Role of the conserved water molecules in the binding of inhibitor to IMPDH-II (human): A study on the water mimic inhibitor design

2009 ◽  
Vol 908 (1-3) ◽  
pp. 31-39 ◽  
Author(s):  
Hridoy R. Bairagya ◽  
Bishnu P. Mukhopadhyay ◽  
S. Bhattacharya
Keyword(s):  
Water Molecules ◽  
Inhibitor Design ◽  
Conserved Water Molecules

scholarly journals Conserved Water Molecules Stabilize the Ω-Loop in Class A β-Lactamases

2008 ◽  
Vol 52 (3) ◽  
pp. 1072-1079 ◽  
Author(s):  
Fabian Bös ◽  
Jürgen Pleiss
Keyword(s):  
Phylogenetic Analysis ◽  
High Resolution ◽  
Evolutionary Relationship ◽  
Water Molecules ◽  
Protein Residues ◽  
Class A ◽  
Conserved Water Molecules ◽  
Dense Cluster ◽  
The Relationship

ABSTRACT A set of 49 high-resolution (≤2.2 Å) structures of the TEM, SHV, and CTX-M class A β-lactamase families was systematically analyzed to investigate the role of conserved water molecules in the stabilization of the Ω-loop. Overall, 13 water molecules were found to be conserved in at least 45 structures, including two water positions which were found to be conserved in all structures. Of the 13 conserved water molecules, 6 are located at the Ω-loop, forming a dense cluster with hydrogen bonds to residues at the Ω-loop as well as to the rest of the protein. This layer of conserved water molecules is packed between the Ω-loop and the rest of the protein and acts as structural glue, which could reduce the flexibility of the Ω-loop. A correlation between conserved water molecules and conserved protein residues could in general not be detected, with the exception of the conserved water molecules at the Ω-loop. Furthermore, the evolutionary relationship between the three families, derived from the number of conserved water molecules, is similar to the relationship derived from phylogenetic analysis.

scholarly journals The role of conserved water molecules in the catalytic domain of protein kinases

2009 ◽  
Vol 76 (3) ◽  
pp. 527-535 ◽  
Author(s):  
James D. R. Knight ◽  
Donald Hamelberg ◽  
J. Andrew McCammon ◽  
Rashmi Kothary
Keyword(s):  
Protein Kinases ◽  
Catalytic Domain ◽  
Water Molecules ◽  
Conserved Water Molecules

CONSERVED WATER MOLECULES IN X-RAY STRUCTURES HIGHLIGHT THE ROLE OF WATER IN INTRAMOLECULAR AND INTERMOLECULAR INTERACTIONS

2008 ◽  
Vol 06 (04) ◽  
pp. 775-788 ◽  
Author(s):  
EVGENIY AKSIANOV ◽  
OLGA ZANEGINA ◽  
ALEXANDER GRISHIN ◽  
SERGEY SPIRIN ◽  
ANNA KARYAGINA ◽  
...  
Keyword(s):  
Intermolecular Interactions ◽  
Protein Interactions ◽  
Active Sites ◽  
Three Dimensional ◽  
Water Molecules ◽  
Macromolecular Complexes ◽  
X Ray ◽  
Conserved Water Molecules ◽  
Related Proteins

Water molecules immobilized on a protein or DNA surface are known to play an important role in intramolecular and intermolecular interactions. Comparative analysis of related three-dimensional (3D) structures allows to predict the locations of such water molecules on the protein surface. We have developed and implemented the algorithm WLAKE detecting "conserved" water molecules, i.e. those located in almost the same positions in a set of superimposed structures of related proteins or macromolecular complexes. The problem is reduced to finding maximal cliques in a certain graph. Despite exponential algorithm complexity, the program works appropriately fast for dozens of superimposed structures. WLAKE was used to predict functionally significant water molecules in enzyme active sites (transketolases) as well as in intermolecular (ETS–DNA complexes) and intramolecular (thiol–disulfide interchange protein) interactions. The program is available online at .

scholarly journals Substrate wettability guided oriented self assembly of Janus particles

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Meneka Banik ◽  
Shaili Sett ◽  
Chirodeep Bakli ◽  
Arup Kumar Raychaudhuri ◽  
Suman Chakraborty ◽  
...  
Keyword(s):  
Self Assembly ◽  
Janus Particles ◽  
Water Molecules ◽  
Functional Coatings ◽  
Hexagonal Close Packed ◽  
Local Densities ◽  
Inhomogeneous Properties ◽  
Metal Polymer ◽  
Specific Orientation

AbstractSelf-assembly of Janus particles with spatial inhomogeneous properties is of fundamental importance in diverse areas of sciences and has been extensively observed as a favorably functionalized fluidic interface or in a dilute solution. Interestingly, the unique and non-trivial role of surface wettability on oriented self-assembly of Janus particles has remained largely unexplored. Here, the exclusive role of substrate wettability in directing the orientation of amphiphilic metal-polymer Bifacial spherical Janus particles, obtained by topo-selective metal deposition on colloidal Polymestyere (PS) particles, is explored by drop casting a dilute dispersion of the Janus colloids. While all particles orient with their polymeric (hydrophobic) and metallic (hydrophilic) sides facing upwards on hydrophilic and hydrophobic substrates respectively, they exhibit random orientation on a neutral substrate. The substrate wettability guided orientation of the Janus particles is captured using molecular dynamic simulation, which highlights that the arrangement of water molecules and their local densities near the substrate guide the specific orientation. Finally, it is shown that by spin coating it becomes possible to create a hexagonal close-packed array of the Janus colloids with specific orientation on differential wettability substrates. The results reported here open up new possibilities of substrate-wettability driven functional coatings of Janus particles, which has hitherto remained unexplored.

A first-principles study of the atomic layer deposition of ZnO on carboxyl functionalized carbon nanotubes: the role of water molecules

2021 ◽  
Vol 23 (5) ◽  
pp. 3467-3478
Author(s):  
J. I. Paez-Ornelas ◽  
H. N. Fernández-Escamilla ◽  
H. A. Borbón-Nuñez ◽  
H. Tiznado ◽  
Noboru Takeuchi ◽  
...  
Keyword(s):  
First Principles ◽  
Ligand Exchange ◽  
Functional Group ◽  
Atomic Layer ◽  
High Reactivity ◽  
Water Molecules ◽  
Exchange Reactions ◽  
Layer Deposition ◽  
The Right

Atomic description of ALD in systems that combine large surface area and high reactivity is key for selecting the right functional group to enhance the ligand-exchange reactions.

scholarly journals The role of the water molecules in novel superconductor, Na0.35CoO2·1.3H2O

2004 ◽  
Vol 412-414 ◽  
pp. 182-186 ◽  
Author(s):  
H. Sakurai ◽  
K. Takada ◽  
F. Izumi ◽  
R.A. Dilanian ◽  
T. Sasaki ◽  
...  
Keyword(s):  
Water Molecules
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