Abstract
A study of isoleucines in protein structures solved using X-ray crystallography revealed a series of systematic trends for the two side-chain torsion angles χ1 and χ2 dependent on the resolution, secondary structure and refinement software used. The average torsion angles for the nine rotamers were similar in high-resolution structures solved using either the REFMAC, CNS or PHENIX software. However, at low resolution these programs often refine towards somewhat different χ1 and χ2 values. Small systematic differences can be observed between refinement software that uses molecular dynamics-type energy terms (for example CNS) and software that does not use these terms (for example REFMAC). Detailing the standard torsion angles used in refinement software can improve the refinement of protein structures. The target values in the molecular dynamics-type energy functions can also be improved.
Highlights
In 1991, Engh and Huber published their landmark article on bond lengths and bond angles (Engh & Huber, 1991)
Other authors have published parameters for planarities (Hooft, Sander et al, 1996b; Sychrovsky et al, 2009; MacArthur & Thornton, 1996) and torsion angles (Wang et al, 2008; Jones & Thirup, 1986; Clore & Kuszewski, 2002; Butterfoss et al, 2005; Hooft et al, 1997; Ponder & Richards, 1987; Dunbrack & Cohen, 1997; Lovell et al, 2000), while several groups have been working on the use of torsion angles in refinement software (Clore & Kuszewski, 2002; Berjanskii et al, 2006; Rice & Brunger, 1994; Brunger, 1992; Adams et al, 2010)
MacArthur & Thornton (1999) realised that the average observed values for side-chain torsion angles are resolution-dependent. They concluded that this is caused by the fact that low-occupancy alternate side-chain conformations are often not observable at low resolution, and hypothesized that refinement of a single conformation in density that reflects multiple conformations leads to systematic torsion-angle deviations
Summary
In 1991, Engh and Huber published their landmark article on bond lengths and bond angles (Engh & Huber, 1991) The parameters that they determined are used in most of today’s macromolecular software. Other authors have published parameters for planarities (Hooft, Sander et al, 1996b; Sychrovsky et al, 2009; MacArthur & Thornton, 1996) and torsion angles (Wang et al, 2008; Jones & Thirup, 1986; Clore & Kuszewski, 2002; Butterfoss et al, 2005; Hooft et al, 1997; Ponder & Richards, 1987; Dunbrack & Cohen, 1997; Lovell et al, 2000), while several groups have been working on the use of torsion angles in refinement software (Clore & Kuszewski, 2002; Berjanskii et al, 2006; Rice & Brunger, 1994; Brunger, 1992; Adams et al, 2010). They concluded that this is caused by the fact that low-occupancy alternate side-chain conformations are often not observable at low resolution, and hypothesized that refinement of a single conformation in density that reflects multiple conformations leads to systematic torsion-angle deviations
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