Structural proteomics Handouts. Proteomics section from book already assigned.

What is structural proteomics/genomics? High-throughput determination of the 3D structure of proteins Goal: to be able to determine or predict the structure of every protein. –Direct determination - X-ray crystallography and nuclear magentic resonance (NMR). –Prediction Comparative modeling - Threading/Fold recognition Ab initio

Why structural proteomics? To study proteins in their active conformation. –Study protein:drug interactions –Protein engineering Proteins that show little or no similarity at the primary sequence level can have strikingly similar structures.

An example FtsZ - protein required for cell division in prokaryotes, mitochondria, and chloroplasts. Tubulin - structural component of microtubules - important for intracellular trafficking and cell division. FtsZ and Tubulin have limited sequence similarity and would not be identified as homologous proteins by sequence analysis.

Burns, R., Nature 391: Picture from E. Nogales FtsZ and tubulin have little similarity at the amino acid sequence level

Are FtsZ and tubulin homologous? Yes! Proteins that have conserved secondary structure can be derived from a common ancestor even if the primary sequence has diverged to the point that no similarity is detected.

Current state of structural proteomics As of Feb ,500 structures –Only 1600 non-redundant structures To identify all possible folds - predicted another 16,000 novel sequences needed for 90% coverage. –Of the 2300 structures deposited in 2000, only 11% contained previously unidentified folds. Overall goal - directly solve enough structures directly to be able to computationally model all future proteins.

Protein domains - structure “clearly recognizable portion of a protein that folds into a defined structure” –Doesn’t have to be the same as the domains we have been investigating with CDD. –RbsB proteins as an example.

Main secondary structure elements  -helix - right handed helical structure  -sheet - composed of two or more  -strands, conformation is more “zig-zag” than helical.

Images from

Folds/motifs - tertiary structure How these secondary structure elements come together to form structure. –Helix-turn-helix Determining the structure of nearly all folds is the goal of structural biology

Quaternary structure Refers to the structure formed by more than one polypeptide. Many proteins function as complexes - best to know the structure of the complex rather than each individual –Proteins may have different conformations when in a complex vs. alone.

X-Ray Crystallography Make crystals of your protein – mm in size –Proteins must be in an ordered, repeating pattern. X-ray beam is aimed at crystal and data is collected. Structure is determined from the diffraction data.

Image from

Schmid, M. Trends in Microbiolgy, 10:s27-s31.

X-ray crystallography Protein must crystallize. –Need large amounts (good expression) –Soluble (many proteins aren’t, membrane proteins). Need to have access to an X-ray beam. Solving the structure is computationally intensive. Time - can take several months to years to solve a structure –Efforts to shorten this time are underway to make this technique high-throughput.

Nuclear Magnetic Resonance Spectroscopy (NMR) Can perform in solution. –No need for crystallization Can only analyze proteins that are <300aa. –Many proteins are much larger. –Can’t analyze multi-subunit complexes Proteins must be stable.

Structure modeling Comparative modeling –Modeling the structure of a protein that has a high degree of sequence identity with a protein of known structure –Must be >30% identity to have reliable structure Threading/fold recognition –Uses known fold structures to predict folds in primary sequence. Ab initio –Predicting structure from primary sequence data –Usually not as robust, computationally intensive

Structure of the ribosome Ribosome - made up of 3 RNA molecules and over 50 proteins. Structure of the 70S ribosome solved by combining several models of the individual 30S and 50S subunits

Bacterial ribosome Ribosome is a 2.3 MDa complex –50S and 30S subunits –54 proteins and 3 RNAs (23S, 16S, and 5S RNAs) –Can account for ~50% of cell mass during rapid growth. –Major target for many antibiotics. Ribosome is a ribozyme! Ramakrishnan (2002) Cell. 108: