Correction

This article refers to:

Structural insight into GRIP1-PDZ6 in Alzheimer’s disease: study from protein expression data to molecular dynamics simulations

Article title: Structural insight into GRIP1-PDZ6 in Alzheimer’s disease: study from protein expression data to molecular dynamics simulations

Authors: Paulami Chatterjee & Debjani Roy

Journal: TBSD: Journal of Biomolecular Structure and Dynamics

Bibliometrics: Volume 35, Number 10, pages 2235- 2247

DOI: http://dx.doi.org/10.1080/07391102.2016.1214085

When this article was first published, there were errors present in Tables 2, 3, 4 and 5. These tables have now been corrected in the online version of the journal and the correct versions have also been reproduced below.

Table 2: Hydrogen bonding pattern of Liprin-alpha residues in 100 ns simulated peptide bound dimer*.

Liprin-alpha residues, atom	Protein residues, atom	Distance, in Å
Arg-4 C, O	Gly-688 A, N	2.99
Tyr-6 C, N	Ile-686 A, O	2.91
Tyr-6 C, OH	Gln-740 A, OE1	3.26
Tyr-6 C, O	Ile-686 A, N	2.83
Cys-8 C, N	Ile-684 A, O	2.93
Ala-1 D, N	Gly-688 B, O	2.99
Thr-2 D, N	Ser-687 B, OG	3.01
Thr-2 D, OG1	Gly-688 B, N	3.42
Thr-2 D, OG1	Arg-4 D, O	2.86
Arg-4 D, NH1	Tyr-6 D, OH	3.08
Tyr-6 D, N	Ile-686 B, O	3.30
Tyr-6 D, O	Ile-686 B, N	2.72
Ser-7 D, OG	Thr-685 B, OG1	2.77
Ser-7 D, OG	Gly-683 B, O	3.38
Cys-8 D, N	Ile-684 B, O	3.18

*Hydrogen bond distances were calculated between the hydrogen bond donor and acceptor atoms (heavy atom to heavy atom) in PyMOL. Hydrogen bonds maintained throughout the simulation are shown in bold.

Table 3: Hydrogen bonding patterns of selected residues present within the 5Å radius of peptide recognition helix in the 100 ns peptide bound and peptide free dimers ^ξ*.

Chain A Residue, atom	Chain A Residue, atom	Distance, Peptide bound, in Å	Chain A Residue, atom	Chain A Residue, atom	Distance, Peptide free, in Å
Pro-731, O	Ala-735, N	3.10	Pro-731, O	Ala-735, N	2.94
Leu-732, N	Thr-689, O	2.70	Ser-733, OG	His-737, NE2	3.01
Leu-732, O	Ile-736, N	3.02	Leu-732, O	Ile-736, N	2.97
Ser-733, N	Glu-690, OE2	2.96	Ser-733, O	His-737, N	2.94
Ser-733, OG	Glu-690,OE1	2.96	Glu-734, N	Lys-730, O	2.88
Glu-734,OE1	His-737, NE2	3.06	Glu-734, OE1	Lys-728, N	2.93
Ile-736, O	Gln-740, N	2.77	Glu-734, OE2	Lys-730, N	3.31
His-737, ND1	Leu-738, N	2.93	Glu-734, O	Leu-738, N	3.19
			His-737, O	Met-741, N	2.95

Chain B Residue, atom	Chain B Residue, atom	Distance, Peptide bound, in Å	Chain B Residue, atom	Chain B Residue, atom	Distance, Peptide free, in Å
Pro-731, O	Ala-735, N	2.60	Pro-731, O	Ala-735, N	3.02
Pro-731, O	Glu-734, N	2.90	Leu-732, O	Ile-736, N	2.57
Leu-732, O	Ile-736, N	2.98	Ser-733, OG	His-737, NE2	3.48
Ser-733, OG	Glu-734, N	2.84	Ser-733, O	His-737, N	2.75
Ser-733, OG	Glu-734,OE1	2.70	Glu-734, O	Leu-738, N	2.91
Ser-733, OG	Glu-734, OE2	3.49	Ile-736, O	Gln-740, N	2.85
Ser 733, O	His 737, N	3.03	His-737, O	Met-741, N	2.95
Glu-734, O	Leu-738, N	3.13
Ile-736, O	Gln-740, N	2.94
His-737, ND1	Gln-740, NE2	3.15
His-737, O	Met-741, N	2.74

ξ Residues showing significant SASA changes are only shown here.

*Hydrogen bond distances were calculated between the hydrogen bond donor and acceptor atoms (heavy atom to heavy atoms) in PyMOL. Hydrogen bonds, maintained throughout the simulation (in comparison to the crystal structure) are shown in italics. Hydrogen bonds, newly evolved in the simulated structure (in comparison to the crystal structure) are shown in bold.

Table 4: Hydrogen bonding patterns of dimeric interface residues of 100 ns simulated peptide bound dimer (chain A) and peptide free dimer (chain A)*.

