当前位置： SCI文献检索 > JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS期刊下所有文献 > Heterodimerization of the Entamoeba histolytica EhCPADH virulence complex through molecular dynamics and protein-protein docking.

Heterodimerization of the Entamoeba histolytica EhCPADH virulence complex through molecular dynamics and protein-protein docking.

Abstract：

:EhCPADH is a protein complex involved in the virulence of Entamoeba histolytica, the protozoan responsible for human amebiasis. It is formed by the EhCP112 cysteine protease and the EhADH adhesin. To explore the molecular basis of the complex formation, three-dimensional models were built for both proteins and molecular dynamics simulations (MDS) and docking calculations were performed. Results predicted that the pEhCP112 proenzyme and the mEhCP112 mature enzyme were globular and peripheral membrane proteins. Interestingly, in pEhCP112, the propeptide appeared hiding the catalytic site (C167, H329, N348); while in mEhCP112, this site was exposed and its residues were found structurally closer than in pEhCP112. EhADH emerged as an extended peripheral membrane protein with high fluctuation in Bro1 and V shape domains. 500 ns-long MDS and protein-protein docking predictions evidenced different heterodimeric complexes with the lowest free energy. pEhCP112 interacted with EhADH by the propeptide and C-terminal regions and mEhCP112 by the C-terminal through hydrogen bonds. In contrast, EhADH bound to mEhCP112 by 442-479 residues, adjacent to the target cell-adherence region (480-600 residues), and by the Bro1 domain (9-349 residues). Calculations of the effective binding free energy and per residue free energy decomposition showed that EhADH binds to mEhCP112 with a higher binding energy than to pEhCP112, mainly through van der Waals interactions and the nonpolar part of solvation energy. The EhADH and EhCP112 structural relationship was validated in trophozoites by immunofluorescence, TEM, and immunoprecipitation assays. Experimental findings fair agreed with in silico results.

journal_name

J Biomol Struct Dyn

journal_title

Journal of biomolecular structure & dynamics

authors

Montaño S,Orozco E,Correa-Basurto J,Bello M,Chávez-Munguía B,Betanzos A

doi

10.1080/07391102.2016.1151831

subject

Has Abstract

pub_date

2017-02-01 00:00:00

pages

486-503

issue

3

eissn

0739-1102

issn

1538-0254

journal_volume

35

pub_type

杂志文章

相关文献

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS文献大全
  • Novel P,C-orthopalladated complexes containing histidine and phenylalanine amino acids: synthesis, DNA and BSA interactions, in vitro antitumoral activity and molecular docking approach.

    abstract：:Novel [Pd(o-CH2C6H4P(o-tolyl)2)(histidine)] (1) and [Pd(o-CH2C6H4P(o tolyl)2)(phenylalanine)] (2) P,C-orthopalladated complexes have been prepared and characterized by elemental analysis, IR and NMR spectroscopy. To study the stability of the compounds in biological media, the complexes were incubated in Tris buffer d...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1865202

    authors： Hashemi S,Karami K,Saberi Dehkordi Z,Momtazi-Borojeni AA,Esmaeili SA

    更新日期：2020-12-24 00:00:00

  • Cyanobacterial metabolites as promising drug leads against the Mpro and PLpro of SARS-CoV-2: an in silico analysis.

    abstract：:A novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) has emerged as the causative agent behind the coronavirus disease 2019 (COVID-19) pandemic. Treatment efforts have been severely impeded due to the lack of specific effective antiviral drugs for the treatment of COVID-associated pathologies. In the pre...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1794972

    authors： Naidoo D,Roy A,Kar P,Mutanda T,Anandraj A

    更新日期：2020-07-21 00:00:00

  • Computational studies of membrane pore formation induced by Pin2.

    abstract：:Understanding, at the molecular level, the effect of AMPs on biological membranes is of crucial importance given the increasing number of multidrug-resistant bacteria. Being part of an ancient type of innate immunity system, AMPs have emerged as a potential solution for which bacteria have not developed resistance. Tr...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1867640

    authors： Velasco-Bolom JL,Garduño-Juárez R

    更新日期：2021-01-05 00:00:00

  • Binding of Folate-G4-PAMAM dendrimer conjugate with indomethacin via ligand diffusion MD simulations.

    abstract：:Preceding experimental findings revealed that the release of indomethacin decreased when a folate conjugate G4-PAMAM (folate-G4-PAMAM) dendrimer was used compared with its unconjugated dendrimer (G4-PAMAM). Further, better encapsulation of the conjugated dendrimer was achieved, information useful for elucidating the s...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1861984

    authors： Martínez-Muñoz A,Correa-Basurto J,Bello M

    更新日期：2020-12-21 00:00:00

  • Exploring the structural interaction of BSA with amine functionalized ruthenium(II) metal complex.

    abstract：:Communicated by Ramaswamy H. Sarma. ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 信件

    doi：10.1080/07391102.2019.1683071

    authors： Anish Babu A,Karthick K,Subramanian R,Swarnalatha K

    更新日期：2020-08-01 00:00:00

  • What is paradoxical about Levinthal paradox?

    abstract：:We would be tempted to state that there has never been a Levinthal paradox. Indeed, Levinthal raised an interesting problem about protein folding, as he realized that proteins have no time to explore exhaustively their conformational space on the way to their native structure. He did not seem to find this paradoxical ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2002.10506850

    authors： Rooman M,Dehouck Y,Kwasigroch JM,Biot C,Gilis D

    更新日期：2002-12-01 00:00:00

  • All-atom molecular dynamics comparison of disease-associated zinc fingers.

    abstract：:An important regulatory domain of NF-[Formula: see text]B Essential Modulator (NEMO) is a ubiquitin-binding zinc finger, with a tetrahedral CYS3HIS1 zinc-coordinating binding site. Two variations of NEMO's zinc finger are implicated in various disease states including ectodermal dysplasia and adult-onset glaucoma. To ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2017.1363662

    authors： Godwin RC,Gmeiner WH,Salsbury FR Jr

    更新日期：2018-08-01 00:00:00

  • NMR conformational studies of micelle-bound orexin-B: a neuropeptide involved in the sleep/awake cycle and feeding regulation.

    abstract：:The preferred conformation of orexin-B, an orphan G-protein coupled receptor agonist (the human sequence is RSGPPGLQGRLQRLLQASGNHAAGILTM-NH(2)) has been determined by (1)H and (13)C 2D NMR spectroscopy and molecular modeling. Orexin-B has been implicated in sleep-wakefulness and feeding regulation. The membrane mimeti...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2003.10506930

    authors： Miskolzie M,Lucyk S,Kotovych G

    更新日期：2003-12-01 00:00:00

  • An NMR study of the polymorphous behavior of the mismatched DNA octamer d(m5C-G-m5C-G-T-G-m5C-G) in solution. The B, Z, and hairpin forms.

    abstract：:The polymorphism exhibited by the mismatched octamer d(m5C-G-m5C-G-T-G-m5C-G), as a function of the temperature, DNA concentration and ionic strength, was investigated by means of NMR spectroscopy. It is shown that this partly self-complementary DNA fragment, under conditions of low DNA concentration (0.4 mM) and low ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1987.10507691

    authors： Orbons LP,van der Marel GA,van Boom JH,Altona C

    更新日期：1987-06-01 00:00:00

  • Loading efficacy and binding analysis of retinoids with milk proteins: a short review.

    abstract：:In this review, the loading efficacies of retinoids with milk proteins are investigated. It has been shown that milk proteins β-lactoglobulin, α-, and β-caseins bind retinol and retinoic acid via hydrophobic, hydrophilic, and H-bonding contacts causing minor alterations of protein secondary structure. Hydrophobic cont...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章,评审

    doi：10.1080/07391102.2017.1411833

    authors： Agudelo D,Bourassa P,Bariyanga J,Tajmir-Riahi HA

    更新日期：2018-12-01 00:00:00

  • An in-silico analysis of ivermectin interaction with potential SARS-CoV-2 targets and host nuclear importin α.

    abstract：:Ivermectin (IVM) is a broad-spectrum antiparasitic agent, having inhibitory potential against wide range of viral infections. It has also been found to hamper SARS-CoV-2 replication in vitro, and its precise mechanism of action against SARS-CoV-2 is yet to be understood. IVM is known to interact with host importin (IM...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1841028

    authors： Azam F,Taban IM,Eid EEM,Iqbal M,Alam O,Khan S,Mahmood D,Anwar MJ,Khalilullah H,Khan MU

    更新日期：2020-11-02 00:00:00

  • Heterogeneous behavior of metalloproteins toward metal ion binding and selectivity: insights from molecular dynamics studies.

    abstract：:About one-third of the existing proteins require metal ions as cofactors for their catalytic activities and structural complexities. While many of them bind only to a specific metal, others bind to multiple (different) metal ions. However, the exact mechanism of their metal preference has not been deduced to clarity. ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2015.1080629

    authors： Gogoi P,Chandravanshi M,Mandal SK,Srivastava A,Kanaujia SP

    更新日期：2016-07-01 00:00:00

  • Structural studies on New Delhi Metallo-β-lactamase (NDM-2) suggest old β-lactam, penicillin to be better antibiotic for NDM-2-harbouring Acinetobacter baumanni.

