Abstract:
:Molecular dynamics simulations of membrane proteins are making rapid progress, because of new high-resolution structures, advances in computer hardware and atomistic simulation algorithms, and the recent introduction of coarse-grained models for membranes and proteins. In addition to several large ion channel simulations, recent studies have explored how individual amino acids interact with the bilayer or snorkel/anchor to the headgroup region, and it has been possible to calculate water/membrane partition free energies. This has resulted in a view of bilayers as being adaptive rather than purely hydrophobic solvents, with important implications, for example, for interaction between lipids and arginines in the charged S4 helix of voltage-gated ion channels. However, several studies indicate that the typical current simulations fall short of exhaustive sampling, and that even simple protein-membrane interactions require at least ca. 1 micros to fully sample their dynamics. One new way this is being addressed is coarse-grained models that enable mesoscopic simulations on multi-micros scale. These have been used to model interactions, self-assembly and membrane perturbations induced by proteins. While they cannot replace all-atom simulations, they are a potentially useful technique for initial insertion, placement, and low-resolution refinement.
journal_name
Curr Opin Struct Bioljournal_title
Current opinion in structural biologyauthors
Lindahl E,Sansom MSdoi
10.1016/j.sbi.2008.02.003subject
Has Abstractpub_date
2008-08-01 00:00:00pages
425-31issue
4eissn
0959-440Xissn
1879-033Xpii
S0959-440X(08)00030-4journal_volume
18pub_type
杂志文章,评审abstract::Toll-like receptors (TLRs) activate the innate immune system in response to invading pathogens. Although nucleic acids are one of the principal TLR ligands, they are not inherently pathogen-specific and, thus, carry the risk of triggering autoimmunity. There are multiple unique regulatory mechanisms aimed at preventin...
journal_title:Current opinion in structural biology
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abstract::The past year has witnessed a tremendous increase in our understanding of the structures and interactions of the GTPases. The highlights include crystal structures of G alpha subunits, as well as the first complex between a GTPase (Rap1A) and an effector molecule (c-Raf1 Ras-binding domain). In the field of elongation...
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journal_title:Current opinion in structural biology
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journal_title:Current opinion in structural biology
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doi:10.1016/j.sbi.2020.10.005
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
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更新日期:1996-06-01 00:00:00
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2007.07.006
更新日期:2007-10-01 00:00:00
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journal_title:Current opinion in structural biology
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2017.01.006
更新日期:2017-02-01 00:00:00
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
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更新日期:2017-06-01 00:00:00
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journal_title:Current opinion in structural biology
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更新日期:2001-04-01 00:00:00
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2009.06.003
更新日期:2009-10-01 00:00:00
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2006.01.009
更新日期:2006-02-01 00:00:00
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2019.02.004
更新日期:2019-12-01 00:00:00
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2020.12.007
更新日期:2021-01-13 00:00:00
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2019.03.030
更新日期:2019-08-01 00:00:00
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journal_title:Current opinion in structural biology
pub_type: 杂志文章
doi:10.1016/s0959-440x(03)00101-5
更新日期:2003-08-01 00:00:00
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2006.10.003
更新日期:2006-12-01 00:00:00
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2009.05.003
更新日期:2009-06-01 00:00:00
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2013.03.006
更新日期:2013-06-01 00:00:00
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journal_title:Current opinion in structural biology
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journal_title:Current opinion in structural biology
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doi:10.1016/j.sbi.2019.05.009
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journal_title:Current opinion in structural biology
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
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更新日期:2020-04-01 00:00:00
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journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
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abstract::Conformational changes are an essential feature of most molecular processes in biology. Optical tweezers have emerged as a powerful tool for probing conformational dynamics at the single-molecule level because of their high resolution and sensitivity, opening new windows on phenomena ranging from folding and ligand bi...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2015.06.006
更新日期:2015-10-01 00:00:00
abstract::The three-dimensional structures of membrane proteins are essential for understanding their functions, interactions and architectures. Their requirement for lipids has hampered structure determination by conventional approaches. With optimized samples, it is possible to apply solution NMR methods to small membrane pro...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
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更新日期:1998-10-01 00:00:00
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journal_title:Current opinion in structural biology
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doi:10.1016/j.sbi.2019.03.031
更新日期:2019-06-01 00:00:00
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journal_title:Current opinion in structural biology
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更新日期:2020-11-21 00:00:00
abstract::Over the past two decades, mass spectrometry (MS) has emerged as a bone fide approach for structural biology. MS can inform on all levels of protein organization, and enables quantitative assessments of their intrinsic dynamics. The key advantages of MS are that it is a sensitive, high-resolution separation technique ...
journal_title:Current opinion in structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.sbi.2011.08.002
更新日期:2011-10-01 00:00:00