Proceeding of the 4 th International Conference on Bioscience and Biotechnology, Vol. 4, 2019, pp. 11-15 Copyright © 2019 TIIKM ISSN 2513-2695 online DOI: https://doi.org/10.17501/25132695.2019.4102 Corresponding Author Email: *mfbhatti@asab.nust.edu.pk STRUCTURAL CHARACTERIZATION OF NPAS4-ARNT DIMERIZATION THROUGH COMPUTATIONAL SIMULATION Ammad Fahim 1 , Zaira Rehman 1 , Muhammad Faraz Bhatti* 1 , Nasar Virk 1 , Rehan Zafar Paracha 2 1 Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan 2 Research Centre of Modeling and Simulation (RCMS), National University of Sciences & Technology (NUST), Islamabad, Pakistan Abstract: Neuronal PAS Domain Protein 4 (Npas4) is an activity dependent transcription factor harboring basic helix-loop-helix (bHLH)-PAS domain, mediating the expression of target genes involved in neuro-transmission. NPAS4 crucially regulates response to various excitatory stimuli and has a role in GABAergic neuronal synapse development. Functionally, NPAS4 as a transcription factor dimerizes with the ARNT protein to serve as complete transcription factor and start the transcription of downstream genes. However, NPAS4 dimerization characteristics with ARNT has not been studied so far. Hence the current study aimed to identify the interaction pattern of NPAS4- ARNT complex through computational docking via HADDOCK. The interaction pattern were determined through pdbSum. The electrostatic surface calculations were performed through APBS plugins in PyMOL. The results indicated that PASB domain of NPAS4 is involved in interactions with the PAS B domain of ARNT. A toll of 136 structures generated by HADDOCK were further grouped into 14 clusters. The cluster with the minimum energy value of -82.6 KJ/mol was then further selected for interaction analysis. The results showed that there is one salt bridge, 12 H- bonding interactions and 156 non-bonded contacts between two proteins. The important interactions among two proteins are Asp224:NPAS4 and Gln421:ARNT, Asp229:NPAS4 and Ser442:ARNT, Glu232:NPAS4 and Thr361:ARNT, Phe240, Glu241:NPAS4, and Arg440:ARNT. The electrostatic potential of these two proteins revealed the binding interface of NPAS4 and ARNT to be neutral hence favoring hydrophobic interactions. The findings can help elucidate Npas4 role in interacting with other neuronal proteins involved in neuronal signaling. Moreover, the interaction findings provide useful comparative insight with other bHLH proteins. Keywords: NPAS4, bHLH proteins, dimerization, neurotransmission, molecular simulation Introduction NPAS4 is an immediate-early gene (IEG) which encodes a transcription factor specific to neurons. This transcription factor is involved in regulation of expression of a large number of genes that mediate diverse effects on synapses. It plays an important role as an early transcription factor which induces late response gene expression in both excitatory and inhibitory neurons. Structurally, NPAS4 belongs to basic Helix-Loop-Helix (HLH) PAS protein family. This protein is specific to, and is highly expressed in brain in response to excitatory activity in the synapse [1]. NPAS4 protein expression is partially induced by calcium influx in neurons. This protein is particularly important in development and repair of inhibitory synapses where it regulates the expression of genes depending on the activity of neuron. These activity-dependent genes are involved in controlling the number of GABA-releasing synapses formed on excitatory neurons. Inhibitory pathways require a balance between neuronal excitation and inhibition [2]. NPAS4 transcription factor regulate the expression of genes which participate in maintaining this balance. NPAS4 regulates and balances the modification of synapses formed on excitatory and inhibitory neurons according to their function within the neuronal circuit. In excitatory neurons NPAS4 promotes BDNF gene expression which controls GABA releasing synapses and increases number of inhibitory synapse formed on excitatory neurons. In inhibitory neurons NPAS4 promotes expression of genes which increase feedback inhibition thereby increasing excitatory input in inhibitory neurons [3]. This