    abstract：:Acinetobacter baumannii, a Gram-negative pathogen causes nosocomial infections including pneumonia, urinary tract and respiratory infections. Carbapenem group of β-lactam antibiotics are routinely used to treat A. baumannii including multidrug-resistant clinical strains. The emergence of New Delhi Metallo-β-lactamase ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2012.706075

    authors： Tiwari V,Moganty RR

    更新日期：2013-01-01 00:00:00

  • Computational studies of essential dynamics of Pseudomonas cepacia lipase.

    abstract：:In order to investigate the interfacial activation of a lipase from Pseudomonas cepacia (PcL), molecular dynamics (MD) simulations and essential dynamics (ED) analysis were performed in different solvent environments: vacuum and explicit water solvents. Starting from the active (open) structure of PcL, the essential d...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2000.10506667

    authors： Lee J,Suh SW,Shin S

    更新日期：2000-10-01 00:00:00

  • Genetic and biochemical manipulations of the small ribosomal subunit from Thermus thermophilus HB8.

    abstract：:Crystals of the small ribosomal subunit from Thermus thermophilus diffract to 3A and exhibit reasonable isomorphism and moderate resistance to irradiation. A 5A MIR map of this particle shows a similar shape to the part assigned to this particle within the cryo-EM reconstructions of the whole ribosome and contains reg...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2000.10506553

    authors： Auerbach T,Pioletti M,Avila H,Anagnostopoulos K,Weinstein S,Franceschi F,Yonath A

    更新日期：2000-02-01 00:00:00

  • A genetic algorithm with conformational memories for structure prediction of polypeptides.

    abstract：:We have developed an iterative hybrid algorithm (HA) to predict the 3D structure of peptides starting from their amino acid sequence. The HA is made of a modified genetic algorithm (GA) coupled to a local optimizer. Each HA iteration is carried out in two phases. In the first phase several GA runs are performed upon t...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2003.10506906

    authors： Garduño-Juárez R,Morales LB

    更新日期：2003-08-01 00:00:00

  • Molecular dynamics studies on troponin (TnI-TnT-TnC) complexes: insight into the regulation of muscle contraction.

    abstract：:Mutations of any subunit of the troponin complex may lead to serious disorders. Rational approaches to managing these disorders require knowledge of the complex interactions among the three subunits that are required for proper function. Molecular dynamics (MD) simulations were performed for both skeletal (sTn) and ca...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2010.10507350

    authors： Varughese JF,Chalovich JM,Li Y

    更新日期：2010-10-01 00:00:00

  • Understanding the thermal response of rice eukaryotic transcription factor eIF4A1 towards dynamic temperature stress: insights from expression profiling and molecular dynamics simulation.

    abstract：:Eukaryotic translation initiation factors (eIFs) are the group of regulatory proteins that are involved in the initiation of translation events. Among them, eIF4A1, a member of the DEAD-box RNA helicase family, participates in a wide spectrum of activities which include, RNA splicing, ribosome biogenesis, and RNA degr...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1751295

    authors： Singha DL,Maharana J,Panda D,Dehury B,Modi MK,Singh S

    更新日期：2020-05-05 00:00:00

  • A possible binding path of ergosterol within elicitins revealed by molecular dynamics.

    abstract：:Elicitins, produced by most of the phytopathogenic fungi of the genus Phytophthora, provoke in the tobacco plant both remote leaf necrosis and the induction of a resistance against subsequent attack by various micro-organisms. The crystal structure of b-cryptogein (CRY), secreted by Phytophthora cryptogea, was previou...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2000.10506680

    authors： Demaret S,Demaret JP,Brunie S

    更新日期：2000-12-01 00:00:00

  • Computational investigation of potential inhibitors of novel coronavirus 2019 through structure-based virtual screening, molecular dynamics and density functional theory studies.

    abstract：:Despite the intensive research efforts towards antiviral drug against COVID-19, no potential drug or vaccines has not yet discovered. Initially, the binding site of COVID-19 main protease was predicted which located between regions 2 and 3. Structure-based virtual screening was performed through a hierarchal mode of e...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1791957

    authors： Mishra SS,Ranjan S,Sharma CS,Singh HP,Kalra S,Kumar N

    更新日期：2020-07-15 00:00:00

  • SARS-CoV-2 mutations and where to find them: an in silico perspective of structural changes and antigenicity of the spike protein.

    abstract：:Communicated by Ramaswamy H. Sarma. ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 信件

    doi：10.1080/07391102.2020.1844052

    authors： Gonçalves RL,Leite TCR,Dias BP,Caetano CCDS,de Souza ACG,Batista UDS,Barbosa CC,Reyes-Sandoval A,Coelho LFL,Silva BM

    更新日期：2020-11-06 00:00:00

  • Comparative binding of Swertiamarin with human serum albumin and α-1 glycoprotein and its cytotoxicity against neuroblastoma cells.

