A monomeric TIM-barrel structure fromPyrococcus furiosusis optimized for extreme temperatures

2012 ◽  
Vol 68 (11) ◽  
pp. 1479-1487 ◽  
Author(s):  
Heidi Repo ◽  
Jesper S. Oeemig ◽  
Janica Djupsjöbacka ◽  
Hideo Iwaï ◽  
Pirkko Heikinheimo
Keyword(s):  
Main Chain ◽  
Pyrococcus Furiosus ◽  
Ion Pairs ◽  
Industrial Applications ◽  
Side Chain ◽  
Water Molecules ◽  
Extreme Temperatures ◽  
Structural Water ◽  
Hyperthermophilic Archaeon ◽  
Tim Barrel

The structure of phosphoribosyl anthranilate isomerase (TrpF) from the hyperthermophilic archaeonPyrococcus furiosus(PfTrpF) has been determined at 1.75 Å resolution. ThePfTrpF structure has a monomeric TIM-barrel fold which differs from the dimeric structures of two other known thermophilic TrpF proteins. A comparison of thePfTrpF structure with the two known bacterial thermophilic TrpF structures and the structure of a related mesophilic protein fromEscherichia coli(EcTrpF) is presented. The thermophilic TrpF structures contain a higher proportion of ion pairs and charged residues compared with the mesophilicEcTrpF. These residues contribute to the closure of the central barrel and the stabilization of the barrel and the surrounding α-helices. In the monomericPfTrpF conserved structural water molecules are mostly absent; instead, the structural waters are replaced by direct side-chain–main-chain interactions. As a consequence of these combined mechanisms, theP. furiosusenzyme is a thermodynamically stable and entropically optimized monomeric TIM-barrel enzyme which defines a good framework for further protein engineering for industrial applications.

Purification and Characterization of Natural Solid-Substrate Degrading and Alcohol Producing Hyperthermostable Alkaline Amylase from Bacillus cereus (sm-sr14)

2020 ◽  
Vol 21 (9) ◽  
pp. 872-881
Author(s):  
Sumit Sahoo ◽  
Sudipta Roy ◽  
Dipannita Santra ◽  
Sayantani Maiti ◽  
Sonali Roul ◽  
...  
Keyword(s):  
Bacillus Cereus ◽  
Main Property ◽  
Solid Substrate ◽  
Industrial Applications ◽  
Starch Degradation ◽  
Significant Similarity ◽  
Alcohol Production ◽  
Cazy Database ◽  
Tim Barrel ◽  
Alkaline Amylase

Objective: Amylases enzymes hydrolyze starch molecules to produce diverse products including dextrins, and progressively smaller polymers. These include glucose units linked through α-1- 1, α-1-4, α-1-6, glycosidic bonds. Methods: This enzyme carrying an (α /β) 8 or TIM barrel structure is also produced containing the catalytic site residues. These groups of enzymes possess four conserved regions in their primary sequence. In the Carbohydrate-Degrading Enzyme (CAZy) database, α-amylases are classified into different Glycoside Hydrolase Families (GHF) based on their amino acid sequence. The present objective was to study one such enzyme based on its molecular characterization after purification in our laboratory. Its main property of solid-natural starch degradation was extensively investigated for its pharmaceutical/ industrial applications. Results: Amylase producing bacteria Bacillus cereus sm-sr14 (Accession no. KM251578.1) was purified to homogeneity on a Seralose 6B-150 gel-matrix and gave a single peak during HPLC. MALDITOF mass-spectrometry with bioinformatics studies revealed its significant similarity to α/β hydrolase family. The enzyme showed an efficient application; favourable Km, Vmax and Kcat during the catalysis of different natural solid starch materials. Analysis for hydrolytic product showed that this enzyme can be classified as the exo-amylase asit produced a significant amount of glucose. Conclusion: Besides the purified enzyme, the present organism Bacillus cereus sm-sr14 could degrade natural solid starch materials like potato and rice up to the application level in the pharmaceutical/ industrial field for alcohol production.

Stereospecific Association of C-20 Epimers of 3β-Hydroxy-16-oxo-24-nor-17-azachol-5-eno-23-nitryle

1997 ◽  
Vol 52 (6) ◽  
pp. 749-756
Author(s):  
Zofia Plesnar ◽  
Stanisław Malanowski ◽  
Zenon Lotowski ◽  
Jacek W. Morzycki ◽  
Jadwiga Frelek ◽  
...  
Keyword(s):  
Proton Nuclear Magnetic Resonance ◽  
Side Chain ◽  
Water Molecules ◽  
Carbonyl Groups ◽  
Nmr Data ◽  
Molecular Modelling Studies ◽  
Modelling Studies ◽  
Lactam Carbonyl ◽  
Self Association ◽  
Chain Conformations

