Loop modeling: Difference between revisions

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{{outdatedupdate|date=March 2015}}

'''Loop modeling''' is a problem in [[protein structure prediction]] requiring the prediction of the [[chemical conformation|conformations]] of [[loop (biochemistry)|loop]] regions in [[protein]]s with or without the use of a structural template. Computer programs that solve these problems have been used to research a broad range of scientific topics from [[Adenosine diphosphate|ADP]] to [[breast cancer]].<ref>{{cite journal|last=Perraud|first=AL |author2=Takanishi, CL |author3=Shen, B |author4=Kang, S |author5=Smith, MK |author6=Schmitz, C |author7=Knowles, HM |author8=Ferraris, D |author9=Li, W |author10=Zhang, J |author11=Stoddard, BL |author12=Scharenberg, AM|title=Accumulation of free ADP-ribose from mitochondria mediates oxidative stress-induced gating of TRPM2 cation channels.|journal=The Journal of Biological Chemistry|date=Feb 18, 2005|volume=280|issue=7|pages=6138–48|pmid=15561722|doi=10.1074/jbc.M411446200}}</ref><ref>{{cite journal|last=Baloria|first=U|author2=Akhoon, BA |author3=Gupta, SK |author4=Sharma, S |author5= Verma, V |title=In silico proteomic characterization of human epidermal growth factor receptor 2 (HER-2) for the mapping of high affinity antigenic determinants against breast cancer.|journal=Amino Acids|date=Apr 2012|volume=42|issue=4|pages=1349–60|pmid=21229277|doi=10.1007/s00726-010-0830-x}}</ref> Because protein function is determined by its shape and the physiochemical properties of its exposed surface, it is important to create an accurate model for protein/ligand interaction studies.<ref>{{cite journal|last=Fiser|first=A|author2=Sali, A |title=ModLoop: automated modeling of loops in protein structures.|journal=Bioinformatics (Oxford, England)|date=Dec 12, 2003|volume=19|issue=18|pages=2500–1|pmid=14668246|doi=10.1093/bioinformatics/btg362}}</ref> The problem arises often in [[homology modeling]], where the [[tertiary structure]] of an [[amino acid sequence]] is predicted based on a [[sequence alignment]] to a ''template'', or a second sequence whose structure is known. Because loops have highly variable sequences even within a given [[structural motif]] or [[protein folding|protein fold]], they often correspond to unaligned regions in sequence alignments; they also tend to be located at the [[solvent]]-exposed surface of [[globular protein]]s and thus are more conformationally flexible. Consequently, they often cannot be modeled using standard homology modeling techniques. More constrained versions of loop modeling are also used in the data fitting stages of solving a protein structure by [[X-ray crystallography]], because loops can correspond to regions of low [[electron density]] and are therefore difficult to resolve.

Regions of a structural model that are predicted by non-template-based loop modeling tend to be much less accurate than regions that are predicted using template-based techniques. The extent of the inaccuracy increases with the number of [[amino acid]]s in the loop. The loop amino acids' [[side chain]]s [[dihedral angle]]s are often approximated from a [[rotamer]] library, but can worsen the inaccuracy of side chain packing in the overall model. [[Andrej Sali]]'s homology modeling suite [[MODELLER]] includes a facility explicitly designed for loop modeling by a satisfaction of spatial restraints method. All methods require an upload of the [[Protein Data Bank (file format)|PDB]] file and some require the specification of the loop ___location.