A Comparative Study of Human Saposins
Abstract
:1. Introduction
2. Results
2.1. Closed and Open Forms of Human Saposins: Structural and Surface Features
2.2. Closed and Open Forms of Human Saposins: Electrostatic Features
2.3. Open Forms of Human Saposins: Dynamic Features
3. Discussion
4. Materials and Methods
4.1. Structural Analyses
4.2. Structural Homology Modeling
4.3. Calculations of pKa and Protonation States
4.4. Poisson-Boltzmann Electrostatic Potentials
4.5. Molecular Dynamics Calculations
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Type | PDB Id | Title | Struct. | Conf. 1 | State | HET 2 | Occ 3 | Year | Ref. |
---|---|---|---|---|---|---|---|---|---|
Saposin A | 2DOB | Human SapA | Xray | Closed | Monom | Ca2+ | No | 2006 | [25] |
4UEX | Human SapA at lysosomal pH | Xray | Closed | Monom | - | Yes | 2015 | [26] | |
4DDJ | SapA in complex with LDAO | Xray | Open | Dimer | LDAO | No | 2012 | [11] | |
Saposin B | 1N69 | Human SapB with PEH | Xray | Open | Dimer | PEH | No | 2003 | [13] |
4V2O | Human SapB in complex with CLQ | Xray | Open | Dimer | CLQ | Yes | 2016 | [27] | |
Saposin C | 1M12 | Human SapC | NMR | Closed | Dimer | - | No | 2003 | [28] |
1SN6 | Human SapC in SDS micelles | NMR | Open | Monom | - | No | 2005 | [29] | |
2GTG | Human SapC | Xray | Closed | Monom | - | No | 2006 | [25] | |
2QYP | Orthorhombic crystal of SapC dimer | Xray | Open | Dimer | - | No | 2008 | [15] | |
2Z9A | Human SapC dimer | Xray | Open | Dimer | - | No | 2008 | [15] | |
Saposin D | 2RB3 | Human SapD | Xray | Closed | Dimer | - | Yes | 2008 | [15] |
2R0R | K9E variant of human SapD | Xray | Closed | Dimer | SO42− | Yes | 2008 | [15] | |
2R1Q | Iodinated SapD in space group C2221 | Xray | Closed | Dimer | IYR | No | 2008 | [15] | |
3BQP | Orthorhombic human SapD | Xray | Closed | Monom | Mg2+ | Yes | 2008 | [17] | |
3BQQ | Triclinic human SapD | Xray | Closed | Monom | - | Yes | 2008 | [17] |
Type | SapA | SapB | SapC | SapD |
---|---|---|---|---|
SapA | 100.0 | 23.08 | 39.74 | 36.71 |
SapB | 23.08 | 100.0 | 16.00 | 22.37 |
SapC | 39.74 | 16.00 | 100.0 | 34.18 |
SapD | 36.71 | 22.37 | 34.18 | 100.0 |
Type | PDB Id | Conf.2 | State | Number of | qT 3 | qT 1 at | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
E | D | R | K | H | pH = 7.0 | pH = 5.0 | pH = 4.5 | |||||
SapA | 2DOB | Closed | Monom | 8 | 7 | 1 | 6 | 0 | −8 | −8 | −8 | −3 |
4UEX | Closed | Monom | 8 | 7 | 1 | 6 | 0 | −8 | −8 | −8 | −2 | |
