Abstract：
:A new method for normal mode analysis is reported for all-atom structures using molecular geometry restraints (MGR). Similar to common molecular mechanics force fields, the MGR potential contains short- and long-range terms. The short-range terms are defined by molecular geometry, i.e., bond lengths, angles and dihedrals; the long-range term is similar to that in elastic network models. Each interaction term uses a single force constant parameter, and is determined by fitting against a set of known structures. Tests on proteins/non-proteins show that MGR can produce low frequency eigenvectors closer to all-atom force-field-based methods than conventional elastic network models. Moreover, the "tip effect", found in low frequency eigenvectors in elastic network models, is reduced in MGR to the same level of the modes produced by force-field-based methods. The results suggest that molecular geometry plays an important role, in addition to molecular shape, in determining low frequency deformational motions. MGR does not require initial energy minimization, and is applicable to almost any structure, including the one with missing atoms, bad contacts, or bad geometries, frequently observed in low-resolution structure determination and refinement. The method bridges the two major representations in normal mode analyses, i.e., the molecular mechanics models and elastic network models.
journal_name
Arch Biochem Biophysjournal_title
Archives of biochemistry and biophysicsauthors
Lu M,Ma Jdoi
10.1016/j.abb.2010.12.031subject
Has Abstractpub_date
2011-04-01 00:00:00pages
64-71issue
1eissn
0003-9861issn
1096-0384pii
S0003-9861(10)00528-Xjournal_volume
508pub_type
杂志文章abstract：:Cell extracts of Methanobacterium thermoautotrophicum possess a methenyl-tetrahydromethanopterin (methenyl-H4MPT) cyclohydrolase. The enzyme catalyzes the hydrolysis of methenyl-H4MPT to formyltetrahydromethanopterin (formyl-H4MPT). The reaction is reversible and both the rate and extent of the reaction depend on the ...
journal_title：Archives of biochemistry and biophysics
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更新日期：1985-11-01 00:00:00
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pub_type： 杂志文章,评审
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pub_type： 杂志文章,评审
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pub_type： 杂志文章
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更新日期：1992-11-01 00:00:00
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pub_type： 杂志文章
doi：10.1006/abbi.1996.9727
更新日期：1997-01-01 00:00:00
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pub_type： 杂志文章
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更新日期：1990-02-15 00:00:00
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journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/0003-9861(92)90738-i
更新日期：1992-05-01 00:00:00
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journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
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更新日期：1984-05-01 00:00:00
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journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/j.abb.2004.06.027
更新日期：2004-09-15 00:00:00
abstract：:The majority of hypertrophic cardiomyopathy mutations in (cTnT) occur within the alpha-helical tropomyosin binding TNT1 domain. A highly charged region at the C-terminal end of TNT1 unwinds to create a flexible "hinge". While this region has not been structurally resolved, it likely acts as an extended linker between ...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/j.abb.2014.01.016
更新日期：2014-06-15 00:00:00
abstract：:Activation of the NLRP3 inflammasome plays an important role in high glucose- induced endothelial dysfunction in patients with type 2 diabetes mellitus (T2DM). Dulaglutide, a newly developed glucagon-like peptide-1 receptor (GLP-1R) agonist, has been approved for the management of T2DM. In the current study, we aimed ...
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pub_type： 杂志文章
doi：10.1016/j.abb.2019.07.008
更新日期：2019-08-15 00:00:00
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pub_type： 杂志文章
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更新日期：2015-06-01 00:00:00
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pub_type： 杂志文章
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更新日期：2013-07-01 00:00:00
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pub_type： 杂志文章
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更新日期：1987-02-15 00:00:00
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pub_type： 杂志文章,评审
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更新日期：2019-01-01 00:00:00
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pub_type： 杂志文章
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更新日期：1987-04-01 00:00:00
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journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
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更新日期：1985-12-01 00:00:00
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pub_type： 杂志文章
doi：10.1006/abbi.1998.0751
更新日期：1998-08-15 00:00:00
abstract：:Pasteurella multocida is a pathogen of veterinary and medical importance. Here, we report the 1.85Å resolution crystal structure of the class C acid phosphatase from this organism (denoted rPmCCAP). The structure shows that rPmCCAP exhibits the same haloacid dehalogenase fold and dimeric assembly as the class C enzyme...
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pub_type： 杂志文章
doi：10.1016/j.abb.2011.02.021
更新日期：2011-05-01 00:00:00
abstract：AIMS:to investigate α2-AR subtype distribution and the relationship between receptor amounts and their functionality in normotensive and spontaneously hypertensive rats. METHODS:experiments were performed on left ventricular cardiomyocytes isolated from Wistar rats and SHR (2-2.5 months). Molecular routine tools (RT-P...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/j.abb.2019.108109
更新日期：2019-10-15 00:00:00
abstract：:The epithelial cells of the gastrointestinal tract have the capacity to engage in biotransformation of ingested chemicals. A principal component of phase I metabolism of xenobiotics is the family of hemeproteins referred to as cytochrome(s) P450. The presence of cytochrome P450 isoforms was examined by Western blot an...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/0003-9861(91)90288-t
更新日期：1991-01-01 00:00:00
abstract：:PFam Clan 0032, also known as the CDE superfamily, is a diverse group of at least 20 protein families sharing a common α,β-barrel domain. Of these, six different groups bind heme inside the barrel's interior, using it alternately as a cofactor, substrate, or product. Focusing on these six, an integrated picture of str...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章,评审
doi：10.1016/j.abb.2015.03.004
更新日期：2015-05-15 00:00:00
abstract：:The level of phosphorylation and activation of phosphofructokinase by serotonin (5-hydroxytryptamine) was studied in intact liver flukes Fasciola hepatica. The enzyme was immunoprecipitated with antiserum prepared against pure enzyme from the liver flukes. The resuspended immunoprecipitated enzyme retained most of its...
journal_title：Archives of biochemistry and biophysics
pub_type： 杂志文章
doi：10.1016/0003-9861(89)90307-x
更新日期：1989-06-01 00:00:00
