学理论。
Mechanics & chemistry of biosystems : MCB Pub Date : 2004-06-01
K Y Volokh
{"title":"A simple phenomenological theory of tissue growth.","authors":"K Y Volokh","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>A simple phenomenological framework for modeling growth of living tissues is proposed. Growth is defined as a change of mass and configuration of the tissue. Tissue is considered as an open system where mass conservation is violated and the full-scale mass balance is applied. A possible structure of constitutive equations is discussed with reference to simple growing materials. 'Thermoelastic' formulation of the simple growing material is specified. Within this framework traction free growth of cylindrical and spherical bodies is examined. It is shown that the theory accommodates the case where stresses are not generated in uniform volumetric growth. It is also found that surface growth corresponds to a boundary layer solution of the governing equations. This finding proves the ability of continuum mechanics to describe surface growth. The latter is contrary to the usual use of purely kinematical theories, which do not involve balance and constitutive equations, for treating surface growth.</p>","PeriodicalId":87411,"journal":{"name":"Mechanics & chemistry of biosystems : MCB","volume":"1 2","pages":"147-60"},"PeriodicalIF":0.0,"publicationDate":"2004-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26097512","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
Encapsulation of pt-labelled DNA molecules inside carbon nanotubes. 铂标记DNA分子在碳纳米管内的封装。
Mechanics & chemistry of biosystems : MCB Pub Date : 2004-06-01
Daxiang Cui, Cengiz S Ozkan, Sathyajith Ravindran, Yong Kong, Huajian Gao
{"title":"Encapsulation of pt-labelled DNA molecules inside carbon nanotubes.","authors":"Daxiang Cui,&nbsp;Cengiz S Ozkan,&nbsp;Sathyajith Ravindran,&nbsp;Yong Kong,&nbsp;Huajian Gao","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Experiments on encapsulating Pt-labelled DNA molecules inside multiwalled carbon nanotubes (MWCNT) were performed under temperature and pressure conditions of 400K and 3 Bar. The DNA-CNT hybrids were purified via agarose gel electrophoresis and analyzed via high resolution transmission electron microscopy (HR-TEM) and energy dispersive X-ray spectroscopy (EDX). The results showed that the Pt-labelled DNA molecules attached to the outside walls of CNTs could be removed by electrophoresis. The HR-TEM and EDX results demonstrated that 2-3% of the Pt-labelled DNA molecules were successfully encapsulated inside the MWCNTs. The experimental study complements our previous molecular dynamics simulations on encapsulation of single stranded DNA oligonucleotides inside single wall carbon nanotubes under similar conditions in water. The van der Waals interaction between CNT and Pt-labelled DNA is believed to be the main driving force for this phenomenon. The DNA-CNT molecular complex could be further explored for potential applications in bio-nanotechnology.</p>","PeriodicalId":87411,"journal":{"name":"Mechanics & chemistry of biosystems : MCB","volume":"1 2","pages":"113-21"},"PeriodicalIF":0.0,"publicationDate":"2004-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26097509","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
Encapsulation of pt-labelled DNA molecules inside carbon nanotubes. 铂标记DNA分子在碳纳米管内的封装。
Mechanics & chemistry of biosystems : MCB Pub Date : 2004-06-01 DOI: 10.3970/MCB.2004.001.113
Daxiang Cui, C. Ozkan, Sathyajith Ravindran, Y. Kong, Huajian Gao
{"title":"Encapsulation of pt-labelled DNA molecules inside carbon nanotubes.","authors":"Daxiang Cui, C. Ozkan, Sathyajith Ravindran, Y. Kong, Huajian Gao","doi":"10.3970/MCB.2004.001.113","DOIUrl":"https://doi.org/10.3970/MCB.2004.001.113","url":null,"abstract":"Experiments on encapsulating Pt-labelled DNA molecules inside multiwalled carbon nanotubes (MWCNT) were performed under temperature and pressure conditions of 400K and 3 Bar. The DNA-CNT hybrids were purified via agarose gel electrophoresis and analyzed via high resolution transmission electron microscopy (HR-TEM) and energy dispersive X-ray spectroscopy (EDX). The results showed that the Pt-labelled DNA molecules attached to the outside walls of CNTs could be removed by electrophoresis. The HR-TEM and EDX results demonstrated that 2-3% of the Pt-labelled DNA molecules were successfully encapsulated inside the MWCNTs. The experimental study complements our previous molecular dynamics simulations on encapsulation of single stranded DNA oligonucleotides inside single wall carbon nanotubes under similar conditions in water. The van der Waals interaction between CNT and Pt-labelled DNA is believed to be the main driving force for this phenomenon. The DNA-CNT molecular complex could be further explored for potential applications in bio-nanotechnology.","PeriodicalId":87411,"journal":{"name":"Mechanics & chemistry of biosystems : MCB","volume":"1 2 1","pages":"113-21"},"PeriodicalIF":0.0,"publicationDate":"2004-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70239032","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: 26
