WordNet

serve in a specific professional capacity; "the priest sat for confession"; "she sat on the jury"
be around, often idly or without specific purpose; "The object sat in the corner"; "We sat around chatting for another hour" (同)sit around
be seated (同)sit_down
be in session; "When does the court of law sit?"
be located or situated somewhere; "The White House sits on Pennsylvania Avenue"
executed with proper legal authority; "a binding contract"
the protective covering on the front, back, and spine of a book; "the book had a leather binding" (同)book binding, cover, back
strip sewn over or along an edge for reinforcement or decoration
the capacity to attract and hold something
the substance that is acted upon by an enzyme or ferment
a surface on which an organism grows or is attached; "the gardener talked about the proper substrate for acid-loving plants" (同)substratum
an indigenous language that contributes features to the language of an invading people who impose their language on the indigenous population; "the Celtic languages of Britain are a substrate for English" (同)substratum
any stratum or layer lying underneath another (同)substratum
the piece of land on which something is located (or is to be located); "a good site for the school" (同)land site
physical position in relation to the surroundings; "the sites are determined by highly specific sequences of nucleotides" (同)situation

PrepTutorEJDIC

(…に)『座る』,座っている《+『at』(『on, in』)+『名』》・着席する《+『down』》・(…に)〈鳥などが〉『止まる』,休む《+『on』+『名』》・〈めんどりが〉卵を抱く,巣に就く / 《場所の副詞[句]を伴って》(ある場所に)『位置する』・ (画家・写真家のために)ポーズをとる・しっとしている,動かないでいる・(議員・委員などの)職に就いている《+『on』+『名』》・〈議会・法廷などが〉開会(開廷)される・(…に)負担となる,重荷となる《+『on』(『upon』)+『名』》・〈衣服などが〉(…に)合う,似合う《+『on』+『名』》・〈人〉‘を'座らせる,着席させる《+『down』+『名,』+『名』+『down』》・〈馬〉‘に'乗る・《英》〈試験〉‘を'受ける
義務的な,拘束力ある / 〈U〉しばること;〈C〉しばる物 / 〈C〉製本,装丁 / 〈U〉縁(‘ふち')取り材料
(町・建物などの)『場所』;敷地,用地 / 遺跡;(事件などの)現場 / 〈建物など〉‘を'位置させる(locate)
=ti

UpToDate Contents

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1. 赤血球産生調節 regulation of erythropoiesis
2. 白血球粘着不全症 leukocyte adhesion deficiency
3. 心筋梗塞既往患者における持続性単形性心室頻拍：治療および予後 sustained monomorphic ventricular tachycardia in patients with a prior myocardial infarction treatment and prognosis
4. 副腎ステロイド生合成 adrenal steroid biosynthesis
5. Vitamin K and the synthesis and function of gamma-carboxyglutamic acid

English Journal

Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms.

Yang LQ, Sang P, Tao Y, Fu YX, Zhang KQ, Xie YH, Liu SQ.Author information a Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education , Yunnan University , Kunming , 650091 , P.R. China .AbstractProteins are dynamic entities in cellular solution with functions governed essentially by their dynamic personalities. We review several dynamics studies on serine protease proteinase K and HIV-1 gp120 envelope glycoprotein to demonstrate the importance of investigating the dynamic behaviors and molecular motions for a complete understanding of their structure-function relationships. Using computer simulations and essential dynamic (ED) analysis approaches, the dynamics data obtained revealed that: (i) proteinase K has highly flexible substrate-binding site, thus supporting the induced-fit or conformational selection mechanism of substrate binding; (ii) Ca(2+) removal from proteinase K increases the global conformational flexibility, decreases the local flexibility of substrate-binding region, and does not influence the thermal motion of catalytic triad, thus explaining the experimentally determined decreased thermal stability, reduced substrate affinity, and almost unchanged catalytic activity upon Ca(2+) removal; (iii) substrate binding affects the large concerted motions of proteinase K, and the resulting dynamic pocket can be connected to substrate binding, orientation, and product release; (iv) amino acid mutations 375 S/W and 423 I/P of HIV-1 gp120 have distinct effects on molecular motions of gp120, facilitating 375 S/W mutant to assume the CD4-bound conformation, while 423 I/P mutant to prefer for CD4-unliganded state. The mechanisms underlying protein dynamics and protein-ligand binding, including the concept of the free energy landscape (FEL) of the protein-solvent system, how the ruggedness and variability of FEL determine protein's dynamics, and how the three ligand-binding models, the lock-and-key, induced-fit, and conformational selection are rationalized based on the FEL theory are discussed in depth.
Journal of biomolecular structure & dynamics.J Biomol Struct Dyn.2014 Mar;32(3):372-93. doi: 10.1080/07391102.2013.770372. Epub 2013 Mar 25.
Proteins are dynamic entities in cellular solution with functions governed essentially by their dynamic personalities. We review several dynamics studies on serine protease proteinase K and HIV-1 gp120 envelope glycoprotein to demonstrate the importance of investigating the dynamic behaviors and mol
PMID 23527883

Molecular dynamics studies on both bound and unbound renin protease.

