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2P-363 Computational Screening of Potential scaffold Proteins Using OCR-based Fingerprint
( Ganapathiraman Munussami ),이선구 한국공업화학회 2017 한국공업화학회 연구논문 초록집 Vol.2017 No.1
The OCR approach generates fingerprints for the family of protein under study by combining conserved residues obtained independently by three alignment methods, i.e. multiple sequence alignment, structure-based alignment and alignment based on the inter-strand hydrogen bonds. An ideal fingerprint was generated for these two superfamily of proteins by aligning the sequentially distant template sequences based on sequence, structure and inter-strand hydrogen bonding patterns independently. The resultant fingerprint was used to scan NR database and to identify potentially novel cystatin-like and lipocalins-like proteins. Finally, these identified proteins were validated by modeling strategies.
Ganapathiraman Munussami,Sriram Sokalingam,Dinesh kumar Sriramulu,이선구 한국공업화학회 2019 Journal of Industrial and Engineering Chemistry Vol.78 No.-
Lipocalins are potential targets for drug development, and therefore it is important to understand thecommon and distinct features of their ligand-binding sites. Here, the sequence and structural features ofligand-binding sites in kernel and outlier lipocalins were analyzed and compared. Ligand-binding sites ofkernel lipocalins were sequentially more diverse than outlier lipocalins. The ligand-binding sites of the twosubgroup lipocalins were relatively hydrophobic and exhibited positive or neutral net-charges, well-correlated with the hydrophobic ligands with neutral or acidic functional groups. There was a propensity ofthree hydrophobic residues, Phe, Leu and Tyr in the ligand-interacting residues of kernel lipocalins, whereasoutlierlipocalins showed relatively lower propensity. Finally, six and ten crucial ligand-interacting positionswere identified in the kernel and outlier lipocalins, respectively. These identified features are expected to bea theoretical reference for the engineering and exploration of kernel and outlier lipocalins.
Ganapathiraman Munussami,Sriram Sokalingam,Sun-Gu Lee 한국생물공학회 2020 KSBB Journal Vol.35 No.2
The incessant expansion of protein sequence data presents a huge challenge in the identification of their structures which relies on laborious and time-consuming experimental approaches. Homology modeling of protein structure is highly accepted as an alternative to experimental approach, but its efficacy tends to decline when the sequence homology between the target and template sequences is low due to the limitation of their sequence alignment. Here, we demonstrated that employing a structure-based fingerprint of a homologous protein set as a constraint for the alignment of distant template and target sequences could improve the efficiency of homology modeling by using lipocalin proteins as a model system. Nine distantly related kernel lipocalins were structurally aligned, which was used to design a structure-based fingerprint consisting of commonly conserved hydrophobic and hydrophilic residues. The fingerprint was introduced as constraint in the alignment of template and target lipocalins, and the homology modeling of target lipocalin was performed based on the aligned sequences. Although the efficiency was marginal, the approach showed a consistent improvement compared to the homology modeling of lipocalin structures without the constraint for sequence alignment.