Understanding actin organization in cell structure through lattice based Monte Carlo simulations. 通过基于晶格的蒙特卡罗模拟了解细胞结构中的肌动蛋白组织。
Mechanics & chemistry of biosystems : MCB Pub Date : 2004-06-01 DOI: 10.3970/MCB.2004.001.123
K. Puskar, Leonard Apeltsin, S. Ta'asan, R. Schwartz, P. Leduc
{"title":"Understanding actin organization in cell structure through lattice based Monte Carlo simulations.","authors":"K. Puskar, Leonard Apeltsin, S. Ta'asan, R. Schwartz, P. Leduc","doi":"10.3970/MCB.2004.001.123","DOIUrl":"https://doi.org/10.3970/MCB.2004.001.123","url":null,"abstract":"Understanding the connection between mechanics and cell structure requires the exploration of the key molecular constituents responsible for cell shape and motility. One of these molecular bridges is the cytoskeleton, which is involved with intracellular organization and mechanotransduction. In order to examine the structure in cells, we have developed a computational technique that is able to probe the self-assembly of actin filaments through a lattice based Monte Carlo method. We have modeled the polymerization of these filaments based upon the interactions of globular actin through a probabilistic model encompassing both inert and active proteins. The results show similar response to classic ordinary differential equations at low molecular concentrations, but a bi-phasic divergence at realistic concentrations for living mammalian cells. Further, by introducing localized mobility parameters, we are able to simulate molecular gradients that are observed in nonhomogeneous protein distributions in vivo. The method and results have potential applications in cell and molecular biology as well as self-assembly for organic and inorganic systems.","PeriodicalId":87411,"journal":{"name":"Mechanics & chemistry of biosystems : MCB","volume":"1 2 1","pages":"123-31"},"PeriodicalIF":0.0,"publicationDate":"2004-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70239275","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: 5
Modeling of surface-tension-driven flow of blood in capillary tubes. 毛细管中表面张力驱动的血流模型。
Mechanics & chemistry of biosystems : MCB Pub Date : 2004-06-01 DOI: 10.3970/MCB.2004.001.161
Jun Wang, Wei Huang, R. S. Bhullar, P. Tong
{"title":"Modeling of surface-tension-driven flow of blood in capillary tubes.","authors":"Jun Wang, Wei Huang, R. S. Bhullar, P. Tong","doi":"10.3970/MCB.2004.001.161","DOIUrl":"https://doi.org/10.3970/MCB.2004.001.161","url":null,"abstract":"Surface-tension-driven blood flow into a capillary tube, as in some medical devices, is studied. In a previous article, we considered the early stages of the entry flow from a drop of blood into a capillary, and solved the problem analytically under the assumption that the resistance of the air is negligible. In the present note we consider a capillary tube of finite length, with the far end containing a small window which opens to the atmosphere. The dynamic reverberation of the air in the capillary tube is analyzed in conjunction with the dynamics of the blood. Existing computing programs are used to solve the Navier-Stokes equations. The interface is characterized by the surface tension between the blood and the air, and the contact angle at the triple point where the air-blood interface meets the capillary tube wall. The results tell us how good our earlier simplified analysis is. The new numerical results show that the smaller the window, the larger is the effect of aerodynamic reverberation. However, even for a window as small as 4% of the capillary cross section, and located at the end of the capillary, the difference of the time of arrival of the interface at the window is less than 5%.","PeriodicalId":87411,"journal":{"name":"Mechanics & chemistry of biosystems : MCB","volume":"1 2 1","pages":"161-7"},"PeriodicalIF":0.0,"publicationDate":"2004-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70239611","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
Illuminating the dynamics of intracellular activity with 'active' molecular reporters. 用“活跃的”分子报告器阐明细胞内活动的动力学。
Mechanics & chemistry of biosystems : MCB Pub Date : 2004-06-01 DOI: 10.3970/MCB.2004.001.133
A. Tsourkas, R. Weissleder