4DDJ | Open | Dimer1 4 | 8 | 7 | 1 | 6 | 0 | −8 | −8 | −6 | −1 | |
SapB | 1N69 | Open | Dimer2 4 | 5 | 6 | 2 | 3 | 2 | −6 | −9 (−6, −5) | −6 (−4, −4) | +1 (−1, 0) |
4V2O | Open | Dimer2 | 5 | 6 | 2 | 3 | 2 | −6 | −10 (−6, −4) | −8 (−4, −4) | −2 (−1, −1) | |
Model | Closed | Monom | 5 | 6 | 2 | 3 | 2 | −6 | −6 | −4 | −1 | |
SapC | 1M12 | Closed | Monom | 11 | 5 | 1 | 7 | 1 | −8 | −8 | −4 | +2 |
1SN6 | Open | Monom | 11 | 5 | 1 | 7 | 1 | −8 | −8 | −6 | +3 | |
2GTG | Closed | Monom | 11 | 5 | 0 | 7 | 1 | −9 | −9 | −8 | −1 | |
2QYP | Open | Dimer2 | 11 | 5 | 0 | 7 | 1 | −9 | −17 (−9, −8) | −6 (−6, −6) | +5 (+4, +2) | |
2Z9A | Open | Dimer2 | 11 | 5 | 0 | 7 | 1 | −9 | −18 (−9, −9) | −8 (−7, −6) | +1 (0, 0) | |
SapD | 2RB3 | Closed | Dimer2 | 8 | 4 | 1 | 7 | 0 | −4 | −8 (−4, −4) | −6 (−3, −3) | 0 (0, −2) |
2R0R 5 | Closed | Dimer2 | 9 | 4 | 1 | 6 | 0 | −6 | −12 (−6, −6) | −8 (−5, −5) | −2 (−2, −2) | |
2R1Q | Closed | Dimer2 | 8 | 4 | 1 | 7 | 0 | −4 | −8 (−4, −4) | −2 (−3, −3) | +3 (0, 0) | |
3BQP | Closed | Monom | 8 | 5 | 1 | 7 | 0 | −5 | −5 | −4 | 0 | |
3BQQ | Closed | Monom | 8 | 5 | 1 | 7 | 0 | −5 | −5 | −3 | −1 | |
Model | Open | Monom | 8 | 4 | 1 | 7 | 0 | −4 | −4 | −2 | +3 |
pH | FATCAT Rigid | CE | TM-Align | |||
---|---|---|---|---|---|---|
p-Value | RMSD1 | Z-Score | RMSD 1 | TM-Score | RMSD 1 | |
Saposin A | ||||||
7 | 4.02 × 10−5 | 6.48 | 4.25 | 5.75 | 0.407 | 3.41 |
5 | 2.08 × 10−9 | 3.71 | 4.74 | 3.99 | 0.579 | 3.26 |
4.5 | 1.01 × 10−8 | 4.00 | 4.58 | 4.22 | 0.563 | 2.62 |
Saposin B | ||||||
7 | 6.93 × 10−12 | 2.89 | 5.04 | 2.79 | 0.683 | 2.77 |
5 | 5.34 × 10−11 | 3.13 | 4.89 | 3.01 | 0.643 | 2.82 |
4.5 | 2.38 × 10−9 | 3.77 | 4.58 | 3.51 | 0.544 | 3.08 |
Saposin C | ||||||
7 | 3.22 × 10−5 | 5.87 | 3.89 | 2.81 | 0.463 | 3.39 |
5 | 1.40 × 10−8 | 3.09 | 4.89 | 2.66 | 0.686 | 2.83 |
4.5 | 2.44 × 10−8 | 3.21 | 4.89 | 3.44 | 0.582 | 3.29 |
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Garrido-Arandia, M.; Cuevas-Zuviría, B.; Díaz-Perales, A.; Pacios, L.F. A Comparative Study of Human Saposins. Molecules 2018, 23, 422. https://doi.org/10.3390/molecules23020422
Garrido-Arandia M, Cuevas-Zuviría B, Díaz-Perales A, Pacios LF. A Comparative Study of Human Saposins. Molecules. 2018; 23(2):422. https://doi.org/10.3390/molecules23020422
Chicago/Turabian StyleGarrido-Arandia, María, Bruno Cuevas-Zuviría, Araceli Díaz-Perales, and Luis F. Pacios. 2018. "A Comparative Study of Human Saposins" Molecules 23, no. 2: 422. https://doi.org/10.3390/molecules23020422