Abstract The cryoscopic measurements show that title compounds are strongly associated in CHCl3 solutions. The association of the 20 R epimer is distinctly less pronounced than that of the 20 S epipmer. Self-association of the 20 S epimer leads to the formation of very large com­plexes. The 20 R epimer forms associates via water molecules. The dissimilarity may be ex­plained in terms of different accessibility of the lactam carbonyl groups in the two epimers for the association. It is proposed that the association process is controlled by the configura­tion at the carbon atom C(20) and conformation around the C(20)-C(22) bond. Populations of side chain conformations of both epimers were determined by means of proton nuclear magnetic resonance. It was found for the 20 R epimer that the t and the -g rotamers are almost equally populated, and the rotamer +g is excluded. For the 20 S epimer the +g rotamer predominates over the t one, and the -g rotamer is excluded. The NMR data are fully consistent with the results of the molecular modelling studies.

scholarly journals Substrate Scope for Human Histone Lysine Acetyltransferase KAT8

2021 ◽  
Vol 22 (2) ◽  
pp. 846
Author(s):  
Giordano Proietti ◽  
Yali Wang ◽  
Chiara Punzo ◽  
Jasmin Mecinović
Keyword(s):  
Main Chain ◽  
Coenzyme A ◽  
Side Chain ◽  
Histone H4 ◽  
Chemical Probes ◽  
Acetyl Coenzyme A ◽  
Acetyl Coenzyme ◽  
Histone Lysine ◽  
Lysine Acetyltransferase

Biomedically important histone lysine acetyltransferase KAT8 catalyses the acetyl coenzyme A-dependent acetylation of lysine on histone and other proteins. Here, we explore the ability of human KAT8 to catalyse the acetylation of histone H4 peptides possessing lysine and its analogues at position 16 (H4K16). Our synthetic and enzymatic studies on chemically and structurally diverse lysine mimics demonstrate that KAT8 also has a capacity to acetylate selected lysine analogues that possess subtle changes on the side chain and main chain. Overall, this work highlights that KAT8 has a broader substrate scope beyond natural lysine, and contributes to the design of new chemical probes targeting KAT8 and other members of the histone lysine acetyltransferase (KAT) family.

scholarly journals Side-Chain to Main-Chain Hydrogen Bonding Controls the Intrinsic Backbone Dynamics of the Amyloid Precursor Protein Transmembrane Helix

2014 ◽  
Vol 106 (6) ◽  
pp. 1318-1326 ◽  
Author(s):  
Christina Scharnagl ◽  
Oxana Pester ◽  
Philipp Hornburg ◽  
Daniel Hornburg ◽  
Alexander Götz ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Amyloid Precursor Protein ◽  
Main Chain ◽  
Transmembrane Helix ◽  
Precursor Protein ◽  
Backbone Dynamics ◽  
Side Chain

scholarly journals Synthesis and Photochemical Reaction of Polymers Containing Norbornadiene Residues Both in the Main Chain and Side Chain.

2000 ◽  
Vol 57 (9) ◽  
pp. 569-576 ◽  
Author(s):  
Makoto SAMPEI ◽  
Ken HIRAMATU ◽  
Atsushi KAMEYAMA ◽  
Tadatomi NISHIKUBO
Keyword(s):  
Photochemical Reaction ◽  
Main Chain ◽  
Side Chain

scholarly journals Dynamics and mechanism of ultrafast water–protein interactions

2016 ◽  
Vol 113 (30) ◽  
pp. 8424-8429 ◽  
Author(s):  
Yangzhong Qin ◽  
Lijuan Wang ◽  
Dongping Zhong
Keyword(s):  
Protein Interactions ◽  
Hydration Shell ◽  
Water Dynamics ◽  
Side Chain ◽  
Water Molecules ◽  
Ultrafast Dynamics ◽  
Hydration Water ◽  
Water Side ◽  
Dynamics And Function ◽  
And Function

Protein hydration is essential to its structure, dynamics, and function, but water–protein interactions have not been directly observed in real time at physiological temperature to our awareness. By using a tryptophan scan with femtosecond spectroscopy, we simultaneously measured the hydration water dynamics and protein side-chain motions with temperature dependence. We observed the heterogeneous hydration dynamics around the global protein surface with two types of coupled motions, collective water/side-chain reorientation in a few picoseconds and cooperative water/side-chain restructuring in tens of picoseconds. The ultrafast dynamics in hundreds of femtoseconds is from the outer-layer, bulk-type mobile water molecules in the hydration shell. We also found that the hydration water dynamics are always faster than protein side-chain relaxations but with the same energy barriers, indicating hydration shell fluctuations driving protein side-chain motions on the picosecond time scales and thus elucidating their ultimate relationship.

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