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HYDROPHOBIC MAPPING OF CHLOROBIUM TEPIDUM, THE ENERGY GENERATING BACTERIA

Anindita Roy Chowdhury, Anushka Kothari
2019 Journal of Harmonized Research in Applied Science  
Among the four major forces responsible for the three dimensional structure of a protein, hydrophobic force is the dominant one.  ...  In this paper, the authors aim to investigate the hydrophobic mapping of protein sequences of Chlorobium tepidum.  ...  Furthermore, hydrophobic contribution of aliphatic amino acids per unit length of the protein sequence in the enzyme classes is more than that of aromatic residues.  ... 
doi:10.30876/johr.7.3.2019.98-106 fatcat:jscfjuetvrgapc66ecmtan5qkm

Anatomy of enzyme channels

Lukáš Pravda, Karel Berka, Radka Svobodová Vařeková, David Sehnal, Pavel Banáš, Roman A Laskowski, Jaroslav Koča, Michal Otyepka
2014 BMC Bioinformatics  
This indicates that enzymes tend to have buried active sites, with channels controlling access to, and egress from, them, and that suggests channels may play a key role in helping determine enzyme substrate  ...  Despite our current knowledge of enzyme structure and function, surprisingly little is known about how often channels are present or about any structural features such channels may have in common.  ...  Hydrophobic aliphatic residues are shown in gray, aromatic amino acids in magenta, polar residues in green, negatively charged in red, positively charged in blue and cysteine in yellow. the active sites  ... 
doi:10.1186/s12859-014-0379-x pmid:25403510 pmcid:PMC4245731 fatcat:7m2avekmengythpacvbwkao2s4

An amino acid at position 142 in nitrilase fromRhodococcus rhodochrousATCC 33278 determines the substrate specificity for aliphatic and aromatic nitriles

Soo-Jin Yeom, Hye-Jung Kim, Jung-Kul Lee, Dong-Eun Kim, Deok-Kun Oh
2008 Biochemical Journal  
Replacing Tyr-142 in the wild-type enzyme with the aromatic amino acid phenylalanine did not alter specificity for either substrate.  ...  Thus aromaticity of substrate or amino acid at position 142 in R. rhodochrous nitrilase is required for enzyme activity.  ...  The wild-type enzyme exhibited activity towards both classes of aromatic and aliphatic substrates, whereas the mutants containing a non-polar aliphatic residue at position 142 and the Y142S mutant had  ... 
doi:10.1042/bj20080440 pmid:18412544 pmcid:PMC2570083 fatcat:sve5zmlhpzfo7nm4o37ptjpssa

A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design

A. Wallqvist, R.L. Jernigan, D.G. Covell
1995 Protein Science  
The main utility of such a scheme lies in the identification of important stabilizing atomic interactions across the receptor-ligand interface.  ...  The free energy approximation of binding strength in this model has a reliability of about * 1.5 kcal/mol, despite limited knowledge of the unbound states.  ...  Wlodawer for generously providing us with the X-ray coordinates of the HIV-I protease inhibitor complexes not in the PDB, and to Dr. Andrew Karplus for valuable comments regarding this manuscript.  ... 
doi:10.1002/pro.5560040923 pmid:8528086 pmcid:PMC2143230 fatcat:sjqwtbuoxzgdfdzyxm7ukkocvu

Bis-isoquinolinium and bis-pyridinium acetylcholinesterase inhibitors: in vitro screening of probes for novel selective insecticides

Veronika Hrabcova, Jan Korabecny, Brigita Manyova, Lenka Matouskova, Tomas Kucera, Rafael Dolezal, Kamil Musilek, Lukas Gorecki, Eugenie Nepovimova, Kamil Kuca, Daniel Jun
2017 RSC Advances  
The work was nancially supported by the by Ministry of Health of the Czech Republic (No. 16-34390A) and by Ministry of Education, Youth and Sports of the Czech Republic (No. SV/UHK2109 and No.  ...  Acknowledgements The authors would like to thank Jitka Turanova for her technical assistance.  ...  Similarly, each aromatic part of the ligand displayed favorable p-p and/or cation-p contacts with aromatic amino acid residues delineating the cavity enzyme.  ... 
doi:10.1039/c7ra05838a fatcat:lbol5mivnvgexeinx7gflz7gj4

