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return kwic search for molecular out of >500 occurrences
333489 occurrences (No.56 in the rank) during 5 years in the PubMed. [no cache] 500 found

230) At this time, we report the interaction of SAP-1 with diverse proteases and its binding partners by CD-spectroscopic and molecular docking methods.

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PMID:24261636 DOI:10.1080/07391102.2013.855882

2015 Journal of biomolecular structure & dynamics

* Studies on the interactions of SAP-1 (an N-terminal truncated form of cystatin S) with its binding partners by CD-spectroscopic and molecular docking methods.

- SAP-1 is a 113 amino acid long single-chain protein which belongs to the type 2 cystatin gene family. In our previous study, we have purified SAP-1 from human seminal plasma and observed its cross-class inhibitory property. At this time, we report the interaction of SAP-1 with diverse proteases and its binding partners by CD-spectroscopic and molecular docking methods. The circular dichroism (CD) spectroscopic studies demonstrate that the conformation of SAP-1 is changed after its complexation with proteases, and the alterations in protein secondary structure are quantitatively calculated with increase of α-helices and reduction of β-strand content. To get insight into the interactions between SAP-1 and proteases, we make an effort to model the three-dimensional structure of SAP-1 by molecular modeling and verify its stability and viability through molecular dynamics simulations and finally complexed with different proteases using ClusPro 2.0 Server. A high degree of shape complementarity is examined within the complexes, stabilized by a number of hydrogen bonds (HBs) and hydrophobic interactions. Using HB analyses in different protein complexes, we have identified a series of key residues that may be involved in the interactions between SAP-1 and proteases. These findings will assist to understand the mechanism of inhibition of SAP-1 for different proteases and provide intimation for further research.

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(1)52 mechanisms	(19)5 docking	(37)3 recognition	(55)2 heparin
(2)26 weight	(20)5 information	(38)3 serotyping	(56)2 identification
(3)18 data	(21)5 methods	(39)3 sieve	(57)2 knowledge
(4)18 mechanism	(22)5 modeling	(40)3 structure	(58)2 mass
(5)16 dynamics	(23)5 phylogenetic	(41)3 techniques	(59)2 mechanisms,
(6)15 and	(24)5 targets	(42)3 variance	(60)2 or
(7)10 analysis	(25)4 diagnosis	(43)2 Dynamics	(61)2 oxygen
(8)10 basis	(26)4 interactions	(44)2 approach	(62)2 perspectives
(9)8 characterization	(27)4 level	(45)2 biological	(63)2 phenotypic
(10)7 epidemiology	(28)4 level,	(46)2 classification	(64)2 phylogenies
(11)7 genetic	(29)4 responses	(47)2 clock	(65)2 probes
(12)7 imaging	(30)4 target	(48)2 dating	(66)2 profiles
(13)6 biology	(31)3 evolution	(49)2 details	(67)2 subtype
(14)6 changes	(32)3 features	(50)2 diffusion	(68)2 therapies
(15)6 markers	(33)3 levels	(51)2 effects	(69)2 underpinnings
(16)6 pathways	(34)3 marker	(52)2 events
(17)5 analyses	(35)3 medicine	(53)2 evidence
(18)5 characteristics	(36)3 orbital	(54)2 genetics

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--- WordNet output for molecular --- =>分子の Overview of adj molecular The adj molecular has 2 senses (first 1 from tagged texts) 1. (6) molecular -- (relating to or produced by or consisting of molecules; "molecular structure"; "molecular oxygen"; "molecular weight is the sum of all the atoms in a molecule") 2. molecular -- (relating to simple or elementary organization; "proceed by more and more detailed analysis to the molecular facts of perception"--G.A. Miller) --- WordNet end ---