Abstract
Two new proteins of approximately 70 amino acids in length, corresponding to an unnaturally-linked N- and C-helix of the ectodomain of the gp41 protein from the human immunodeficiency virus (HIV) type 1, were designed and characterized. A designed tripeptide links the C-terminus of the C-helix with the N-terminus of the N-helix in a circular permutation so that the C-helix precedes the N-helix in sequence. In addition to the artificial peptide linkage, the C-helix is truncated at its N-terminus to expose a region of the N-helix known as the “Trp-Trp-Ile” binding pocket. Sedimentation, crystallographic, and nuclear magnetic resonance studies confirmed that the protein had the desired trimeric structure with an unoccupied binding site. Spectroscopic and centrifugation studies demonstrated that the engineered protein had ligand binding characteristics similar to previously reported constructs. Unlike previous constructs which expose additional, shallow, non-conserved, and undesired binding pockets, only the single deep and conserved Trp-Trp-Ile pocket is exposed in the proteins of this study. This engineered version of gp41 protein will be potentially useful in research programs aimed at discovery of new drugs for therapy of HIV-infection in humans.
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Acknowledgment
This manuscript is dedicated to Yvonne Connolly Martin. The precepts of molecular properties and architectures promulgated by Yvonne in 41 years at Abbott extend even to the level of protein design. All of the authors thank her for being a steadfast source of inspiration and scientific role-model of the highest degree. Crystallographic data were collected at beamline 17-ID in the facilities of the Industrial Macromolecular Crystallography Association Collaborative Access Team (IMCA-CAT) at the Advanced Photon Source. These facilities are supported by the companies of the Industrial Macromolecular Crystallography Association.
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Stewart, K.D., Steffy, K., Harris, K. et al. Design and characterization of an engineered gp41 protein from human immunodeficiency virus-1 as a tool for drug discovery. J Comput Aided Mol Des 21, 121–130 (2007). https://doi.org/10.1007/s10822-007-9107-1
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DOI: https://doi.org/10.1007/s10822-007-9107-1