Biophysical Mechanism of the SAHA Inhibition of Zn2+-Histone Deacetylase-Like Protein (FB188 HDAH) Assessed via Crystal Structure Analysis

Cynthia Raquel Trejo-Muñoz, Ricardo Vázquez-Ramírez, Luis Mendoza, Carlos Kubli-Garfias
2018 Computational Molecular Bioscience  
Significant differences were observed in the areas and volumes of the binding pocket, as well as hydrophobic interactions, dipole moments, atomic charges and electrostatic potential, among other properties  ...  The zinc-containing enzyme HDAC-like amidohydrolase (FB188 HDAH), identified in the Bordetella alcaligenes bacteria, is similar to enzymes that participate in epigenetic mechanisms such as histone modifications  ...  Seven amino acids-five aromatic and two aliphatic-form the hydrophobic core that surrounds the SAHA molecule.  ... 
doi:10.4236/cmb.2018.82005 fatcat:tj2sro25vzawnpz2q2of27sorq

Unique Features of a New Baeyer–Villiger Monooxygenase from a Halophilic Archaeon

Niero, Righetto, Beneventi, Polverino de Laureto, Fraaije, Filippini, Bergantino
2020 Catalysts  
The enzyme was characterized in terms of its salt-dependent activity and resistance to some water–organic-solvent mixtures.  ...  Nevertheless, we managed to express HtBVMO in Escherichia coli and could purify it as active enzyme.  ...  HtBVMO and in the GC-MS analysis of whole-cell transformations, respectively.  ... 
doi:10.3390/catal10010128 fatcat:juql5rlqxzc5lekp7fqrnsql3i

Novel 8-Substituted Coumarins That Selectively Inhibit Human Carbonic Anhydrase IX and XII

Kerem Buran, Silvia Bua, Giulio Poli, F. Önen Bayram, Tiziano Tuccinardi, Claudiu T. Supuran
2019 International Journal of Molecular Sciences  
µM concentration in the assay system.  ...  Molecular modeling studies provided a rationale for explaining the selectivity profile of these non-classic hCA inhibitors and their interactions with the enzymes, according to their specific mechanism  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms20051208 fatcat:u4kkvxmvfzfprlevrt6nxe3aye

In silico analysis of heme oxygenase structural homologues identifies group-specific conservations

Joseph Irvin, Alexander J. Ropelewski, John Perozich
2017 FEBS Open Bio  
AR performed functional residue prediction analyses and interpreted the results.  ...  JP supervised the project, participated in the analysis of the alignment, helped to write the initial and final drafts of the manuscript, and addressed reviewer's comments.  ...  This position also has 84% similarity with aliphatic hydrophobic residues (I, V, L, and M) throughout the entire alignment.  ... 
doi:10.1002/2211-5463.12275 pmid:28979838 pmcid:PMC5623701 fatcat:gm4uz7h4k5ethal6cfqdy3lgpy

In silico identification of T-type calcium channel blockers: A ligand-based pharmacophore mapping approach

Tamanna Gandhi, Anu R. Melge, C. Gopi Mohan
2016 Journal of Advanced Research  
HipHop pharmacophore map of the selective T-type CCBs contained six different chemical features, namely ring aromatic (R), positive ionizable (P), two hydrophobic aromatic (Y), hydrophobic aliphatic (Z  ...  Limited progress has been made in the quest to identify both selective and non-toxic T-type calcium channel blocking compounds.  ...  Supplementary material Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j.jare.2016. 09.004.  ... 
doi:10.1016/j.jare.2016.09.004 pmid:27713840 pmcid:PMC5045570 fatcat:kpdhif2ldzga3pz2eqjnpumoea

A Critical Mathematical Review on Protein Sequence Comparison Using Physio-Chemical Properties of Amino Acids

