Recognition of errors in three‐dimensional structures of proteins

Abstract

A major problem in the determination of the three-dimensional structure of proteins concerns the quality of the structural models obtained from the interpretation of experimental data. New developments in X-ray crystallography and nuclear magnetic resonance spectroscopy have accelerated the process of structure determination and the biological community is confronted with a steadily increasing number of experimentally determined protein folds. However, in the recent past several experimentally determined protein structures have been proven to contain major errors, indicating that in some cases the interpretation of experimental data is difficult and may yield incorrect models. Such problems can be avoided when computational methods are employed which complement experimental structure determinations. A prerequisite of such computational tools is that they are independent of the parameters obtained from a particular experiment. In addition such techniques are able to support and accelerate experimental structure determinations. Here we present techniques based on knowledge based mean fields which can be used to judge the quality of protein folds. The methods can be used to identify misfolded structures as well as faulty parts of structural models. The techniques are even applicable in cases where only the C alpha trace of a protein conformation is available. The capabilities of the technique are demonstrated using correct and incorrect protein folds.

Six new candidate members of the α/β twisted open‐sheet family detected by sequence similarity to flavodoxin

“…The program PROSAII, employed for energy analysis of the structural models, was obtained from the Center of Applied Molecular Engineering (CAME), Salzburg, Austria (Sippl, 1993a(Sippl, , 1993b; PROSAII, PROtein Structure Analysis, version 2.0, instruction manual, 1994, copyright by CAME, Salzburg, Austria).…”

“…As an additional test of the hypothesis that the 6 proteins examined here have a flavodoxin fold, we used a recently developed knowledge-based potential function for residue-pair interactions (Sippl & Weitckus, 1992;Sippl, 1993a) to evaluate the unoptimized structural models implied by the alignment in Figure 1. These potentials are derived from empirical frequency distributions of CP-CP distances on the basis of Boltzmann's principle in order to describe the mean force field acting in a natively folded structure.…”

“…Because the potentials are derived from CP-CP distances, the method evaluates compatibility between amino acid sequence and main-chain topology independently of assumptions about the conformation of the side chains. The method has been shown to be sensitive to deliberately misfolded proteins and incorrectly modeled regions within experimentally determined native structures (Sippl, 1993a). Such regions correlate with positive peaks of the energy function, whereas correct structures typically give all-negative functions fluctuating between -2and -0.5 kcal/mol.…”

“…The program PROSAII tests all the possible conformations generated by sliding the input sequence along a hypothetical polyprotein of known structural domains. Z scores range between -5 and -10 for native proteins of about 150 residues, whereas incorrectly folded proteins typically give values between -2 and 5 kcal/mol (Sippl, 1993a). Table 1 reports the Z scores from the global energy values of the 6 sequences folded in the flavodoxin conformation, and those of the controls described above.…”

“…The Z scores derived from surface potentials (Sippl, 1993b) and from their combination with pair-interaction potentials are also shown in Table 1 aNative structures are indicated only by their PDB identifier, whereas models are indicated by the sequence name followed by the PDB identifier of the structure used as a template. Values were calculated from database screening with the program PROSAII (Sippl, 1993a). Z scores from pair interaction energy (pair), surface energy (surf), and combined energy (comb) (Sippl, 1993b).…”