scholarly journals Molecular dynamics study to improve the substrate adsorption of Saccharomycopsis fibuligera R64 alpha-amylase by designing a new surface binding site

2019 ◽  
Vol Volume 12 ◽  
pp. 1-13
Author(s):  
Umi Baroroh ◽  
Muhammad Yusuf ◽  
Saadah Diana Rachman ◽  
Safri Ishmayana ◽  
Khomaini Hasan ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Binding Site ◽  
Alpha Amylase ◽  
Surface Binding ◽  
Saccharomycopsis Fibuligera ◽  
Surface Binding Site

scholarly journals Computational Model of the Effect of a Surface-Binding Site on the Saccharomycopsis fibuligera R64 α-Amylase to the Substrate Adsorption

2017 ◽  
Vol 11 ◽  
pp. 117793221773876 ◽  
Author(s):  
*Muhammad Yusuf ◽  
*Umi Baroroh ◽  
Khomaini Hasan ◽  
Saadah Diana Rachman ◽  
Safri Ishmayana ◽  
...  
Keyword(s):  
Computational Model ◽  
Binding Site ◽  
Positive Control ◽  
Model Structure ◽  
Structural Comparison ◽  
Surface Binding ◽  
Processing Industry ◽  
Saccharomycopsis Fibuligera ◽  
Lower Temperature ◽  
Surface Binding Site

α-Amylase is one of the important enzymes in the starch-processing industry. However, starch processing requires high temperature, thus resulting in high cost. The high adsorptivity of α-amylase to the substrate allows this enzyme to digest the starch at a lower temperature. α-Amylase from Saccharomycopsis fibuligera R64 (Sfamy R64), a locally sourced enzyme from Indonesia, has a high amylolytic activity but low starch adsorptivity. The objective of this study was to design a computational model of Sfamy R64 with increased starch adsorptivity using bioinformatics method. The model structure of Sfamy R64 was compared with the positive control, ie, Aspergillus niger α-amylase. The structural comparison showed that Sfamy R64 lacks the surface-binding site (SBS). An SBS was introduced to the structure of Sfamy R64 by S383Y/S386W mutations. The dynamics and binding affinity of the SBS of mutant to the substrate were also improved and comparable with that of the positive control.

Selectivity of the surface binding site (SBS) on barley starch synthase I

Biologia ◽  
2014 ◽  
Vol 69 (9) ◽  
Author(s):  
Casper Wilkens ◽  
Jose Cuesta-Seijo ◽  
Monica Palcic ◽  
Birte Svensson
Keyword(s):  
Crystal Structure ◽  
Surface Plasmon Resonance ◽  
Binding Site ◽  
Active Site ◽  
Mutational Analysis ◽  
Starch Synthase ◽  
Surface Binding ◽  
Binding Studies ◽  
A Chain ◽  
Surface Binding Site

AbstractStarch synthase I (SSI) from various sources has been shown to preferentially elongate branch chains of degree of polymerisation (DP) from 6–7 to produce chains of DP 8–12. In the recently determined crystal structure of barley starch synthase I (HvSSI) a so-called surface binding site (SBS) was seen, which was found by mutational analysis to be essential for the activity of HvSSI on glycogen. We now show in binding studies using surface plasmon resonance that HvSSI has no detectable affinity for malto-triose and -tetraose, but clearly binds maltopentaose, -hexaose, -heptaose (M7) and β-cyclodextrin (β-CD) albeit with a measurable K D for only β-CD and M7. Moreover, an HvSSI SBS mutant F538A lost the ability to bind β-CD and maltooligosaccharides. This behaviour suggests that a chain in the α-glucan molecule (amylopectin) that is undergoing extension attaches itself at the SBS and that the active site itself, likely working on a different end chain, has low affinity for both substrate and product.

Fragment screening of inhibitors for MIF tautomerase reveals a cryptic surface binding site

2010 ◽  
Vol 20 (6) ◽  
pp. 1821-1824 ◽  
Author(s):  
Larry R. McLean ◽  
Ying Zhang ◽  
Hua Li ◽  
Yong-Mi Choi ◽  
Zuoning Han ◽  
...  
Keyword(s):  
Binding Site ◽  
Surface Binding ◽  
Fragment Screening ◽  
Surface Binding Site

scholarly journals The Importance of Surface-Binding Site towards Starch-Adsorptivity Level in α-Amylase: A Review on Structural Point of View

2017 ◽  
Vol 2017 ◽  
pp. 1-11 ◽  
Author(s):  
Umi Baroroh ◽  
Muhammad Yusuf ◽  
Saadah Diana Rachman ◽  
Safri Ishmayana ◽  
Mas Rizky A. A. Syamsunarno ◽  
...  
Keyword(s):  
Binding Site ◽  
Large Scale ◽  
Point Of View ◽  
Carbohydrate Binding ◽  
Surface Binding ◽  
Raw Starch ◽  
Amylolytic Enzymes ◽  
Stacking Interaction ◽  
Structural Point ◽  
Surface Binding Site