    abstract：:Communicated by Ramaswamy H. Sarma. ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 信件

    doi：10.1080/07391102.2019.1695672

    authors： Dubey S,Kallubai M,Subramanyam R

    更新日期：2020-10-01 00:00:00

  • General acid-base catalysis in nucleobase amino proton exchange: cytidine.

    abstract：:A useful property of DMSO solvent has been exploited to reveal a new catalytic route for cytidine amino proton exchange, relevant to exchange in the macromolecular state, but hidden in aqueous solution. Additional exchange mechanisms in aqueous monomeric cytidine (and adenosine) are obscured by the formation of a fast...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1986.10506359

    authors： McConnell B

    更新日期：1986-12-01 00:00:00

  • Characterization of the structural conformation adopted by (TTAGGG)n telomeric DNA repeats of different length in closed circular DNA.

    abstract：:Telomeric DNA sequences are known to adopt unusual DNA structures upon protonation when contained into negatively supercoiled DNA. In this paper, the structural properties of (T2AG3)n telomeric sequences of different length is analyzed in detail. Transition to the protonated form is observed at very low pH for (T2AG3)...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：

    authors： Huertas D,Lipps H,Azorín F

    更新日期：1994-08-01 00:00:00

  • A novel major groove binding site in B-form DNA for ethidium cation.

    abstract：:A stably-bound external binding site for ethidium cation in the major groove of B-form DNA is proposed. This complex is stabilized by hydrogen bonding between this ligand and the nucleophilic centers O6 and N7 of guanine, both of which are accessible via the major groove. This binding site is not the same as the well-...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2007.10507160

    authors： Monaco RR

    更新日期：2007-10-01 00:00:00

  • Design of sequence-specific DNA binding ligands that use a two-stranded peptide motif for DNA sequence recognition.

    abstract：:The design and DNA binding activity of beta-structure-forming peptides and netropsin-peptide conjugates are reported. It is found that a pair of peptides-S,S'-bis(Lys-Gly-Val-Cys-Val-NH-NH-Dns)-bridged by an S-S bond binds at least 10 times more strongly to poly(dG).poly(dC) than to poly(dA).poly(dT). This peptide can...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1996.10508927

    authors： Nikolaev VA,Grokhovsky SL,Surovaya AN,Leinsoo TA,Sidorova NYu,Zasedatelev AS,Zhuze AL,Strahan GA,Shafer RH,Gursky GV

    更新日期：1996-08-01 00:00:00

  • Investigating specificity of the anti-hypertensive inhibitor WNK463 against With-No-Lysine kinase family isoforms via multiscale simulations.

    abstract：:The With-No-Lysine (WNK) kinase family plays a significant role in regulating cation-chloride cotransporters, blood pressure and body fluid homeostasis. Mutations in the gene of WNK family, especially in WNK1 and WNK4 are responsible for pseudohypoaldosteronism type II (PHAII), characterized by hypertension. The selec...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2019.1602079

    authors： Jonniya NA,Kar P

    更新日期：2020-03-01 00:00:00

  • 7-Azido-actinomycin D: a photoaffinity probe of the sequence specificity of DNA binding by actinomycin D.

    abstract：:Actinomycin D (ActD) is a DNA-binding antitumor antibiotic that appears to act in vivo by inhibiting RNA polymerase. The mechanism of DNA binding of ActD has attracted much attention because of its strong preference for 5'-dGpdC-3' sequences. Binding is thought to involve intercalation of the tricyclic aromatic phenox...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1989.10508509

    authors： Rill RL,Marsch GA,Graves DE

    更新日期：1989-12-01 00:00:00

  • Identification of potential non-nucleoside MraY inhibitors for tuberculosis chemotherapy using structure-based virtual screening.

    abstract：:The efforts to limit the spread of the tuberculosis epidemic have been challenged by the rise of drug-resistant strains of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis. It is critical to discover new chemical scaffolds acting on novel or unexploited targets to beat this drug-resistant pathogen...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1862705

    authors： Pandey P,Chatterjee S,Berida T,Doerksen RJ,Roy S

    更新日期：2020-12-22 00:00:00

  • Exploration of good and bad structural fingerprints for inhibition of indoleamine-2,3-dioxygenase enzyme in cancer immunotherapy using Monte Carlo optimization and Bayesian classification QSAR modeling.

    abstract：:Indoleamine-2,3-dioxygenase 1 (IDO1) is an extrahepatic, heme-containing and tryptophan-catalyzing enzyme responsible for causing blockade of T-cell proliferation and differentiation by depleting tryptophan level in cancerous cells. Therefore, inhibition of IDO1 may be a useful strategy for immunotherapy against cance...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2019.1615000

    authors： Jain S,Bhardwaj B,Amin SA,Adhikari N,Jha T,Gayen S

    更新日期：2020-04-01 00:00:00