Reg : EOM structures and RDC refinement

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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vas2201
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Posts: 6
Joined: 2018.08.13 23:27

Reg : EOM structures and RDC refinement

#1 Post by vas2201 » 2018.08.14 00:00

Dear ATSAS users,

We are currently working on flexible protein (HNRNP proteins ), consist of two domains with the flexible linker. We would like to use EOM generated structures as starting structures for further RDC refinement using amber MD protocols. When we ran the EOM, it generated mainly three subsets of protein structures with different domain orientations with X2 value of 1.6 to 3.2 We knew that EOM can only represent the flexibility of the system. we aim to calculate the conformational ensemble that represents the flexibility of the system and validate both SAX and RDC data.

we are following the below protocol

EOM ---> Genrate 10000 PDBS ---> select the 50-100 pdbs with low X2 vlaue ---> Genrate the emap restaints for each pdb ---> RDC refinement (MAP constaints self-guided langevin dynamics) ---> extract the pdbs from trajectoy ---> select the set of pdbs (conformational ensemble) from MD trajectory which agree with both RDC and SAX.

However, I have few questions about EOM generated structures!

can we obtain the global orientation of the domains from the EOM generated structures, so that can we use these models ( which have low X2 value) for RDC refinement?.

is this is valid protocol to obtain the global orientation of the domains as starting models for or we should use any other method to validate the structures that refined with RDC data?

but we can't sure that whether those structures can be used as starting models for further refinement for the RDC (NMR restraints ) or not ?.

Thank you !

Eom OUT PUT
Ense Average Radius of gyration = 23.34
Ense Histogram Radius of gyration = 23.12
Pool Average Radius of gyration = 0.00
Pool Histogram Radius of gyration = 20.99
Rg Pool freq. Sel. freq.
16.26 0.0000000000 0.0000000000
16.47 0.0002000000 0.0000000000
16.68 0.0003600000 0.0000000000
16.89 0.0007800000 0.0000000000
17.11 0.0016400000 0.0000000000
17.32 0.0027400000 0.0000000000
17.53 0.0049800000 0.0003748828
17.74 0.0081800000 0.0003748828
17.95 0.0114600000 0.0013120900
18.16 0.0154000000 0.0026241799
18.38 0.0197400000 0.0035613871
18.59 0.0236800000 0.0048734770
18.80 0.0275800000 0.0088097470
19.01 0.0320200000 0.0129334583
19.22 0.0357800000 0.0185567010
19.43 0.0395600000 0.0262417994
19.65 0.0427200000 0.0346766635
19.86 0.0445600000 0.0429240862
20.07 0.0456000000 0.0476101218
20.28 0.0453600000 0.0476101218
20.49 0.0447600000 0.0438612933
20.70 0.0444400000 0.0404873477
20.92 0.0435200000 0.0335520150
21.13 0.0421600000 0.0284910965
21.34 0.0411800000 0.0236176195
21.55 0.0399000000 0.0202436739
21.76 0.0381000000 0.0146204311
21.98 0.0360400000 0.0095595127
22.19 0.0341600000 0.0058106842
22.40 0.0317800000 0.0043111528
22.61 0.0293200000 0.0031865042
22.82 0.0264800000 0.0022492971
23.03 0.0237200000 0.0020618557
23.25 0.0205200000 0.0011246485
23.46 0.0181000000 0.0005623243
23.67 0.0153400000 0.0059981256
23.88 0.0125800000 0.0106841612
24.09 0.0107000000 0.0134957826
24.30 0.0094400000 0.0134957826
24.52 0.0078000000 0.0258669166
24.73 0.0063200000 0.0202436739
24.94 0.0052400000 0.0181818182
25.15 0.0042400000 0.0256794752
Last edited by vas2201 on 2018.08.16 18:19, edited 1 time in total.

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Hayds
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Posts: 100
Joined: 2008.05.21 19:01
Location: EMBL, Hamburg

Re: Reg : EOM structures and RDC refinement

#2 Post by Hayds » 2018.08.16 11:15

Dear vas2201,

can you explain a little more what you mean by the "global orientation of the domains from the EOM structures" ?

I assume you don't mean the orientation of the domains relative to each other in each model as that is pretty straight forward. I'm not sure what you're after exactly.

Cheers,

hayds

vas2201
Member
Posts: 6
Joined: 2018.08.13 23:27

Re: Reg : EOM structures and RDC refinement

#3 Post by vas2201 » 2018.08.16 18:46

Dear Hayds,

Thanks for your reply! yes! I mean that global orientation of the domains is the orientation of the domains relative to each other in each model.

can we obtain the relative domain orientation from EOM structures or at least can we use those structures (the subset of structures which have low X2 values from EOM output) as starting models for further conformational sampling while doing MD that includes RDC data?

because our NMR data (T1, T2, HETNOE and molecular correlation time ) suggest that the molecular system is flexible and that agrees with EOM data. Since the two domains are tumbling independently, it is hard to obtain the single set of conformation that agrees with experimental data (SAX and RDC). So Our aim is to calculate the models (conformational ensemble) that better agree with NMR (RDC) and SAX data.

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