1. The RCSB Protein Data Bank Teaching an Old Dog New Tricks
Philip E. Bourne

2. A Tribute
From the guardian of a resource (institution) to all those men and women who make biology possible – may we never take you for granted
Biocurator Perspectives

3. Agenda The old dog New tricks
Thinking differently about proteins
Virtual Communities
Internal (wwPDB)
External
What will the resource look like in 2-5 years?

4. History of the Old Dog
1970s
Community discussions about how to establish an archive of protein structures
Cold Spring Harbor meeting in protein crystallography
PDB established at Brookhaven (October 1971; 7 structures)
1980s
Number of structures increases as technology improves
Community discussions about requiring depositions
IUCr guidelines established
Number of structures deposited increases
1990s
Ontology defined
Structural genomics begins
PDB moves to RCSB
2000s
wwPDB formed

5. History of the Old Dog
1970s
Community discussions about how to establish an archive of protein structures
Cold Spring Harbor meeting in protein crystallography
PDB established at Brookhaven (October 1971; 7 structures)
1980s
Number of structures increases as technology improves
Community discussions about requiring depositions
IUCr guidelines established
Number of structures deposited increases
1990s
Ontology defined
Structural genomics begins
PDB moves to RCSB
2000s
wwPDB formed

6. Unchanging Core Mission
Create and maintain a well-curated database of macromolecular structure data derived using experimental methods
that is…
Always accessible to a diverse user community worldwide
Developed in collaboration with that community
that will…
Facilitate and support scientific research and education

7. Challenges - Scientific
More complex structures – molecular machines, complexes
New methods (e.g. EM)
Lack of a vocabulary to provide reductionism in complex structures
Partially solved problems in analyzing structures – structure alignments, domain definitions, functional site determination and characterization, pathway relationships, interaction partners
Integrating microscopic and macroscopic views
Disease relationships

8. Growth and Complexity
Number of released entries
Year:

9. Data Integration Primary References Derived References Some Actions
Human Proteome &
Homology Models
Function Coverage
Target Selection
CATH
Domains/
Families
Source Organism Browser
CATH Browser
SCOP Browser
PFAM Display
Structure
SCOP
PFAM
Source
Organism
SWISS-PROT/
GenBank IDs
Pubmed
Enzyme
Commission
NCBI Taxonomy
Abstract Search
Enzyme Browser
Reactome
Gene Ontology
OMIM/
Disease
Genomes
(NCBI Gene)
Structural Genomics
Targets
Disease Browser
Target Search
Genome Browser
SNPs Mapped to Structure
Find Structures by SP ID
GO Browsers
Find Structures by GO ID
NAR 2005, 33: D233-D237

10. Challenges - Technical
Sheer numbers
Efficient visualization
Improved annotation
Demands from a more diverse user base
Centralization versus decentralization
Web V2

11. Diverse User Community (180,000 individuals per month) and Diversifying Further
Structural biologists
Computational biologists
Experimental biologists
Educators
Students
Lay public

12. Agenda The old dog New tricks
Thinking differently about proteins
Virtual Communities
Internal (wwPDB)
External
What will the resource look like in 2-5 years?

13. New Tricks – Protein Representation
The conventional view of a protein (left) has had a remarkable impact on our understanding of living systems, but is it time for a new view? It is not how one protein sees another after all.

14. Limitations of a Cartesian Viewpoint
A local viewpoint – does not capture the global properties of the protein
Limited to a single scale descriptor
Limits comparative analysis
New Tricks – Protein Representation

15. Protein Kinase A – Open Book View

16. Superfamily Members – The Same But Different

17. Alignment Violates the Triangle Inequality
Many of the features in the distance matrix may be due to “distortions” induced by the failure to satisfy the TI.
Poor distinguishing based on rmsd – illustrated by the breakdown of inequality
Protein kinase like superfamily. Left - rmsd distance matrix. Right – number of violations of the triangle inequality at each pair of proteins.
New Tricks – Protein Representation

18. An Alternative Approach: Multipolar Representation
Roots in spherical harmonics
Parameter space and boundary conditions can be a variety of properties
Order of the multipoles defines the granularity of the descriptors
Bottom line – interpreted as shape descriptors
Gramada & Bourne 2006 BMC Bioinformatics 7:242

19. Results – Protein Kinase Like Superfamily Alignment Scheeff & Bourne 2005 PLoS Comp. Biol., 1(5) e49
Clear distinction between families.
Some clustering seen inside TPKs that resemble various groups, even though there is little shape discrimination at this level.
New Tricks – Protein Representation

20. Possibilities – Structure Based Phylogenetic Analysis
Scheeff & Bourne
Multipoles
New Tricks – Protein Representation

21. New Tricks – Protein Motion
Structures exist in a spectrum from
order to disorder
Ordered
Structures
Disordered
Structures

22. Obtaining Protein Dynamic Information Protein Structures Treated as a 3-D Elastic Network
Bahar, I., A.R. Atilgan, and B. Erman
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential.
Folding & Design, (3): p
New Tricks – Protein Motion

23. Gaussian Network Model
Each Ca is a node in the network.
Each node undergoes Gaussian-distributed fluctuations influenced by neighboring interactions within a given cutoff distance. (7Å)
Decompose protein fluctuation into a summation of different modes.
New Tricks – Protein Motion

