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pH-Dependent conformational stability of SpeB from Thermus thermophilus HB8: insights from molecular dynamics simulation

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journal contribution
posted on 2023-11-20, 18:01 authored by Malaisamy Veerapandian, Nagarajan Hemavathy, Alagesan Karthika, Jayaraman Manikandan, Umashankar Vetrivel, Jeyaraman Jeyakanthan

N(1)-aminopropyl agmatine ureohydrolase (SpeB) is considered an essential enzyme for the growth and survival of thermophiles, it is involved in the biosynthesis of polyamines. The present study investigates the conformational stability and flexibility of Thermus thermophilus HB8 SpeB and its interactions with substrate, N1-aminopropyl agmatine at different physiological conditions to probe the optimal conditions that provide insights on biotechnological applications. As the 3D structure of SpeB is yet to be crystallized, it was modelled and validated using structural bioinformatics methods. To understand the conformational dynamics and also to assess the impact of pH and temperature variables on the tertiary structure of SpeB , atomistic molecular dynamics simulation (MDS) was employed. The MD investigation revealed that 300 K is not optimal for SpeB (apo form) at both acidic pH 4.5, and alkaline pH 8.5, since it exhibited decreased stability and compactness with higher residual flexibility. Further, the stable and strong binding of N1-aminopropyl agmatine with SpeB was observed at following conditions, neutral pH 7 at 353.15 K and alkaline pH 11 at 300 K. Thus, this in silico study provides significant insights into the structural investigations on SpeB along with optimal pH as well as temperature for its ideal enzymatic function.


This work was supported by Department of Science and Technology (DST) -INDO-TAIWAN: [Grant No. GITA/DST/TWN/P-86/2019]; Department of Biotechnology (DBT) -Bioinformatics Centre: [Grant No. (BIC)-No.BT/PR40154/BTIS/137/34/2021]; Ministry of Human Resource Development- Rashtriya Uchchatar Shiksha Abhiyan (MHRD-RUSA 2.0) : [Grant No. F.24e51/2014-U, Policy (TNMulti-Gen)]; Tamil Nadu State Council for Higher Education (TANSCHE) : [Grant No. RGP/2019-20/ALU/HECP-0049 dated:27/04/2021]; Department of Science and Technology (DST)-Promotion of University Research and Scientific Excellence (PURSE phase II): [Grant No. SR/PURSE Phase 2/38 (G), 2017]; Department of Biotechnology- National Network Project (DBT-NNP) [Grant No. BT/PR40156/BTIS/137/54/2023]; Department of Science and Technology (DST)-Fund for Improvement of S&T Infrastructure in Universities & Higher Educational Institutions (FIST): [Grant No. (SR/FST/LSI-667/2016) (C)].