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Article ; Online: Agent-Based Modeling in Molecular Systems Biology.

Soheilypour, Mohammad / Mofrad, Mohammad R K

BioEssays : news and reviews in molecular, cellular and developmental biology

2018 Volume 40, Issue 7, Page(s) e1800020

Abstract: Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior ... ...

Abstract	Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially-detailed and computationally-efficient approaches. In this review, we summarize the capabilities of agent-based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease.
MeSH term(s)	Computational Biology/trends ; Computer Simulation ; Humans ; Models, Theoretical ; Systems Analysis ; Systems Biology/trends
Language	English
Publishing date	2018-06-08
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.201800020
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Article ; Online: Quality control of mRNAs at the entry of the nuclear pore: Cooperation in a complex molecular system.

Soheilypour, Mohammad / Mofrad, Mohammad R K

Nucleus (Austin, Tex.)

2018 Volume 9, Issue 1, Page(s) 202–211

Abstract: Despite extensive research on how mRNAs are quality controlled prior to export into the cytoplasm, the exact underlying mechanisms are still under debate. Specifically, it is unclear how quality control proteins at the entry of the nuclear pore complex ( ... ...

Abstract	Despite extensive research on how mRNAs are quality controlled prior to export into the cytoplasm, the exact underlying mechanisms are still under debate. Specifically, it is unclear how quality control proteins at the entry of the nuclear pore complex (NPC) distinguish normal and aberrant mRNAs. While some of the involved components are suggested to act as switches and recruit different factors to normal versus aberrant mRNAs, some experimental and computational evidence suggests that the combined effect of the regulated stochastic interactions between the involved components could potentially achieve an efficient quality control of mRNAs. In this review, we present a state-of-the-art portrait of the mRNA quality control research and discuss the current hypotheses proposed for dynamics of the cooperation between the involved components and how it leads to their shared goal: mRNA quality control prior to export into the cytoplasm.
MeSH term(s)	Cell Nucleus/metabolism ; Cytoplasm/metabolism ; Humans ; Nuclear Pore/metabolism ; Quality Control ; RNA, Messenger/metabolism
Chemical Substances	RNA, Messenger
Language	English
Publishing date	2018-02-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	2619626-8
ISSN	1949-1042 ; 1949-1034
ISSN (online)	1949-1042
ISSN	1949-1034
DOI	10.1080/19491034.2018.1439304
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Article ; Online: FG nucleoporins feature unique patterns that distinguish them from other IDPs.

Peyro, Mohaddeseh / Soheilypour, Mohammad / Nibber, Vikrum S / Dickson, Andrew M / Mofrad, Mohammad R K

Biophysical journal

2021 Volume 120, Issue 16, Page(s) 3382–3391

Abstract: FG nucleoporins (FG Nups) are intrinsically disordered proteins and are the putative regulators of nucleocytoplasmic transport. They allow fast, yet selective, transport of molecules through the nuclear pore complex, but the underlying mechanism of ... ...

Abstract	FG nucleoporins (FG Nups) are intrinsically disordered proteins and are the putative regulators of nucleocytoplasmic transport. They allow fast, yet selective, transport of molecules through the nuclear pore complex, but the underlying mechanism of nucleocytoplasmic transport is not yet fully discovered. As a result, FG Nups have been the subject of extensive research in the past two decades. Although most studies have been focused on analyzing the conformation and function of FG Nups from a biophysical standpoint, some recent studies have investigated the sequence-function relationship of FG Nups, with a few investigating amino acid sequences of a large number of FG Nups to understand common characteristics that might enable their function. Previously, we identified an evolutionarily conserved feature in FG Nup sequences, which are extended subsequences with low charge density, containing only positive charges, and located toward the N-terminus of FG Nups. We named these patterns longest positive like charge regions (lpLCRs). These patterns are specific to positively charged residues, and negatively charged residues do not demonstrate such a pattern. In this study, we compare FG Nups with other disordered proteins obtained from the DisProt and UniProt database in terms of presence of lpLCRs. Our results show that the lpLCRs are virtually exclusive to FG Nups and are not observed in other disordered proteins. Also, lpLCRs are what differentiate FG Nups from DisProt proteins in terms of charge distribution, meaning that excluding lpLCRs from the sequences of FG Nups make them similar to DisProt proteins in terms of charge distribution. We also previously showed the biophysical effect of lpLCRs in conformation of FG Nups. The results of this study are in line with our previous findings and imply that lpLCRs are virtually exclusive and functionally significant characteristics of FG Nups and nucleocytoplasmic transport.
MeSH term(s)	Active Transport, Cell Nucleus ; Glycine/metabolism ; Nuclear Pore/metabolism ; Nuclear Pore Complex Proteins/metabolism ; Phenylalanine/metabolism
Chemical Substances	Nuclear Pore Complex Proteins ; Phenylalanine (47E5O17Y3R) ; Glycine (TE7660XO1C)
Language	English
Publishing date	2021-07-06
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2021.06.031
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Article: Agent‐Based Modeling in Molecular Systems Biology

