PROJECT #19301 RESEARCH FOR MG2-ION-BINDING
FOLDING PERFORMANCE PROFILE

PROJECT SUMMARY

Atomistic insights into AAA+ protein superfamily ATPases Associated with diverse cellular Activities (AAA+) comprise a superfamily of proteins that perform a large variety of functions essential to cell physiology, including control of protein homeostasis, DNA replication, recombination, chromatin remodeling, ribosomal RNA processing, molecular targeting, organelle biogenesis, and membrane fusion.

Members of this superfamily are defined by the presence of what is termed the AAA+ domain containing the canonical Walker A and B motifs required for ATP binding and hydrolysis.

Typically, genomes encode approximately ten to several hundred AAA+ family members, each of which is thought to be adapted to specific functional niches that necessitate precise mechanisms of substrate recognition and processing.

The striking adaptive radiation of AAA+ proteins to operate in diverse settings illustrates the versatile utility of the AAA+ domain.

AAA+ proteins typically form hexameric complexes and act as motors to remodel other proteins, DNA/RNA, or multicomponent complexes.

Indeed, many chaperones and ATP-dependent proteases are or have subunits that belong to this superfamily.

Rubisco activase (Rca) belongs to the AAA+ superfamily of proteins and it hydrolyzes ATP to ADP.

The complementarity of nucleotide-binding sites between AAA+ interfaces, the mechanism of ATP hydrolysis and the conformational changes activating or deactivating their ATP-binding pocket ensure a functional cycle that creates mechanical force to promote remodeling of substrates.

In this study, we will investigated the ADP/ATP and Mg2+ ion binding mechanism in Rca monomer and homodimers using extensive longtime scale simulations.

We will also try to find the binding pathway for ADP and ATP.

Simulations will also helps to predicts the crucial residues that involved in this binding process..

PROJECT INFO

Manager(s): Rabindranath Paul

Institution: University of Illinois at Urbana-Champaign

PROJECT WORK UNIT SUMMARY

Atoms: 200,176

Core: OPENMM_22

Status: Public

PROJECT FOLDING PPD AVERAGES BY GPU

PPDDB data as of Sunday, 04 December 2022 18:13:18

Rank
Project
Model Name
Folding@Home Identifier
Make
Brand
GPU
Model
PPD
Average
Points WU
Average
WUs Day
Average
WU Time
Average
1 GeForce RTX 3090
GA102 [GeForce RTX 3090]
Nvidia GA102 7,463,005 255,043 29.26 0 hrs 49 mins
2 GeForce RTX 3080 Ti
GA102 [GeForce RTX 3080 Ti]
Nvidia GA102 6,183,167 240,224 25.74 0 hrs 56 mins
3 GeForce RTX 2080 Ti Rev. A
TU102 [GeForce RTX 2080 Ti Rev. A] M 13448
Nvidia TU102 5,285,281 228,618 23.12 1 hrs 2 mins
4 GeForce RTX 2080 Ti
TU102 [GeForce RTX 2080 Ti] M 13448
Nvidia TU102 5,228,619 228,390 22.89 1 hrs 3 mins
5 GeForce RTX 3080 Lite Hash Rate
GA102 [GeForce RTX 3080 Lite Hash Rate]
Nvidia GA102 5,156,812 225,795 22.84 1 hrs 3 mins
6 GeForce RTX 3070 Ti
GA104 [GeForce RTX 3070 Ti]
Nvidia GA104 4,568,035 218,128 20.94 1 hrs 9 mins
7 GeForce RTX 3070 Lite Hash Rate
GA104 [GeForce RTX 3070 Lite Hash Rate]
Nvidia GA104 4,279,480 214,363 19.96 1 hrs 12 mins
8 GeForce RTX 3070
GA104 [GeForce RTX 3070]
Nvidia GA104 3,982,444 208,507 19.10 1 hrs 15 mins
9 GeForce RTX 3060 Ti Lite Hash Rate
GA104 [GeForce RTX 3060 Ti Lite Hash Rate]
Nvidia GA104 3,165,724 192,734 16.43 1 hrs 28 mins
10 GeForce RTX 2080 Super
TU104 [GeForce RTX 2080 SUPER]
Nvidia TU104 3,076,286 191,775 16.04 1 hrs 30 mins
11 GeForce RTX 2060 Super
TU106 [GeForce RTX 2060 SUPER]
Nvidia TU106 2,425,511 176,293 13.76 2 hrs 45 mins
12 GeForce RTX 3060 Lite Hash Rate
GA106 [GeForce RTX 3060 Lite Hash Rate]
Nvidia GA106 2,194,980 169,617 12.94 2 hrs 51 mins
13 Quadro RTX 4000
TU104GL [Quadro RTX 4000]
Nvidia TU104GL 2,055,827 166,454 12.35 2 hrs 57 mins
14 Radeon RX 6800/6800 XT / 6900 XT
Navi 21 [Radeon RX 6800/6800 XT / 6900 XT]
AMD Navi 21 1,572,645 153,432 10.25 2 hrs 20 mins
15 GeForce RTX 2060
TU104 [GeForce RTX 2060]
Nvidia TU104 1,393,298 146,864 9.49 3 hrs 32 mins
16 GeForce GTX 1070 Ti
GP104 [GeForce GTX 1070 Ti] 8186
Nvidia GP104 1,372,519 146,999 9.34 3 hrs 34 mins
17 GeForce GTX 1070
GP104 [GeForce GTX 1070] 6463
Nvidia GP104 1,338,924 141,560 9.46 3 hrs 32 mins
18 GeForce GTX 1080
GP104 [GeForce GTX 1080] 8873
Nvidia GP104 1,178,770 139,166 8.47 3 hrs 50 mins
19 Tesla M40
GM200GL [Tesla M40] 6844
Nvidia GM200GL 1,160,055 137,484 8.44 3 hrs 51 mins
20 GeForce GTX 1660 SUPER
TU116 [GeForce GTX 1660 SUPER]
Nvidia TU116 1,131,782 136,467 8.29 3 hrs 54 mins
21 Radeon RX 5600 OEM/5600 XT/5700/5700 XT
Navi 10 [Radeon RX 5600 OEM/5600 XT/5700/5700 XT]
AMD Navi 10 961,960 129,100 7.45 3 hrs 13 mins
22 P104-100
GP104 [P104-100]
Nvidia GP104 885,332 127,004 6.97 3 hrs 27 mins
23 Radeon RX 6600/6600 XT/6600M
Navi 23 [Radeon RX 6600/6600 XT/6600M]
AMD Navi 23 294,505 85,192 3.46 7 hrs 57 mins
24 Radeon RX Vega 7
Lucienne [Radeon RX Vega 7]
AMD Lucienne 43,326 41,898 1.03 23 hrs 13 mins

PROJECT FOLDING PPD AVERAGES BY CPU BETA

PPDDB data as of Sunday, 04 December 2022 18:13:18

Rank
Project
CPU Model Logical
Processors (LP)
PPD-PLP
AVG PPD per 1 LP
ALL LP-PPD
(Estimated)
Make