2020 https://researchopenworld.com/category/journal-of-molecular-genetics/  
The review tries to list out maximum number of physical and chemical properties of amino acids, which are being used directly or indirectly in protein sequence comparison.  ...  It also tries to examine critically all the methods under mathematical precision. Finally it tries to point out how to modify the methods, in case they are not sound.  ...  Again it is sure that C does not belong to neither of the classes POL and HPO. But in this paper, C is placed in the HPO class. Also no sufficient reference is given in support of class (i) (b).  ... 
doi:10.31038/jmg.2020332 fatcat:d6yrznffxjgebpzbyn33djid4i

Identification of protein functions using a machine-learning approach based on sequence-derived properties

Bum Lee, Moon Shin, Young Oh, Hae Oh, Keun Ryu
2009 Proteome Science  
The primary contribution of this paper is to propose new PNPRD features representing global and/or local differences in sequences, based on positively and/ or negatively charged residues, to assist in  ...  Our results indicate that sequence-based classifiers can provide good results among a broad range of proteins, that the proposed features are useful in predicting several functions, and that the combination  ...  Acknowledgements This work was supported by a grant from the Korean Ministry of Education, Science, and Technology (The Regional Core Research Programme  ... 
doi:10.1186/1477-5956-7-27 pmid:19664241 pmcid:PMC2731080 fatcat:x7lv35en2behle3kbbbdlkofqq

Computer-aided drug design guided by hydrogen/deuterium exchange mass spectrometry: A powerful combination for the development of potent and selective inhibitors of Group VIA calcium-independent phospholipase A 2

Varnavas D. Mouchlis, Christophe Morisseau, Bruce D. Hammock, Sheng Li, J. Andrew McCammon, Edward A. Dennis
2016 Bioorganic & Medicinal Chemistry  
Molecular docking and dynamics simulations in the presence of a membrane were guided by the DXMS data in order to identify the binding mode of OTFP.  ...  The SAR showed that the sulfur atom is vital for the potency of beta-thioether analogues, while the hydrophobic chain is important for selectivity.  ...  An alternative hypothesis is that the sulfur atom may participates in π-stacking interactions with aromatic residues in the enzyme active site [26] .  ... 
doi:10.1016/j.bmc.2016.05.009 pmid:27320659 pmcid:PMC5053890 fatcat:2heuqnqtwnbkbpjgcjn3pl2pm4

Probing the origins of human acetylcholinesterase inhibition via QSAR modeling and molecular docking

Saw Simeon, Nuttapat Anuwongcharoen, Watshara Shoombuatong, Aijaz Ahmad Malik, Virapong Prachayasittikul, Jarl E.S. Wikberg, Chanin Nantasenamat
2016 PeerJ  
and hydrophobic interaction inside the binding pocket.  ...  Acetylcholinesterase (AChE) is an enzyme that catalyzes the breakdown of the neurotransmitter acetylcholine that is essential for cognition and memory.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.7717/peerj.2322 pmid:27602288 pmcid:PMC4991866 fatcat:x5m5666zdnajbinl6m2kchx3lu

Inhibition of secreted phospholipases A2 by 2-oxoamides based on α-amino acids: Synthesis, in vitro evaluation and molecular docking calculations

Varnavas D. Mouchlis, Victoria Magrioti, Efrosini Barbayianni, Nathan Cermak, Rob C. Oslund, Thomas M. Mavromoustakos, Michael H. Gelb, George Kokotos
2011 Bioorganic & Medicinal Chemistry  
In this study, the synthesis of 2-oxoamides based on a-amino acids and the in vitro evaluation against three secreted sPLA 2 s (GIIA, GV and GX) are described.  ...  Group IIA secreted phospholipase A 2 (GIIA sPLA 2 ) is a member of the mammalian sPLA 2 enzyme family and is associated with various inflammatory conditions.  ...  Acknowledgments The project is co-funded by the European Social Fund and National Resources (EPEAEK II) (G.K.) and by a grant from the National Institutes of Health (HL36235) (M.H.G.). V. D.  ... 
doi:10.1016/j.bmc.2010.12.030 pmid:21216150 pmcid:PMC3050527 fatcat:zcc7ftnybfeqngnszhd5tf6p7u
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