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PDB ID	Description

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The structural classification of TMPad is derived from the SCOP database.

• • - Alpha and beta proteins (a/b) (1)
  • - Membrane and cell surface proteins and peptides (24)
  • - Low resolution protein structures (3)
  • - Peptides (1)

General Description

Helix-helix interactions are critical for folding, function, dynamics and oligomerization of membrane proteins, however the details of how these interactions establish the native protein conformations remain elusive. The TMPad (TransMembrane protein helix-Packing Database) addresses the above issues by integrating quantitative measures of helix-packing geometries with other sequence and structural information. This public repository serves as an information gateway for gaining insights into the relationship between helix-helix interactions and higher levels of organization in protein structure and function.

TMPad offers a collection of experimentally observed helix-helix interactions and related structural information of membrane proteins. Specifically, TMPad collects the geometric descriptors of helix-packing interface including residue contacts, interhelical distances and crossing angles, and helical rotational angles. In addition, TMPad also contains the corresponding sequence, topology, lipid accessibility, ligand and binding site information for each selected protein chain.

Each protein is shown with an overview of experimental details, comparison of complete and TM-only chains, structural and functional classifications, cross references, and sequence in FASTA format; for each selected chain of the protein, the topology information, helix-helix interactions, lipid accessibility, and binding sites are also shown in graphical representations and molecular visualization.

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Search

(i)Search by PDB ID or keywords

Proteins can be searched by their four-character PDB¹ IDs or by keywords in one or multiple fields of the following: (1) from the PDB file (the corresponding field name in TMPad): TITLE (Title), SOURCE (Source), KEYWDS (keywords), EXPDTA (Method), AUTHOR (Authors), JRNL (Key reference), (2) "Biological Process", "Cellular Component", or "Molecular Function" terms from Gene Ontology² (GO); accession number from UniProt³, Structural Classification of Proteins (SCOP) database⁴ keywords and (3) Ligand names. Users can perform a quick search by PDB IDs on the top left field on every page. If the search is by PDB ID, the result will be automatically directed to the Overview page. Users can also search by multiple keywords and more search fields can be added. An example is displayed when one of the above search types is selected. Note that the keyword search finds exact matches of the string entered, even if spaced by delimiters. The keyword search result is returned in a list of entries sorted in a descending order of relevance. The matched texts in the field by the keyword searched are highlighted in bold. Select a protein of interest from the search result to proceed to the Overview page.

(ii)Search by multiple identifiers

If the user already has a list of proteins and wishes to retrieve them by their PDB IDs, UniProt accession numbers/name, or GO terms or a combination of the above, they can do so by copying and pasting the identifiers into the text box. The search result is returned in a list of entries sorted in a descending order of relevance.

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Browse

Browse by SCOP classification

The database can be browsed and searched in a tree using the classification schemes according to the SCOP database⁴. Initially, the tree displays the top of the hierarchy and can be expanded by clicking on the + to show the sub-levels. The order of hierarchy shown, from top level to leaf-node level is Class>Fold>Superfamily>Family>Domain>Protein. The number in parenthesis indicates the number of immediate sub-level under the current level. If the tree at Protein level contains only one entry, the tree will expand automatically to the Species level. At the Species level, the PDB ID and chain number for a particular entry is shown with a link to retrieve the information.

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Overview

This is the default page for displaying the quick summary of an entry in the TMPad. The Overview page shows a static snapshot of the protein structure generated by PyMol⁵ and a summary of experimental details and annotations including PDB ID, Title, Source, Chain information, SCOP classification, Resolution (if by X-ray), R-factor (if by X-ray), Authors, Key Reference, Release Date and Cross References from records in PDB and PDBsum⁶. Inside the Chain (information), we list the comparison of the complete and TM-only chains and their corresponding UniProt and GO terms associated with each chain (if available). The associated GO terms of each chain can be further expanded. The key reference of the structure (if published) is listed and links to the article on PUBMED and its DOI are provided. The list of complete SCOP classification (if available) for each chain can also be expanded. In the cross reference, we provide links to external databases including PDB, PDBsum, PDBTM⁷, JenaLib⁸, OPM⁹, TOPDB¹⁰, UniProt, and GO databases. Related entries (released on an older date) for the current structure are also shown.

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Topology

For each entry, the topology (the number of TM helices and their orientations with respect to the membrane) of the chains making up the protein is shown. The constituent chains of each protein are taken from the BIOMOLECULE record in the PDB file. Additionally, only chains that have at least one TM helix is kept for topology and lipid accessibility calculations (two for helix-helix interactions). This does not apply for the ligand information and all chains including mainly non-TM domains are shown. The topology of the individual chains can be viewed by clicking on the chain letter/number. Here, the topology is derived from multiple sources. For helical locations and boundaries, we extracted the definitions by PDBTM. However, since the topology of every TM protein does not have full annotations, especially those of newly solved proteins, we derived this information from sources including OPM, TOPDB, and predictions by SVMtop¹¹, TOPCONS¹², and Memsat3¹³. We have divided the topology into 5 different evidence types depending on the information source:

Topology Evidence	Description
By OPM	By OPM only (100% sequence identity)
By TOPDB	By TOPDB only (100% sequence identity)
By similarity to OPM	By strong similarity (70% sequence identity) to OPM entries
By similarity to TOPDB	By strong similarity (70% sequence identity) to TopDB entries
By consensus prediction	By consensus (majority) prediction of SVMtop, TOPCONS, and Memsat3

For illustration, the topology of the selected chain is displayed in a cartoon, highlighting the inner (blue)/outer (red) sides of membrane, TM helices, and the sequence positions of the start and end of helices. The topology, sequence, start and end positions of helices, lengths, tilt angles and helical curvature classification are also shown in a table. The sequence positions here are indexed by the "SEQRES" field in the PDB, or as "Seq. Index". The tilt angles are calculated as the angle between the membrane normal and the principle helical axis. The helical curvature classification designates FOUR types of TM helices: "Linear", "Curved", "Kinked", or "None". We followed the same definition as used in HELANAL¹⁴ to classify helical geometries. Users can also examine the 3D structure of a selected TM helix in Jmol viewer. The chain sequence can be found at the bottom of the page, and there is an available option to label the sequence by topology.

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Helix-helix interactions

For each selected protein, only chains with at least one helix-helix interaction are shown. This includes any intra- or inter-chain helix-helix interactions. If no helix-helix interaction is found for a chain, this tab is automatically disabled.

NEW: Users now have the option to define helix-helix interactions by the minimum number of observed VDW contacts and the default value is 3. All contents on this page are automatically updated when a new cutoff is chosen.

(i)Summary

For each chain, the summary of helix-helix interactions found is shown in a table. The summary table lists the interacting helical pairs from the selected chain. Each helix of the entry is numbered using the chain letter, followed by a column and helix number in the order they appear in the sequence. For example, A:H1 denotes the first helix in chain A. For each helix-helix interaction the table also lists the orientation (anti-parallel or parallel), handedness, crossing angles, minimum distance between the closest C_α atoms, and the number of contacts found between the selected helical pair. The definition of contacts is described in the following section in (ii). This table can be further expanded upon clicking and the details of helix-helix interaction geometric descriptors will be shown as described in (iii). The structure plus the selected helical pair can be visualized using Jmol¹⁵, as described in (iv).

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(ii)Helical contacts

Here, a helix-helix interaction is defined as a pair of TM helices sharing one or more contacts satisfying the following two distance-based criteria: (i) the distance between C_β atoms of two residues, one from each helix, are less than 6Å, and (ii) the atomic distances between any two heavy atoms, one from each helix, are less than the sum of their van der Waals radii plus 0.6Å. These distance thresholds are also used by Walters and DeGrado¹⁶. We list the contact residues, their positions in the helix-packing details table. The helix-helix interactions graph on the right side of the page provides a top view of the helical interactions in the selected chain, where the nodes represent the TM helices, and the edges represent the interactions. Move the cursor of a node and its interacting partners will be highlighted in red, with the number of contacts with each partner labeled on the edge.