Soheilypour, Mohammad / Mohammad R. K. Mofrad

BioEssays. 2018 July, v. 40, no. 7

2018

Abstract	Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially‐detailed and computationally‐efficient approaches. In this review, we summarize the capabilities of agent‐based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease.
Keywords	computational methodology ; models ; researchers
Language	English
Dates of publication	2018-07
Size	p. e1800020.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	REVIEW
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.201800020
Database	NAL-Catalogue (AGRICOLA)

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Article: Quality control of mRNAs at the entry of the nuclear pore: Cooperation in a complex molecular system

Soheilypour, Mohammad / Mofrad, Mohammad R. K

Nucleus. 2018 Dec. 31, v. 9, no. 1

2018

Abstract	Despite extensive research on how mRNAs are quality controlled prior to export into the cytoplasm, the exact underlying mechanisms are still under debate. Specifically, it is unclear how quality control proteins at the entry of the nuclear pore complex (NPC) distinguish normal and aberrant mRNAs. While some of the involved components are suggested to act as switches and recruit different factors to normal versus aberrant mRNAs, some experimental and computational evidence suggests that the combined effect of the regulated stochastic interactions between the involved components could potentially achieve an efficient quality control of mRNAs. In this review, we present a state-of-the-art portrait of the mRNA quality control research and discuss the current hypotheses proposed for dynamics of the cooperation between the involved components and how it leads to their shared goal: mRNA quality control prior to export into the cytoplasm.
Keywords	cytoplasm ; nuclear pore ; quality control
Language	English
Dates of publication	2018-1231
Size	p. 202-211.
Publishing place	Taylor & Francis
Document type	Article
ZDB-ID	2619626-8
ISSN	1949-1042 ; 1949-1034
ISSN (online)	1949-1042
ISSN	1949-1034
DOI	10.1080/19491034.2018.1439304
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Characterizing Binding Interactions That Are Essential for Selective Transport through the Nuclear Pore Complex.

Lennon, Kathleen M / Soheilypour, Mohammad / Peyro, Mohaddeseh / Wakefield, Devin L / Choo, Grace E / Mofrad, Mohammad R K / Jovanovic-Talisman, Tijana

International journal of molecular sciences

2021 Volume 22, Issue 19

Abstract: Specific macromolecules are rapidly transported across the nuclear envelope via the nuclear pore complex (NPC). The selective transport process is facilitated when nuclear transport receptors (NTRs) weakly and transiently bind to intrinsically disordered ...

Abstract	Specific macromolecules are rapidly transported across the nuclear envelope via the nuclear pore complex (NPC). The selective transport process is facilitated when nuclear transport receptors (NTRs) weakly and transiently bind to intrinsically disordered constituents of the NPC, FG Nups. These two types of proteins help maintain the selective NPC barrier. To interrogate their binding interactions in vitro, we deployed an NPC barrier mimic. We created the stationary phase by covalently attaching fragments of a yeast FG Nup called Nsp1 to glass coverslips. We used a tunable mobile phase containing NTR, nuclear transport factor 2 (NTF2). In the stationary phase, three main factors affected binding: the number of FG repeats, the charge of fragments, and the fragment density. We also identified three main factors affecting binding in the mobile phase: the avidity of the NTF2 variant for Nsp1, the presence of nonspecific proteins, and the presence of additional NTRs. We used both experimentally determined binding parameters and molecular dynamics simulations of Nsp1FG fragments to create an agent-based model. The results suggest that NTF2 binding is negatively cooperative and dependent on the density of Nsp1FG molecules. Our results demonstrate the strengths of combining experimental and physical modeling approaches to study NPC-mediated transport.
MeSH term(s)	Active Transport, Cell Nucleus ; Cell Nucleus/metabolism ; Models, Molecular ; Molecular Dynamics Simulation ; Mutation ; Nuclear Pore/physiology ; Nuclear Pore Complex Proteins/genetics ; Nuclear Pore Complex Proteins/metabolism ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Nucleocytoplasmic Transport Proteins/genetics ; Nucleocytoplasmic Transport Proteins/metabolism ; Protein Interaction Domains and Motifs ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/growth & development ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	NSP1 protein, S cerevisiae ; NTF2 protein, S cerevisiae ; Nuclear Pore Complex Proteins ; Nuclear Proteins ; Nucleocytoplasmic Transport Proteins ; Saccharomyces cerevisiae Proteins
Language	English
Publishing date	2021-10-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms221910898
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Article ; Online: Torsional behavior of axonal microtubule bundles.