Starch is a polymeric carbohydrate composed of glucose. As a source of energy, starch can be degraded by various amylolytic enzymes, including α-amylase. In a large-scale industry, starch processing cost is still expensive due to the requirement of high temperature during the gelatinization step. Therefore, α-amylase with raw starch digesting ability could decrease the energy cost by avoiding the high gelatinization temperature. It is known that the carbohydrate-binding module (CBM) and the surface-binding site (SBS) of α-amylase could facilitate the substrate binding to the enzyme’s active site to enhance the starch digestion. These sites are a noncatalytic module, which could interact with a lengthy substrate such as insoluble starch. The major interaction between these sites and the substrate is the CH/pi-stacking interaction with the glucose ring. Several mutation studies on the Halothermothrix orenii, SusG Bacteroides thetaiotamicron, Barley, Aspergillus niger, and Saccharomycopsis fibuligera α-amylases have revealed that the stacking interaction through the aromatic residues at the SBS is essential to the starch adsorption. In this review, the SBS in various α-amylases is also presented. Therefore, based on the structural point of view, SBS is suggested as an essential site in α-amylase to increase its catalytic activity, especially towards the insoluble starch.

scholarly journals Asp271 is critical for substrate interaction with the surface binding site in β-agarase a from Zobellia galactanivorans

2018 ◽  
Vol 87 (1) ◽  
pp. 34-40
Author(s):  
Casper Wilkens ◽  
Manish K. Tiwari ◽  
Helen Webb ◽  
Murielle Jam ◽  
Mirjam Czjzek ◽  
...  
Keyword(s):  
Binding Site ◽  
Surface Binding ◽  
Substrate Interaction ◽  
Surface Binding Site

Interaction of Poliovirus with its Cell Surface Binding Site

Virology ◽  
1994 ◽  
Vol 201 (1) ◽  
pp. 107-115 ◽  
Author(s):  
James A. Bibb ◽  
Gary Witherell ◽  
Günter Bernhardt ◽  
Eckard Wimmer
Keyword(s):  
Cell Surface ◽  
Binding Site ◽  
Surface Binding ◽  
Cell Surface Binding ◽  
Surface Binding Site

scholarly journals Identification of a New Hormone-Binding Site on the Surface of Thyroid Hormone Receptor

2014 ◽  
Vol 28 (4) ◽  
pp. 534-545 ◽  
Author(s):  
P.C.T. Souza ◽  
A.C. Puhl ◽  
L. Martínez ◽  
R. Aparício ◽  
A.S. Nascimento ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Thyroid Hormone ◽  
Ligand Binding ◽  
Molecular Dynamics Simulations ◽  
Binding Site ◽  
Nuclear Receptor ◽  
Surface Binding ◽  
X Ray ◽  
Protein Dissociation ◽  
Dynamics Simulations

Abstract Thyroid hormone receptors (TRs) are members of the nuclear receptor superfamily of ligand-activated transcription factors involved in cell differentiation, growth, and homeostasis. Although X-ray structures of many nuclear receptor ligand-binding domains (LBDs) reveal that the ligand binds within the hydrophobic core of the ligand-binding pocket, a few studies suggest the possibility of ligands binding to other sites. Here, we report a new x-ray crystallographic structure of TR-LBD that shows a second binding site for T3 and T4 located between H9, H10, and H11 of the TRα LBD surface. Statistical multiple sequence analysis, site-directed mutagenesis, and cell transactivation assays indicate that residues of the second binding site could be important for the TR function. We also conducted molecular dynamics simulations to investigate ligand mobility and ligand-protein interaction for T3 and T4 bound to this new TR surface-binding site. Extensive molecular dynamics simulations designed to compute ligand-protein dissociation constant indicate that the binding affinities to this surface site are of the order of the plasma and intracellular concentrations of the thyroid hormones, suggesting that ligands may bind to this new binding site under physiological conditions. Therefore, the second binding site could be useful as a new target site for drug design and could modulate selectively TR functions.

scholarly journals Characterization of the starch surface binding site on Bacillus paralicheniformis α-amylase

2020 ◽  
Vol 165 ◽  
pp. 1529-1539
Author(s):  
Nataša Božić ◽  
Henriëtte J. Rozeboom ◽  
Nikola Lončar ◽  
Marinela Šokarda Slavić ◽  
Dick B. Janssen ◽  
...  
Keyword(s):  
Binding Site ◽  
Surface Binding ◽  
Bacillus Paralicheniformis ◽  
Surface Binding Site

Surface binding site analysis of Ca2+-homoionized clay–humic acid complexes

2010 ◽  
Vol 352 (2) ◽  
pp. 526-534 ◽  
Author(s):  
Raul E. Martinez ◽  
Prasesh Sharma ◽  
Andreas Kappler
Keyword(s):  
Humic Acid ◽  
Binding Site ◽  
Surface Binding ◽  
Site Analysis ◽  
Surface Binding Site
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