{"title":"Illuminating the dynamics of intracellular activity with 'active' molecular reporters.","authors":"A. Tsourkas, R. Weissleder","doi":"10.3970/MCB.2004.001.133","DOIUrl":"https://doi.org/10.3970/MCB.2004.001.133","url":null,"abstract":"Traditionally, fluorescent and luminescent reporter proteins have been used as indicators of gene expression and protein localization. However, insightful mutagenesis and protein engineering strategies have transformed these simple passive reporters into active biological sensors. Molecular reporters are now being designed to alter their intrinsic optical properties in response to specific biomolecular interactions. Applications for these novel biological sensors range from monitoring intracellular pH and ion fluxes to detecting protein-protein interactions and enzymatic activity. The ability to monitor the dynamics of intracellular activity in response to external stimuli can help elucidate the cascade of events involved in complex processes such as mechanotransduction. Here we review some of the approaches used to create these novel biological sensors, including resonance energy transfer (RET) between reporter proteins and protein fragmentation strategies.","PeriodicalId":87411,"journal":{"name":"Mechanics & chemistry of biosystems : MCB","volume":"1 2 1","pages":"133-45"},"PeriodicalIF":0.0,"publicationDate":"2004-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70239387","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
Forced dissociation of the strand dimer interface between C-cadherin ectodomains. c -钙粘蛋白外结构域间链二聚体界面的强制解离。
Mechanics & chemistry of biosystems : MCB Pub Date : 2004-06-01
M V Bayas, K Schulten, D Leckband
{"title":"Forced dissociation of the strand dimer interface between C-cadherin ectodomains.","authors":"M V Bayas,&nbsp;K Schulten,&nbsp;D Leckband","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The force-induced dissociation of the strand dimer interface in C-cadherin has been studied using steered molecular dynamics simulations. The dissociation occurred, without domain unraveling, after the extraction of the conserved trypthophans (Trp2) from their respective hydrophobic pockets. The simulations revealed two stable positions for the Trp2 side chain inside the pocket. The most internal stable position involved a hydrogen bond between the ring Nepsilon of Trp2 and the backbone carbonyl of Glu90. In the second stable position, the aromatic ring is located at the pocket entrance. After extracting the two tryptophans from their pockets, the complex exists in an intermediate bound state that involves a close packing of the tryptophans with residues Asp1 and Asp27 from both domains. Dissociation occurred after this residue association was broken. Simulations carried out with a complex formed between W2A mutants showed that the mutant complex dissociates more easily than the wild type complex does. These results correlate closely with the role of the conserved tryptophans suggested previously by site directed mutagenesis.</p>","PeriodicalId":87411,"journal":{"name":"Mechanics & chemistry of biosystems : MCB","volume":"1 2","pages":"101-11"},"PeriodicalIF":0.0,"publicationDate":"2004-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26097508","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
Modeling of surface-tension-driven flow of blood in capillary tubes. 毛细管中表面张力驱动的血流模型。
Mechanics & chemistry of biosystems : MCB Pub Date : 2004-06-01
Jun Wang, Wei Huang, Raghbir S Bhullar, Pin Tong
{"title":"Modeling of surface-tension-driven flow of blood in capillary tubes.","authors":"Jun Wang,&nbsp;Wei Huang,&nbsp;Raghbir S Bhullar,&nbsp;Pin Tong","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Surface-tension-driven blood flow into a capillary tube, as in some medical devices, is studied. In a previous article, we considered the early stages of the entry flow from a drop of blood into a capillary, and solved the problem analytically under the assumption that the resistance of the air is negligible. In the present note we consider a capillary tube of finite length, with the far end containing a small window which opens to the atmosphere. The dynamic reverberation of the air in the capillary tube is analyzed in conjunction with the dynamics of the blood. Existing computing programs are used to solve the Navier-Stokes equations. The interface is characterized by the surface tension between the blood and the air, and the contact angle at the triple point where the air-blood interface meets the capillary tube wall. The results tell us how good our earlier simplified analysis is. The new numerical results show that the smaller the window, the larger is the effect of aerodynamic reverberation. However, even for a window as small as 4% of the capillary cross section, and located at the end of the capillary, the difference of the time of arrival of the interface at the window is less than 5%.</p>","PeriodicalId":87411,"journal":{"name":"Mechanics & chemistry of biosystems : MCB","volume":"1 2","pages":"161-7"},"PeriodicalIF":0.0,"publicationDate":"2004-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26097513","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
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