Evolutionary conservation of protein dynamics: insights from all-atom molecular dynamics simulations of ‘peptidase’ domain of Spt16

2021 ◽  
pp. 1-13
Author(s):  
Neeraj K. Gaur ◽  
Biplab Ghosh ◽  
Venuka Durani Goyal ◽  
Kiran Kulkarni ◽  
Ravindra D. Makde
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Protein Dynamics ◽  
Evolutionary Conservation ◽  
Dynamics Simulations

scholarly journals Active-site protein dynamics and solvent accessibility in nativeAchromobacter cycloclastescopper nitrite reductase

IUCrJ ◽  
2017 ◽  
Vol 4 (4) ◽  
pp. 495-505 ◽  
Author(s):  
Kakali Sen ◽  
Sam Horrell ◽  
Demet Kekilli ◽  
Chin W. Yong ◽  
Thomas W. Keal ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Protein Dynamics ◽  
Nitrite Reductase ◽  
Active Site ◽  
Solvent Accessibility ◽  
Nitrite Reduction ◽  
Protonation State ◽  
Dynamics Simulations

Microbial nitrite reductases are denitrifying enzymes that are a major component of the global nitrogen cycle. Multiple structures measured from one crystal (MSOX data) of copper nitrite reductase at 240 K, together with molecular-dynamics simulations, have revealed protein dynamics at the type 2 copper site that are significant for its catalytic properties and for the entry and exit of solvent or ligands to and from the active site. Molecular-dynamics simulations were performed using different protonation states of the key catalytic residues (AspCATand HisCAT) involved in the nitrite-reduction mechanism of this enzyme. Taken together, the crystal structures and simulations show that the AspCATprotonation state strongly influences the active-site solvent accessibility, while the dynamics of the active-site `capping residue' (IleCAT), a determinant of ligand binding, are influenced both by temperature and by the protonation state of AspCAT. A previously unobserved conformation of IleCATis seen in the elevated temperature series compared with 100 K structures. DFT calculations also show that the loss of a bound water ligand at the active site during the MSOX series is consistent with reduction of the type 2 Cu atom.

scholarly journals Interaction of the TonB dependent transporter HasR with its cognate TonB-like protein HasB in a membrane environment

2021 ◽  
Author(s):  
Kamolrat Somboon ◽  
Oliver Melling ◽  
Maylis Lejeune ◽  
Glaucia M.S. Pinheiro ◽  
Annick Paquelin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Protein Dynamics ◽  
Periplasmic Space ◽  
Geometrical Constraints ◽  
Flexible Region ◽  
Tonb Protein ◽  
Dynamics Simulations

Energized nutrient import in bacteria needs the interaction between a TonB-dependent transporter (TBDT) and a TonB protein. The mechanism of energy and signal transfer between these two proteins is not well understood. They belong to two membranes separated by the periplasmic space and possess each a disordered and flexible region. Therefore, the membranes, their distance and geometrical constraints together with the protein dynamics are important factors for deciphering this trans-envelope system. Here we report the first example of the interaction of a TBDT with a TonB protein in the presence of both membranes. By combining molecular dynamics simulations in a membrane model, in vitro and in vivo phenotypic experiments we obtained the comprehensive network of interaction between HasR, a heme/hemophore receptor and its dedicated TonB protein, HasB.

scholarly journals ROLE OF SUBSTRATE BINDING ON THE PROTEIN DYNAMICS OF AN ENDOGLUCANASE FROM FUSARIUM OXYSPORUM AT DIFFERENT TEMPERATURES

2018 ◽  
Vol 19 (1) ◽  
pp. 307-314
Author(s):  
ABDUL AZIZ AHMAD ◽  
Hamzah Mohd. Salleh ◽  
IBRAHIM ALI NOORBATCHA
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Fusarium Oxysporum ◽  
Protein Dynamics ◽  
Substrate Binding ◽  
Solvent Accessible Surface Area ◽  
Enzyme Complex ◽  
Different Temperatures ◽  
Endoglucanase I ◽  
Dynamics Simulations

: Thermostability is an important requirement for protein function, and one goal of protein engineering is improvement of activity of the enzymes at higher temperatures, particularly for industrial applications. Computational approaches to investigate factors influencing thermostability of proteins are becoming researchers’ choice. This study investigates the influence of substrate binding on the protein dynamics by comparing the molecular dynamics simulations of substrate-enzyme complex against un-bound enzyme, using endoglucanase I from Fusarium oxysporum. Endoglucanase-substrate complex was prepared by docking and molecular dynamics simulations were carried out at three different temperatures, 313 K, 333 K and 353 K. Our finding shows that the secondary structures for substrate-enzyme complex show more fluctuations relative to un-complexed structure. The same trend was observed for solvent accessible surface area and radius of gyration. At the highest temperature studied (353 K), the substrate-enzyme complex form showed the highest fluctuations. The fluctuations around the active site regions reach a minimum at the optimum temperature, compared to the other structural regions and other temperatures. ABSTRAK: Kestabilan (ketahanan) terhadap haba merupakan keperluan yang penting untuk fungsi protin, salah satu matlamat kejuruteraan protin adalah penambahbaikan aktiviti enzim pada suhu yang tinggi khususnya untuk aplikasi industri. Kini para penyelidik memilih kaedah komputasi, bagi mengkaji faktor yang mempengaruhi kestabilan terhadap haba. Kajian ini menyelidik pengaruh ikatan substrat pada protin dengan membandingkan simulasi molekular dinamik diantara substrat-enzim kompleks dan enzim sahaja, menggunakan endoglucanase I dari Fusarium oxysporum. Kompleks endoglucanase-substrat disediakan melalui kaedah docking dan simulasi molekular dinamik dilakukan pada suhu 313 K, 333 K dan 353 K. Kajian kami menunjukkan struktur sekunder bagi substrat-enzim kompleks kurang stabil berbanding enzim sahaja. Pola yang sama bagi luas permukaan boleh dicapai pelarut (SASA) dan jejari gyrasi. Pada suhu tertinggi dikaji (353 K), substrat-enzim kompleks paling tidak stabil. Pada suhu optimum, kadar ubah-ubah sekitar amino asid aktif adalah minimum berbanding struktur dan suhu lain.  

scholarly journals Druggability assessment of mammalian Per–Arnt–Sim [PAS] domains using computational approaches

MedChemComm ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 1126-1137 ◽  
Author(s):  
João V. de Souza ◽  
Sylvia Reznikov ◽  
Ruidi Zhu ◽  
Agnieszka K. Bronowska
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Protein Dynamics ◽  
Computational Approaches ◽  
P Protein ◽  
Dynamics Simulations

Protein dynamics finely tune the “druggability” of mammalian PAS-B domains, as assessed by atomistic molecular dynamics simulations and hotspot mapping.

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