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(iii)Geometric descriptors of helix-helix interactions

By clicking on an interacting helical pair, the summary table can be expanded and the complete details of helix-packing geometric descriptors for the selected pair are shown. The information displayed includes the orientation, handedness, and crossing angle (Ω) of the helical pair; the rotational angle for each helix (α and β), and the scalar shift for each helix (s1 and s2). The minimal distances (D_min) between the selected helical pair are calculated on three different levels: between the closest C_α atoms, between any two atoms, and between the principle helical axes. The calculations of helical principal axis were based on the definitions by Chothia¹⁷, and Lee and Im¹⁸. The definitions for the helix-packing descriptors were derived from Pappu et al.¹⁹ The contact list shows the details of calculated contacts of the helical pair, where the total number of contacts, amino acid types, and sequence position are listed.

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Figure 1. Definitions of geometric descriptors of helix-helix interaction.

(iv)Structure visualization

Each structure in the TMPad can be examined by clicking on the Jmol icon in the expanded summary table. A Jmol viewer will initialize in a pop-up window on the right side of the page. The viewer displays the structure of the protein and the selected helical pair highlighted in yellow and blue. The PDB ID, chain number, helix number, and the positions are shown in the viewer. The sequence positions here are indexed by the residues available in the PDB structure or by "PDB index", where unstructured residues have been removed. The boundaries of the membrane planes, derived from PDBTM are shown in red (OUT) and grey (IN). We also provide options to show contacts in "spacefill" style for the selected helical pair and to hide non-interacting chains. The contacts are colored based on the physicochemical property of each amino acid: hydrophobic (green), polar (blue), aromatic (white), and charged (red).

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Lipid accessibility

The lipid accessibilities of the TM helical domains, and the molecular visualization of global lipid accessible surfaces, interior and exterior cavities can be accessed on the Lipid Accessibility page. Each of them is described below:

NEW: Users now have the option to define helix-helix interactions by the minimum number of observed VDW contacts. All contents on this page are automatically updated when a new cutoff is chosen.

(i)Lipid accessibility

The top view of the protein highlighting the helix-helix interactions and the relative lipid accessibility arranged in helical wheels are shown. The lipid accessibility is first calculated from the total lipid accessible area (LAA) per residue by using a probe radius of 2.0Å to simulate the -CH2- lipid tails using the NACCESS program²⁰. The relative lipid accessibility (RLA) of each residue is then calculated from LAA normalized by the reference value of accessible surface of the amino acid. Each residue is then colored in a scale between red (very buried; RLA=0-0.05) to dark blue (very exposed; RLA=0.75-1.00) in FIVE classes. The starting sequence position of each helix is also labeled. The lipid accessibility of each helix is shown in a helix-helix interaction graph, where the nodes represent and helices and the edges represent the interactions mediated by at least one residue pair contact. The edge is also labeled with the number of contact and crossing angle. On the top right corner, the box shows the composition viewer of RLA in each class from "very buried" to "very exposed" in a selected helix. The lower right corner shows the detailed single helical wheel and the amino acid types, and the direction of rotation for the selected helix. The first residue of the helix in the helical wheel is encircled in purple. To change the composition and single helical wheel view to another helix, roll the cursor over a new helix and both views will be updated.

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(ii)Lipid/Solvent accessible surface, cavities, and ligand visualization

The visualization of global lipid accessible surfaces, interior and exterior cavities, and ligand-binding sites of each protein can be viewed by Jmol. In a separate window by clicking on View TM Domain Surface and Cavities, the lipid accessibility surface is shown in blue wireframes and the boundaries of the membrane planes, derived from PDBTM are shown in red and grey. There is an option to show the selected protein chain in cartoon. We highlighted the interior cavities in yellow and exterior cavities (open pockets on the surface) in green. The cavity radius has been set to 1.2Å and for the envelop radius we set it to 10Å to define the outer limit of the molecule. These probe radii are set for finding interior and exterior cavities within Jmol visualization, respectively. The interior cavities do not extend to the outer surface while the exterior cavities may appear as open pockets on the outer surface.