Lazarus, Carole / Soheilypour, Mohammad / Mofrad, Mohammad R K

Biophysical journal

2015 Volume 109, Issue 2, Page(s) 231–239

Abstract: Axonal microtubule (MT) bundles crosslinked by microtubule-associated protein (MAP) tau are responsible for vital biological functions such as maintaining mechanical integrity and shape of the axon as well as facilitating axonal transport. Breaking and ... ...

Abstract	Axonal microtubule (MT) bundles crosslinked by microtubule-associated protein (MAP) tau are responsible for vital biological functions such as maintaining mechanical integrity and shape of the axon as well as facilitating axonal transport. Breaking and twisting of MTs have been previously observed in damaged undulated axons. Such breaking and twisting of MTs is suggested to cause axonal swellings that lead to axonal degeneration, which is known as "diffuse axonal injury". In particular, overstretching and torsion of axons can potentially damage the axonal cytoskeleton. Following our previous studies on mechanical response of axonal MT bundles under uniaxial tension and compression, this work seeks to characterize the mechanical behavior of MT bundles under pure torsion as well as a combination of torsional and tensile loads using a coarse-grained computational model. In the case of pure torsion, a competition between MAP tau tensile and MT bending energies is observed. After three turns, a transition occurs in the mechanical behavior of the bundle that is characterized by its diameter shrinkage. Furthermore, crosslink spacing is shown to considerably influence the mechanical response, with larger MAP tau spacing resulting in a higher rate of turns. Therefore, MAP tau crosslinking of MT filaments protects the bundle from excessive deformation. Simultaneous application of torsion and tension on MT bundles is shown to accelerate bundle failure, compared to pure tension experiments. MAP tau proteins fail in clusters of 10-100 elements located at the discontinuities or the ends of MT filaments. This failure occurs in a stepwise fashion, implying gradual accumulation of elastic tensile energy in crosslinks followed by rupture. Failure of large groups of interconnecting MAP tau proteins leads to detachment of MT filaments from the bundle near discontinuities. This study highlights the importance of torsional loading in axonal damage after traumatic brain injury.
MeSH term(s)	Axons/metabolism ; Elasticity ; Microtubules/metabolism ; Models, Neurological ; Torsion, Mechanical ; tau Proteins/metabolism
Chemical Substances	tau Proteins
Language	English
Publishing date	2015-07-21
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2015.06.029
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Article ; Online: Characterizing Binding Interactions That Are Essential for Selective Transport through the Nuclear Pore Complex

Kathleen M. Lennon / Mohammad Soheilypour / Mohaddeseh Peyro / Devin L. Wakefield / Grace E. Choo / Mohammad R. K. Mofrad / Tijana Jovanovic-Talisman