24. Functional Flexibility Score
Utilize correlated movements to help define regional flexibility with functional importance.
Functionally Flexible Score
For each residue:
Find Maximum and Minimum Correlation.
Use to scale normalized fluctuation to determine functional importance.
Gu, Gribskov & Bourne 2006 PLoS Comp. Biol. 2(7) e90

25. Identifying FFRs in HIV Protease
Gu, Gribskov & Bourne 2006 PLoS Comp. Biol. 2(7) e90

26. Other Examples BPTI and Calmodulin
Gu, Gribskov & Bourne 2006 PLoS Comp. Biol. 2(7) e90

27. Side Note: Gaussian Network Model vs Molecular Dynamics
GNM relatively course grained
GNM fast to compute vs MD
Look over larger time scales
Suitable for high throughput
New Tricks – Protein Motion

28. An Active Research Program Around the Resource is Good for the Resource

29. Agenda The old dog New tricks
Thinking differently about proteins
Virtual Communities
Internal (wwPDB)
External
What will the resource look like in 2-5 years?

30. Single worldwide archive of macromolecular structural data
Ensures that the PDB remains a single & uniform archive publicly available to the worldwide community
3 founding members: RCSB PDB, PDBj, MSD-EBI
Virtual Communities - Internal

31. wwPDB Activities Collaborative projects Remediation
taxonomy, ligands, literature
Single data processing system
Virtual Communities - Internal

32. Agenda The old dog New tricks
Thinking differently about proteins
Virtual Communities
Internal (wwPDB)
External (modeling, other….)
What will the resource look like in 2-5 years?

33. Virtual Communities - External
Consider the PDB a gathering point through which a virtual and real community interacts with each other around a common interest

34. Virtual Communities - External
Real
Traveling art exhibit for lay audiences
NJ Science Olympiad
Science Expo
Virtual
Website Tutorials/Feedback
Molecule of the Month
PDB-in-a-CAVE

35. Virtual Communities - Modelers
Recommendations of Workshop
PDB depositions should be restricted to atomic coordinates that are substantially determined by experimental measurements on specimens containing biological macromolecules
A central, publicly available archive (or technical equivalent thereof) or portal should be established for models
It was unanimously agreed that methods for assessing model quality are essential
Structure 2006 To be published

36. Agenda The old dog New tricks
Thinking differently about proteins
Virtual Communities
Internal (wwPDB)
External
What will the resource look like in 2-5 years?

37. What Will the Resource Look Like in the Next 2-5 Years?
Upwards of 75,000 structures
Consensus (and different) views at the micro and macro scale – domains, SNPs, gene structure, cell localization, pathways, interactions, post-translational modification…
Community annotation cf Wikipedia
Distributed subsets - External Reference Files (XML)
MyPDB
PDB-in-a-box
Specialized visualization tools (mbt.sdsc.edu)

38. Is a database really different than a biological journal?
The Knowledge and Data Cycle
0. Full text of PLoS papers stored
in a database
4. The composite view has
links to pertinent blocks
of literature text and back to the PDB
Is a database really different than a biological journal?
PloS Comp Biol (3) e34 4. 1.
3. A composite view of
journal and database
content results
1. A link brings up figures
from the paper 3.
Now assigning DOIs to
structures 2.
2. Clicking the paper figure retrieves
data from the PDB which is
analyzed

39. Acknowledgements The RCSB PDB NIH, NSF, DOE Apostol Gramada
Multipole Analysis
Jenny Gu
Protein Motions

40. A Protein is More than the Union of its Parts
Breaking the protein into parts changes the object of the comparison
This is interpreted in many cases to imply that the rmsd measure is inadequate.
The reality is that it is the aligning of structure that breaks the triangle inequality and not the measure per se. The reason for failure is that we effectively compare different objects then we say we do.
Transitivity is not guaraneteed
From Røgen & Fain (2003), PNAS 100:
New Tricks – Protein Representation

41. An Alternative Approach: Multipolar Representation Roots in Spherical Harmonics
Spatial distribution of
a scalar quantity
Parameterization
+ boundary conditions
Charge distribution
(i.e. structure)
Scalar
potential
Justifies use of multipoles as a distribution of charge also geometry of spatial distribution of atoms
Multipole expresses distortions in the spherical distribution
Gramada & Bourne 2006 BMC Bioinformatics 7:242
New Tricks – Protein Representation

42. An Alternative Approach: Multipolar Representation
“Out” Multipoles
For a given rank l, they form a 2l+1 dimensional vector under 3D rotations
Vector algebra applies => metric properties
Gramada & Bourne 2006 BMC Bioinformatics 7:242
New Tricks – Protein Representation

43. An Alternative Approach: Multipolar Representation
The multipoles can be interpreted as shape descriptors
In principle, from the entire series of multipoles one can reconstruct the scalar field and therefore the density, i.e the entire set of Cartesian coordinates, i. e. of the structure with a geometric level of detail
The partitioning of the multipole series according to various representation of the rotational group allows for a multi-scale description of the structure
Gramada & Bourne 2006 BMC Bioinformatics 7:242
New Tricks – Protein Representation