Brás NF, Fernandes PA, Ramos MJ.Author information a REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade do Porto , Rua do Campo Alegre s/n, 4169-007 , Porto , Portugal .AbstractThe aspartic protease renin (REN) catalyses the rate-limiting step in the Renin-Angiotensin-Aldosterone System (RAAS), which regulates cardiovascular and renal homoeostasis in living organisms. Renin blockage is therefore an attractive therapeutic strategy for the treatment of hypertension. Herein, computational approaches were used to provide a structural characterization of the binding site, flap opening and dynamic rearrangements of REN in the key conserved residues and water molecules, with the binding of a dodecapeptide substrate or different inhibitors. All these structural insights during catalysis may assist future studies in developing novel strategies for REN inactivation. Our molecular dynamics simulations of several unbound-REN and bound-REN systems indicate similar flexible-segments plasticity with larger fluctuations in those belonging to the C-domain (exposed to the solvent). These segments are thought to assist the flap opening and closure to allow the binding of the substrate and catalytic water molecules. The unbound-REN simulation suggests that the flap can acquire three different conformations: closed, semi-open and open. Our results indicate that the semi-open conformation is already sufficient and appropriate for the binding of the angiotensinogen (Ang) tail, thus contributing to the high specificity of REN, and that both semi-open and open flap conformations are present in free and complexed enzymes. We additionally observed that the Tyr75-Trp39 H-bond has an important role in assisting flap movement, and we highlight several conserved water molecules and amino acids that are essential for the proper catalytic activity of REN.
Journal of biomolecular structure & dynamics.J Biomol Struct Dyn.2014 Mar;32(3):351-63. doi: 10.1080/07391102.2013.768553. Epub 2013 Mar 25.
The aspartic protease renin (REN) catalyses the rate-limiting step in the Renin-Angiotensin-Aldosterone System (RAAS), which regulates cardiovascular and renal homoeostasis in living organisms. Renin blockage is therefore an attractive therapeutic strategy for the treatment of hypertension. Herein,
PMID 23527826

Pore-exposed tyrosine residues of p-glycoprotein are important hydrogen-bonding partners for drugs.

Dönmez Cakil Y, Khunweeraphong N, Parveen Z, Schmid D, Artaker M, Ecker GF, Sitte HH, Pusch O, Stockner T, Chiba P.Author information Institutes of Medical Chemistry (Y.D.C., N.K., Z.P., P.C.), Pharmacology (Y.D.C., H.H.S., T.S.), and Physiology (D.S.), Department of Medical Biochemistry, Max F. Perutz Laboratories (M.A.), and Department of Cell and Developmental Biology (O.P.), Medical University of Vienna, Vienna, Austria; Department of Biochemistry, Abdul Wali Khan University Mardan, Pakistan (Z.P.); and Emerging Field Pharmacoinformatics, Department of Medicinal Chemistry, University of Vienna, Vienna, Austria (G.F.E.).AbstractThe multispecific efflux transporter, P-glycoprotein, plays an important role in drug disposition. Substrate translocation occurs along the interface of its transmembrane domains. The rotational C2 symmetry of ATP-binding cassette transporters implies the existence of two symmetry-related sets of substrate-interacting amino acids. These sets are identical in homodimeric transporters, and remain evolutionary related in full transporters, such as P-glycoprotein, in which substrates bind preferentially, but nonexclusively, to one of two binding sites. We explored the role of pore-exposed tyrosines for hydrogen-bonding interactions with propafenone type ligands in their preferred binding site 2. Tyrosine 953 is shown to form hydrogen bonds not only with propafenone analogs, but also with the preferred site 1 substrate rhodamine123. Furthermore, an accessory role of tyrosine 950 for binding of selected propafenone analogs is demonstrated. The present study demonstrates the importance of domain interface tyrosine residues for interaction of small molecules with P-glycoprotein.
Molecular pharmacology.Mol Pharmacol.2014 Mar;85(3):420-8. doi: 10.1124/mol.113.088526. Epub 2013 Dec 23.
The multispecific efflux transporter, P-glycoprotein, plays an important role in drug disposition. Substrate translocation occurs along the interface of its transmembrane domains. The rotational C2 symmetry of ATP-binding cassette transporters implies the existence of two symmetry-related sets of su
PMID 24366667

Japanese Journal

Structure of β-1,4-mannanase from the common sea hare Aplysia kurodai at 1.05 Å resolution.

Mizutani Kimihiko,Tsuchiya Sae,Toyoda Mayuko,Nanbu Yuko,Tominaga Keiko,Yuasa Keizo,Takahashi Nobuyuki,Tsuji Akihiko,Mikami Bunzo
Acta crystallographica. Section F, Structural biology and crystallization communications 68(Part 10), 1164-1168, 2012-10-00
… No obvious binding residue was found in subsite +1 and the substrate-binding site was exposed to the molecular surface, which may account for the enzymatic properties of mannanases that can digest complex substrates such as glucomannan and branched mannan. …
NAID 120004920435

Amino Acid Sequence of Egyptian Goose Egg-White Lysozyme and Effects of Amino Acid Substitution on the Enzymatic Activity

KAWAMURA Shunsuke,TOSHIMA Gen,CHIJIIWA Yuki [他],TORIKATA Takao,ARAKI Tomohiro
Bioscience, biotechnology, and biochemistry 76(4), 691-698, 2012-04-23
… Tyr34 and Gly37 were found at subsites E and F of the active site when compared with HEL. … The experimental time-course characteristics of EGL against the N-acetylglucosamine pentamer substrate, (GlcNAc)5, revealed higher production of (GlcNAc)4 … The saccharide-binding ability of subsites A–C in EGL was also found to be weaker than in HEL. …
NAID 10030751484