Structural Basis for the Nucleic Acid Binding Cooperativity of Bacteriophage T4 Gene 32 Protein: The (Lys/Arg)3(Ser/Thr)2(LAST) Motif

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 89; no. 3; pp. 1050 - 1054
• Main Authors: Casas-Finet, Jose R., Fischer, Kenneth R., Karpel, Richard L.
• Format: Journal Article
• Language: English
• Published: Washington, DC National Academy of Sciences of the United States of America 01.02.1992; National Acad Sciences
• Subjects: Amino Acid Sequence; Amino acids; Analytical, structural and metabolic biochemistry; Base Sequence; Binding and carrier proteins; Biochemistry; Biological and medical sciences; Blue shift; Chromatography; Cooperation; DNA-Binding Proteins - chemistry; Fluorescence; Fundamental and applied biological sciences. Psychology; Macromolecular Substances; Molecular Sequence Data; Nuclear interactions; Nucleic acids; Peptides - chemistry; Polynucleotides; Protein Binding; Proteins; Spectrometry, Fluorescence; Structure-Activity Relationship; T-Phages - chemistry; Tryptophan - chemistry; Viral Proteins - chemistry; Peptides; Gene product; Molecular interaction; Myoviridae; Virus; Site specificity; Binding protein; T even phage; Synthetic product; N terminal-Sequence; Nucleic acid; Cooperative phenomenon; Phage; Phage T4
• DOI: 10.1073/pnas.89.3.1050
• ISSN: 0027-8424

To identify the functional residues of the N-terminal B region of bacteriophage T4 gene 32 protein involved in its cooperative binding to single-stranded nucleic acids, a process dependent on homotypic protein-protein interaction, we have studied the interaction of the protein with synthetic peptides containing different portions of this domain. Gel-permeation chromatography showed that a 6-acryloyl-2-dimethylaminonaphthalene (acrylodan)-labeled fluorescent peptide corresponding to the first 17 residues of gene 32 protein formed a complex with whole protein. The fluorescence was blue-shifted 14 nm upon interaction with intact protein, and somewhat less so (7-11 nm) with cleavage products of the protein lacking B domains. The intrinsic tryptophan fluorescence of whole and truncated protein was quenched by this peptide and by the nonderivatized peptide. The peptide bound tightly to truncated protein at both 0.015 and 0.44 M Na+, with a stoichiometry of 1:1. Similar tryptophan quenching or acrylodan blue shifts were obtained with peptides corresponding to residues 1-9 and 3-8, but not residues 1-4, 5-9, or 5-17, indicating that the essential amino acids are contained within positions 3-8, Lys-Arg-Lys-Ser-Thr-Ala. Several other DNA binding proteins contain a LAST motif with documented involvement of these residues in nucleic acid interaction. The amino acid and coding sequence of residues 110-114, a region proposed to be involved in nucleic acid binding, is virtually identical to that of residues 3-7. Based on these observations, we have formulated a model for the cooperative interactions of gene 32 protein with single-stranded nucleic acids.