TY - JOUR
T1 - Effects of compact volume and chain stiffness on the conformations of native proteins
AU - Hao, M. H.
AU - Rackovsky, S.
AU - Liwo, A.
AU - Pincus, M. R.
AU - Scheraga, H. A.
PY - 1992/7/15
Y1 - 1992/7/15
N2 - An investigation of the statistical properties of the native conformations of proteins, observed from crystal structures, is reported. Protein conformations were analyzed in terms of a bond vector correlation function and molecular volume. It was observed that, while the volume of a protein structure varies nearly linearly with the number of residues, the bond vector correlation function exhibits a universal feature for all sizes of proteins. To interpret the nature of the bond vector correlation function of native protein structures quantitatively, Monte Carlo simulations of realistic polypeptide chains of specific but arbitrary amino acid sequence were carried out. The molecule was constrained in an ellipsoidal volume determined by its chain length, and conformations with unacceptable nonbonded contacts between different amino acid residues were excluded. The interactions within a terminally blocked single residue, which correlate two nearest-neighbor peptide groups in a chain, were taken into account by an energetically biased sampling of its φ-ψ space. The simulated chain correlation functions were found to be in good agreement with those of the crystal structures of β-sheet-type and mixed-type (α + β) proteins of similar length. On the basis of these calculations, it is concluded that the observed conformations of these native proteins may arise from two basic factors: the compactness of structures under hydrophobic interactions and the intrinsic stiffness of polypeptide chains due to the interactions within each terminally blocked residue.
AB - An investigation of the statistical properties of the native conformations of proteins, observed from crystal structures, is reported. Protein conformations were analyzed in terms of a bond vector correlation function and molecular volume. It was observed that, while the volume of a protein structure varies nearly linearly with the number of residues, the bond vector correlation function exhibits a universal feature for all sizes of proteins. To interpret the nature of the bond vector correlation function of native protein structures quantitatively, Monte Carlo simulations of realistic polypeptide chains of specific but arbitrary amino acid sequence were carried out. The molecule was constrained in an ellipsoidal volume determined by its chain length, and conformations with unacceptable nonbonded contacts between different amino acid residues were excluded. The interactions within a terminally blocked single residue, which correlate two nearest-neighbor peptide groups in a chain, were taken into account by an energetically biased sampling of its φ-ψ space. The simulated chain correlation functions were found to be in good agreement with those of the crystal structures of β-sheet-type and mixed-type (α + β) proteins of similar length. On the basis of these calculations, it is concluded that the observed conformations of these native proteins may arise from two basic factors: the compactness of structures under hydrophobic interactions and the intrinsic stiffness of polypeptide chains due to the interactions within each terminally blocked residue.
KW - Bond vector correlation function
KW - Conformational statistics
KW - Monte Carlo simulation
KW - Regular structures
UR - http://www.scopus.com/inward/record.url?scp=0026716018&partnerID=8YFLogxK
U2 - 10.1073/pnas.89.14.6614
DO - 10.1073/pnas.89.14.6614
M3 - Article
C2 - 1631164
AN - SCOPUS:0026716018
SN - 0027-8424
VL - 89
SP - 6614
EP - 6618
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 14
ER -