Peptide bound Chain A Residue, atom	H-bonded Residue, atom	Distance in Å	Peptide free Chain A, Residue, atom	H-bonded Residue, atom	Distance in Å
Ile-670 A, O	Lys-676 B, N	2.80	Ile-670 A, N	Ala-668 A, O	2.86
Tyr-671 A, N	Ile-750 A, O	2.76	Tyr-671 A, N	Ile-750 A, O	3.00
Tyr-671 A, OH	Ala-712 A, O	3.31	Tyr-671 A, OH	Ala-712 B, N	2.95
Tyr-671 A, O	Ile-750 A, N	3.15	Tyr-671 A, OH	Asp-717 A, OD2	2.81
Thr -672 A, N	Glu-674 B, O	3.12	Tyr-671 A, O	Ile-750 A, N	3.15
Thr-672 A, O	Glu-674 B, N	2.84	Thr-672 A, O	Glu-674 B, N	3.04
Val-673 A, N	Leu-748 A, O	2.94	Val-673 A, N	Leu-748 A, O	2.81
Val-673 A, O	Leu-748 A, N	3.06	Val-673 A, O	Leu-748 A, N	3.19
Glu-674 A, N	Thr-672 B, O	3.14	Glu-674 A, N	Thr-672 B, O	2.91
Glu-674 A, O	Thr-672 B, N	3.08	Glu-674 A, OE2	Thr-672 B, N	3.02
Glu-674 A, O	Thr-672 B, OG1	3.18	Glu-674 A, OE2	Thr-672 B, OG1	2.61
Leu-675 A, N	Val-746 A, O	2.86	Leu-675 A, N	Val-746 A, O	2.91
Leu-675 A, O	Val-746 A, N	2.77	Leu-675 A, O	Val-746 A, N	2.59
Lys-676 A, N	Ile-670 B, O	3.33	Lys-676 A, N	Thr-710 A, OG1	2.97
Ala-712 A, O	Tyr-671 A, OH	3.31	His-714 A, N	Gly-711 B, O	2.82
His-714 A, N	Asp-717 A, OD2	2.92	His-714 A, ND1	Leu-701 A, N	3.08
Ile-715 A, O	Ser-700 A, N	3.30	Ile-715 A, O	Asp-717 A, N	3.08
Asp-717 A, N	Ile-698 A, O	3.15	Gly-716 A, N	Ile-698 A, O	2.71
Asp-717 A, O	Ile-698 A, N	3.12	Asp-717 A, OD2	Tyr-671 A, OH	2.81
			Asp-717 A, OD2	Gly-711 B, N	2.88
			Asp-717 A, O	Ile-698 A, N	2.95

*Hydrogen bond distances were calculated between the hydrogen bond donor and acceptor atoms (heavy atom to heavy atoms) in PyMOL.

Hydrogen bonds newly appeared in 100 ns simulated peptide bound dimer compared to the crystal structure. Hydrogen bonds present in peptide bound dimer and absent in peptide free dimer are shown in bold. Hydrogen bonds, maintained throughout the simulation (in comparison to the crystal structure) are shown in italics. All dimeric interface residues (βA strand: residues 670-676 and αA-βD loop: residues 712-717) were taken into consideration for studying their hydrogen bonding pattern.

Table 5: Hydrogen bonding patterns of dimeric interface residues of 100 ns simulated peptide bound dimer (chain B) and peptide free dimer (chain B)*.

Peptide bound Chain B Residue, atom	H-bonded Residue, atom	Distance in Å	Peptide free Chain B Residue, atom	Residue	Distance in Å
Ile-670 B, N	Tyr-678 A, OH	2.94	Tyr-671 B, N	Ile-750 B, O	3.22
Ile-670 B, O	Lys-676 A, N	3.33	Tyr-671 B, O	Ile-750 B, N	2.78
Tyr-671 B, N	Ile-750 B, O	2.92	Thr-672 B, N	Glu-674 A, OE2	3.02
Tyr-671 B, OH	Asp-717 B,OD2	2.71	Thr-672 B, OG1	Glu-674 A, OE2	2.61
Tyr-671 B, OH	Ala-712 B, O	3.39	Thr-672 B, O	Glu-674 A, N	2.91
Tyr-671 B, O	Ile-750 B, N	3.09	Val-673 B, N	Leu-748 B, O	2.79
Thr-672 B, N	Glu-674 A, O	3.08	Val-673 B, O	Leu-748 B, N	2.83
Thr-672 B, OG1	Glu-674 A, O	3.18	Glu-674 B, N	Thr-672 A, O	3.04
Thr-672 B, O	Glu-674 A, N	3.14	Leu-675 B, N	Val-746 B, O	2.89
Val-673 B, N	Leu-748 B, O	2.97	Leu-675 B, O	Val-746 B, N	3.13
Val-673 B, O	Leu-748 B, N	2.98	Ala-712 B, N	Tyr-671 A, OH	2.95
Glu-674 B, N	Thr-672 A, O	2.84	His-714 B, ND1	Ile-715 B, N	3.05
Glu-674 B, O	Thr-672 A, N	3.12	His-714 B, O	Ser-700 B, N	3.26
Leu-675 B, N	Val-746 B, O	2.90	Gly-716 B, N	Ile-698 B, O	3.20
Leu-675 B, O	Val-746 B, N	2.86	Asp-717 B, O	Ile-698 B, N	2.80
Lys-676 B, N	Ile-670 A, O	2.80
Lys-676 B, NZ	Thr-745 B,OG1	3.11
Ala-712 B, O	Lys-752 B, NZ	3.13
Ile-713 B, N	Thr-710 B, O	3.05
His-714 B, ND1	Lys-752 B, NZ	2.80
His-714 B, NE2	Gly-711 B, O	2.94
His-714 B, O	Asp-717 B, N	3.35
His-714 B, O	Asp-717 B,OD1	3.03
Gly-716 B, N	Ile-698 B, O	2.86
Asp-717 B, O	Ile-698 B, N	2.87

* Hydrogen bond distances were calculated between the hydrogen bond donor and acceptor atoms (heavy atom to heavy atoms) in PyMOL.

Hydrogen bonds newly appeared in 100 ns simulated peptide bound dimer compared to the crystal structure. Hydrogen bonds present in peptide bound dimer and absent in peptide free dimer are shown in bold. Hydrogen bonds, maintained throughout the simulation (in comparison to the crystal structure) are shown in italics. All dimeric interface residues (βA strand: residues 670-676 and αA-βD loop: residues 712-717) were taken into consideration for studying their hydrogen bonding pattern.