High-resolution structure of an HIV zinc fingerlike domain via a new NMR-based distance geometry approach

Journal Article · Tue Jan 16 04:00:00 EST 1990 · Biochemistry; (USA)

DOI:https://doi.org/10.1021/bi00454a005· OSTI ID:6698082

Summers, M F; South, T L; Kim, B ^[1]; Hare, D R ^[2]

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1. Univ. of Maryland Baltimore County (USA)
2. Hare Research, Inc., Woodinville, WA (USA)

A new method is described for determining molecular structures from NMR data. The approach utilizes 2D NOESY back-calculations to generate simulated spectra for structures obtained from distance geometry (DG) computations. Comparison of experimental and back-calculated spectra, including analysis of cross-peak buildup and auto-peak decay with increasing mixing time, provides a quantitative measure of the consistence between the experimental data and generated structures and allows for use of tighter interproton distance constraints. For the first time, the goodness of the generated structures is evaluated on the basis of their consistence with the actual experimental data rather than on the basis of consistence with other generated structures. This method is applied to the structure determination of an 18-residue peptide with an amino acid sequence comprising the first zinc fingerlike domain from the gag protein p55 of HIV. This is the first structure determination to atomic resolution for a retroviral zinc fingerlike complex. The peptide (Zn(p55F1)) exhibits a novel folding pattern that includes type I and type II NH-S tight turns and is stabilized both by coordination of the three Cys and one His residues to zinc and by extensive internal hydrogen bonding. The backbone folding is significant different from that of a classical DNA-binding zinc finger. The side chains of conservatively substituted Phe and Ile residues implicated in genomic RNA recognition form a hydrophobic patch on the peptide surface.

• OSTI ID: 6698082
• Journal Information: Biochemistry; (USA), Journal Name: Biochemistry; (USA) Vol. 29:2; ISSN 0006-2960; ISSN BICHA
• Country of Publication: United States
• Language: English

Related Subjects

550601* -- Medicine-- Unsealed Radionuclides in Diagnostics
62 RADIOLOGY AND NUCLEAR MEDICINE
AMINO ACID SEQUENCE
AMINO ACIDS
CARBOXYLIC ACIDS
CHEMICAL SHIFT
GEOMETRY
LEUCINE
MAGNETIC RESONANCE
MATHEMATICS
METALLOPROTEINS
MOLECULAR STRUCTURE
NUCLEAR MAGNETIC RESONANCE
NUCLEIC ACIDS
ORGANIC ACIDS
ORGANIC COMPOUNDS
OVERHAUSER EFFECT
PEPTIDES
PHENYLALANINE
PROTEINS
RESONANCE
RNA
ZINC COMPOUNDS