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Ligands

The ligands category including any ions, small molecules, natural or synthetic compounds, protein scaffolds, nucleic acids, or peptides and the list of their binding residues were extracted from the HETATM fields in the PDB annotations or from the JenaLib database if this information was not available. We also derived the IUPAC names of each ligand from the JenaLib database and their corresponding common names (if available) from the DrugBank database²¹. Note that only the ligands that satisfy the side-chain contact distance criteria were selected for display. The page will automatically load and display the ligand view for the whole protein in Jmol and a list of ligands by type on the right side of the viewer. Click on "Reload" if the loading is not successful. The list can be expanded to reveal a collection of individual ligands with customized options for display. Each individual ligand can be selected by checking the boxin the list and displayed as singleton or jointly with other ligands. The selected ligand(s) will appear in the Jmol viewer initially with their probe spheres in wireframes and the labeled contact residues with interacting side-chains. Uncheck the box to hide the ligand(s) There are four additional options to customize this view: (i) ligands can be centered in the Jmol viewer by clicking on "Center"; (ii) the contact residues can be either shown or hidden; (iii) zoom in/out options on the structures can be selected on magnitudes of 0.8, 1.0, 1.5, 2.0, 3.0, 5.0, or 10.0 times of the original size; (iv) "Slab" mode can be selected at a preset scale of 60, or showing 60% of the model by visualizing the cross-section. On the lower part of the page, the complete list of ligands bound to the selected protein chain containing at least one TM domains is shown. This information is shown in a table, summarizing list of different types of ligands bound to the protein chain by its name (three-letter code), the number of counts, ligand type, and the full name in IUPAC standard. Each item in the table can be expanded by clicking on the field, and details are shown for each binding site. In the detailed view, each record contains the name, hetero sequence ID, binding-site residues and their and positions.

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References

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2. Ashburner, M., et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet, 25, 25-29.
3. Apweiler, R., et al. (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res, 38, D142-148.
4. Andreeva, A., et al. (2008) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res, 36, D419-425.
5. DeLano, W.L. (2002) The PyMOL Molecular Graphics System on World Wide Web. http://www.pymol.org
6. Laskowski, R.A. (2009) PDBsum new things. Nucleic Acids Res, 37, D355-359.
7. Tusnady, G.E., et al. (2005) PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res, 33, D275-278.
8. Reichert, J. and Suhnel, J. (2002) The IMB Jena Image Library of Biological Macromolecules: 2002 update. Nucleic Acids Res, 30, 253-254.
9. Lomize, M.A., et al. (2006) OPM: orientations of proteins in membranes database. Bioinformatics, 22, 623-625.
10. Tusnady, G.E., et al. (2008) TOPDB: topology data bank of transmembrane proteins, Nucleic Acids Res, 36, D234-239.
11. Lo, A., et al. (2008) Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function, J Proteome Res, 7, 487-496.
12. Bernsel, A., et al. (2009) TOPCONS: consensus prediction of membrane protein topology, Nucleic Acids Res, 37, W465-468.
13. Jones, D.T. (2007) Improving the accuracy of transmembrane protein topology prediction using evolutionary information, Bioinformatics, 23, 538-544.
14. Bansal, M., et al. (2000) HELANAL: a program to characterize helix geometry in proteins. J Biomol Struct Dyn, 17, 811-819.
15. Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org
16. Walters, R.F. and DeGrado, W.F. (2006) Helix-packing motifs in membrane proteins. Proc Natl Acad Sci U S A, 103, 13658-13663.
17. Chothia, C., et al. (1981) Helix to helix packing in proteins. J Mol Biol, 145, 215-250.
18. Lee, J. and Im, W. (2007) Implementation and application of helix-helix distance and crossing angle restraint potentials. J Comput Chem, 28, 669-680.
19. Pappu, R.V., et al. (1999) A potential smoothing algorithm accurately predicts transmembrane helix packing. Nat Struct Biol, 6, 50-55.
20. Hubbard,S.J. & Thornton, J.M. (1993), 'NACCESS', Computer Program, Department of Biochemistry and Molecular Biology, University College London.
21. Wishart, D.S., et al. (2008) DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res, 36, D901-906.