Databanks + New tools = New insights THE AXIOM S imple A tom D epth I ndex C alculator protein fold barcoding CATH – ADAPT…

protein foldingBirth of the Earth Digging inside objects to discover their origins SADIC: a new tool to analyze atom depth

* Chakravarty S, Varadarajan R. Residue depth: a novel parameter for the analysis of protein structure and stability. Structure Fold Des : * Pintar A, Carugo O, Pongor S. Atom depth as a descriptor of the protein interior. Biophys J : atom depth calculated as the distance with: the closest external water* the closest dot of the water accessible surface* the closest surface exposed atom* atom depth HEWL 4lzt 2D

atom depth 2D Daniele Varrazzo, Andrea Bernini1, Ottavia Spiga, Arianna Ciutti, Stefano Chiellini,Vincenzo Venditti, Luisa Bracci and Neri Niccolai. Three-dimensional Computation of Atomic Depth in Complex Molecular Structures Bioinformatics : Calculation of exposed volumes 3D HEWL 4lzt 2D

atom depth Calculation of exposed volumes HEWL 4lzt 3D Daniele Varrazzo, Andrea Bernini1, Ottavia Spiga, Arianna Ciutti, Stefano Chiellini,Vincenzo Venditti, Luisa Bracci and Neri Niccolai. Three-dimensional Computation of Atomic Depth in Complex Molecular Structures Bioinformatics :

Calculation of exposed volumes Depth index: D i,r = 2V i,r / V 0,r where V i,r is the exposed volume of a sphere of radius r centered on atom i of the molecule and V 0,r is the exposed volume of the same sphere when centered on an isolated atom HEWL 4lzt atom depth 3D Daniele Varrazzo, Andrea Bernini1, Ottavia Spiga, Arianna Ciutti, Stefano Chiellini,Vincenzo Venditti, Luisa Bracci and Neri Niccolai. Three-dimensional Computation of Atomic Depth in Complex Molecular Structures Bioinformatics : the sphere radius r should have the biggest value which makes V i = 0 for the most buried atom

Thr 47 α carbon D i,9 = 1.59 Ile 58 α carbon D i,9 = 0.13 Trp 28 α carbon D i.9 = atom depth 3D vs 2D HEWL 4lzt

3D atom depth analysis from PDB ID 1UBQ DiDi

SBL Bioinformatics Projects Projects SADIC correlated: 1.fold dependent aa compositions of protein cores; 2.towards i-SADIC Projects SADIC uncorrelated: 1.systematic analysis of PPI

D i analysis of protein atoms defining strutural layers in protein 3D structures each strutural layer includes atoms with similar D i ’s fast and accurate analysis of aa content of structural layers

3 VTR (chitinolytic enzyme 572 aa) D i analysis of protein atoms

N 0.19 CA 0.30 C 0.25 O 0.23 CB 0.50 CG 0.68 CD 0.91 CE 1.11 NZ 1.29 K63 N 0.38 CA 0.52 C 0.50 O 0.52 CB 0.76 CG 0.95 CD 1.17 OE OE E24 3D atom depth analysis N 0.10 CA 0.05 C 0.11 O 0.18 CB 0.02 CG 0.02 CD CD L43 D imax from PDB ID 1UBQ

D imax analysis of protein residues defining aa occupancy in protein strutural layers each strutural layer includes residues with similar D imax ’s fast and accurate analysis of aa distribution in protein structures

D imax analysis of protein singles quite a few proteins like to stay single (at least in the crystalline state) Bioinformatiha 2, Firenze 18 ottobre -9

a database of protein singles Experimental Method: X-RAY (79,770) Chain Type: Protein (74,456) Only 1 chain in asym. unit: (28,803) Oligomeric state: 1 (21,193) Number of Entities: 1 (3,517) Homologue 95% identity (2,410) 2,410 proteins in the dataset 4,657,574 atoms 589,383 residues DOOPS:

a database of protein singles 2,410 proteins in the dataset 4,657,574 atoms 589,383 residues DOOPS: Swiss-Prot: 540,958 proteins in the dataset (192 Maa)

calculation of % amino acid content in L 0 the first quantitative analysis of a large array of protein cores! D imax analysis of protein cores 2,410 proteins; 4,657,574 atoms; 589,383 residues DOOPS: ~20 % of total molecular volume Σ DOOPS aa(L 0 ) = 106,088 (from 2410 proteins) core aa if D imax < 0.2

ClassArchitecturesTopology Homologous superfamily Domains 1 (mainly α) ,038 2 (mainly β) ,881 3 (α & β) ,029 4 (few sec. str.) ,588 Total ,536 D i analysis of protein cores folding clues from aa core composition? :

total Proteins mono 213 (84) 84 (40) 19 (17) 10 (3) 17 (13) 57 (37) 94 (73) 134 (110) 12 (12) 84 (73) 52 (44) 139 (106) (8) 49 (49) 1,190 (872) ( ) D i analysis of protein cores folding clues from aa core composition? # domain DOOPS + CATH selected Architectures with ≥ 10 PDB files :

