Modeling Non-Peptide Structures ChemBE 414/614 Guest Lecture

The Big Picture “Form follows function.” Biology involves more than just proteins. We need to understand the “form” of more than just amino acid polymers.

Cellular Make-Up

Small Molecules Important to model for certain docking and design applications Two categories: – Ligands/Substrates Targets for binding proteins/antibodies (docking problems) Undergo chemistry within active sites (design problems) – Cofactors/Vitamins Do chemistry that AAs can’t do Can be thought of as part of the protein (holo vs. apo)

Cofactors Metals – act as strong positive charges for binding highly negative substrates, such as ATP – involved in electron- transfer reactions, such as oxidations/reductions

Cofactors Organic Cofactors/Vitamins – hydride transfers – methyl transfers – etc.

Modeling Challenges Sampling Scoring

The Sampling Problem Cartesian Coordinates vs. Internal Coordinates Not all torsions are created equal. – Linear vs. Branching – Backbone vs. Side Chains – Open vs. Closed Paths (i.e., Rings)

The Scoring Problem Physics-based approaches Statistics-based approaches

Macromolecules Biopolymers are made from repeating residues. – Protein/peptides Amino acids – DNA/RNA Nucleic acids – Carbohydrates Monosaccharides

CARBOHYDRATES Detailed Example

The Sampling Problem Oligo/Polypeptides effectively 2 main-chain torsions (φ, ψ) 1 side chain per residue (χs) no rings (w/ 1 exception) linear Oligo/Polysaccharides 2 or 3 main-chain torsions (φ, ψ, ω) multiple side chains per residue (χs) many ring conformers often branched 12 Glycans have many DoF to sample!

13 Sugar Topology in Rosetta φ(2) (1, BB, 1) (1, BB, 2) (1, BB, 3) (1, BB, 4) (1, BB, 5) 4 ψ(2) Drew et al. PLoS ONE 2013, 8, e Different linkages require different.params files. φ & ψ have unique definitions. NU records were added. CUT_BONDS and virtual atoms are required. VO5 VC1 reducing end maltotriose α- D -Glcp(1→4)-α- D -Glcp(1→4)- D -Glcp

Main-Chain Flexibility SmallMoverRingConformationMover 14

Branching & Conjugation N-linked 14-mer Glycolipid 15

The Scoring Problem 16 Grant & Woods Curr. Opin. Struct. Biol. 2014, 28C, 47–55. all φ/ψ from PDB (~42,000) -α- D -Glcp-(1→4)-α- D -Glcp- φ/ψ from PDB (~1,200) -α- D -Glcp-(1→4)-α- D -Glcp- φ/ψ from PDB (~1,200) φ ψ φ ψ 2-equatorial 3-axial 4-equatorial β (1′-equatorial) 2-axial 3-equatorial 4-axial α (1′-axial)

Tour of Residue Diversity Non-Canonical AAs (NCAAs)Problems & Solutions use unique topology files use unique rotamer libraries use peptide backbone- sampling use Ramachandran statistics can’t rely on Dunbrack statistics

Tour of Residue Diversity Post-Translational Modifications Problems & Solutions use patch files might be able to re-use rotamer libraries use peptide backbone-sampling use Ramachandran statistics might be able to use Dunbrack statistics potential difficult electrostatics

Tour of Residue Diversity D -Amino AcidsProblems & Solutions use opposite rotamers use peptide backbone- sampling use opposite Ramachandran statistics use opposite Dunbrack statistics

Tour of Residue Diversity β-Amino AcidsProblems & Solutions include extra backbone torsion use same rotamer libraries

Tour of Residue Diversity PeptoidsProblems & Solutions must use new rotamer libraries cis and trans ω must be allowed