International Journal of Molecular Sciences, Vol 22, Iss 10898, p

2021 Volume 10898

Abstract	Specific macromolecules are rapidly transported across the nuclear envelope via the nuclear pore complex (NPC). The selective transport process is facilitated when nuclear transport receptors (NTRs) weakly and transiently bind to intrinsically disordered constituents of the NPC, FG Nups. These two types of proteins help maintain the selective NPC barrier. To interrogate their binding interactions in vitro, we deployed an NPC barrier mimic. We created the stationary phase by covalently attaching fragments of a yeast FG Nup called Nsp1 to glass coverslips. We used a tunable mobile phase containing NTR, nuclear transport factor 2 (NTF2). In the stationary phase, three main factors affected binding: the number of FG repeats, the charge of fragments, and the fragment density. We also identified three main factors affecting binding in the mobile phase: the avidity of the NTF2 variant for Nsp1, the presence of nonspecific proteins, and the presence of additional NTRs. We used both experimentally determined binding parameters and molecular dynamics simulations of Nsp1FG fragments to create an agent-based model. The results suggest that NTF2 binding is negatively cooperative and dependent on the density of Nsp1FG molecules. Our results demonstrate the strengths of combining experimental and physical modeling approaches to study NPC-mediated transport.
Keywords	nuclear pore complex ; FG Nups ; nuclear transport receptors ; NPC barrier mimic ; agent-based modeling ; molecular dynamics ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The LINC and NPC relationship - it's complicated!

Jahed, Zeinab / Soheilypour, Mohammad / Peyro, Mohaddeseh / Mofrad, Mohammad R K

Journal of cell science

2016 Volume 129, Issue 17, Page(s) 3219–3229

Abstract: The genetic information of eukaryotic cells is enclosed within a double-layered nuclear envelope, which comprises an inner and outer nuclear membrane. Several transmembrane proteins locate to the nuclear envelope; however, only two integral protein ... ...

Abstract	The genetic information of eukaryotic cells is enclosed within a double-layered nuclear envelope, which comprises an inner and outer nuclear membrane. Several transmembrane proteins locate to the nuclear envelope; however, only two integral protein complexes span the nuclear envelope and connect the inside of the nucleus to the cytoplasm. The nuclear pore complex (NPC) acts as a gateway for molecular exchange between the interior of the nucleus and the cytoplasm, whereas so-called LINC complexes physically link the nucleoskeleton and the cytoskeleton. In this Commentary, we will discuss recent studies that have established direct functional associations between these two complexes. The assembly of NPCs and their even distribution throughout the nuclear envelope is dependent on components of the LINC complex. Additionally, LINC complex formation is dependent on the successful localization of inner nuclear membrane components of LINC complexes and their transport through the NPC. Furthermore, the architecture of the nuclear envelope depends on both protein complexes. Finally, we will present recent evidence showing that LINC complexes can affect nucleo-cytoplasmic transport through the NPC, further highlighting the importance of understanding the associations of these essential complexes at the nuclear envelope.
MeSH term(s)	Animals ; Cytoskeleton/metabolism ; Humans ; Mitosis ; Models, Biological ; Nuclear Envelope/metabolism ; Nuclear Pore/metabolism ; Protein Transport
Language	English
Publishing date	2016-09-01
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2993-2
ISSN	1477-9137 ; 0021-9533
ISSN (online)	1477-9137
ISSN	0021-9533
DOI	10.1242/jcs.184184
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Article ; Online: Looking "Under the Hood" of Cellular Mechanotransduction with Computational Tools: A Systems Biomechanics Approach across Multiple Scales.

Shams, Hengameh / Soheilypour, Mohammad / Peyro, Mohaddeseh / Moussavi-Baygi, Ruhollah / Mofrad, Mohammad R K

ACS biomaterials science & engineering

2017 Volume 3, Issue 11, Page(s) 2712–2726

Abstract: Signal modulation has been developed in living cells throughout evolution to promote utilizing the same machinery for multiple cellular functions. Chemical and mechanical modules of signal transmission and transduction are interconnected and necessary ... ...

Abstract	Signal modulation has been developed in living cells throughout evolution to promote utilizing the same machinery for multiple cellular functions. Chemical and mechanical modules of signal transmission and transduction are interconnected and necessary for organ development and growth. However, due to the high complexity of the intercommunication of physical intracellular connections with biochemical pathways, there are many missing details in our overall understanding of mechanotransduction processes, i.e., the process by which mechanical signals are converted to biochemical cascades. Cell-matrix adhesions are mechanically coupled to the nucleus through the cytoskeleton. This modulated and tightly integrated network mediates the transmission of mechanochemical signals from the extracellular matrix to the nucleus. Various experimental and computational techniques have been utilized to understand the basic mechanisms of mechanotransduction, yet many aspects have remained elusive. Recently,
Language	English
Publishing date	2017-06-29
Publishing country	United States
Document type	Journal Article
ISSN	2373-9878
ISSN (online)	2373-9878
DOI	10.1021/acsbiomaterials.7b00117
Database	MEDical Literature Analysis and Retrieval System OnLINE

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