Cys PDB ID 1UZK(A01) aa % average value (av) av + σ av + 2σ av - σ av - 2σ Towards protein folding barcodes ribbon Leu Phe PDB ID 1RG8(A00) trefoil Val PDB ID 2IMH(A01) four layer sandwich ClassArchitecturesTopology Homologous superfamily Total % L overall ALA 13,2810,3221,4612,749,2610,058,439,325,510,6910,0812,5811,8814,9512, ARG 0,61,280,241,3900,641,720,7500,551,111,750,30,470, ASN 0,672,620,732,771,852,041,771,3602,12,90,961,522,82, ASP 1,612,620,242,911,231,272,031,7902,12,93,021,772,340, CYS 3,352,995,370,8322,842,041,464,420,922,832,11,491,861,43, GLN 0,61,50,241,111,231,151,811,6900,461,562,150,991,41, GLU 1,481,440,731,5201,151,191,0400,912,592,411,080,930, GLY 8,058,729,7613,8516,059,9216,210,829,178,7811,8111,3512,6413,089, HIS 1,011,62,441,110,620,760,790,5602,651,963,021,910,472, ILE 12,689,9510,738,596,7913,6110,6810,7813,7612,811,7712,5311,537,0111, LEU 23,8818,3422,4411,778,0217,1812,9713,9833,9416,5411,914,3314,2215,4213, LYS 0,670,9101,1100,380,490,5600,090,621,360,5500, MET 2,624,171,714,9902,82,653,151,832,932,762,412,393,271, PHE 6,446,792,934,574,327,127,066,7315,67,224,956,186,074,216, PRO 1,342,463,412,633,093,3132,7803,292,91,842,251,41, SER 3,494,553,665,963,095,345,565,132,752,835,354,434,236,075, THR 2,284,814,157,25,563,315,124,470,923,25,224,254,945,145, TRP 1,011,5502,773,70,381,632,782,752,191,520,661,260,472, TYR 2,623,690,244,572,471,272,694,380,923,293,121,582,3202, VAL 12,349,689,517,629,8816,2812,7513,5111,9314,5312,8811,716,2919,1615, # PDB 213 (84) 84 (40) 19 (17) 10 (3) 17 (13) 57 (37) 94 (73) 134 (110) 12 (12) 84 (73) 52 (44) 139 (106) (8) 49 (49) 2,410 D i of 173,536 CATH domains 28 h, 5’ (average comp. time 1.72 s/domain) Calculations performed on 6 cores 990X CPU based computer Ala PDB ID 3CKC(A02) alpha horseshoe CATH-ADAPT CATHa da pt CATH - atom d epth a ssisted protein tomography

Towards protein folding barcodes Putting the protein universe in order

Towards protein folding barcodes Putting the protein universe in order

towards i-SADIC (implemented SADIC)

towards i-SADIC (implemented SADIC) H/D exchange rate profiles

towards i-SADIC (implemented SADIC) H/D exchange rate profiles D D D D D D D D D D D D D D

towards i-SADIC (implemented SADIC) H/D exchange rate profiles

towards i-SADIC (implemented SADIC) H/D exchange rate profiles

towards i-SADIC (implemented SADIC) H/D exchange rate profiles

2D atom depth or 3D atom depth H/D exchange rate profiles data from Pedersen TG, Thomsen NK, Andersen KV, Madsen JC, Poulsen FM. Determination of the rate constants k1 and k2 of the Linderstrom-Lang model for protein amide hydrogen exchange. A study of the individual amides in hen egg-white lysozyme. J Mol Biol (2): dnw i = or atom distance with the nearest water molecule D i,9 = or atom depth index with a probe od radius 9 Å

iSADIC atom depth 3D atom depth H/D exchange rate profiles data from Pedersen TG, Thomsen NK, Andersen KV, Madsen JC, Poulsen FM. Determination of the rate constants k1 and k2 of the Linderstrom-Lang model for protein amide hydrogen exchange. A study of the individual amides in hen egg-white lysozyme. J Mol Biol (2): D i,9 = or atom depth index with a probe od radius 9 Å iD i,9 = aD i,9 + bASA i cD i,9 + dDnw i

iSADIC atom depth 3D atom depth H/D exchange rate profiles iD i,9 = aD i,9 + bASA i cD i,9 + dDnw i

protein-protein interface analysis biological vs crystallographic interfaces

crystallographic dimers biological dimers

vs N ARG CA ARG C ARG O ARG CB ARG CG ARG CD ARG NE ARG CZ ARG NH1 ARG NH2 ARG H ARG HA ARG HB2 ARG HB3 ARG HG2 ARG HG3 ARG HD2 ARG HD3 ARG HE ARG HH11 ARG HH12 ARG HH21 ARG HH22 ARG N LYS CA LYS C LYS O LYS CB LYS CG LYS CD LYS CE LYS NZ LYS H LYS HA LYS HB2 LYS HB3 LYS HG2 LYS HG3 LYS HD2 LYS HD3 LYS HE2 LYS HE3 LYS HZ1 LYS HZ2 LYS HZ3 LYS