Modeling of Complex of Hexameric Insulin and 4'-Hydroxyacetanilide

Title: The structure of a complex of hexameric insulin and 4'-hrydroxyacetanilide
Compound: Insulin (T3R3) (pH 6.4, 0.75 M NaCl) Complexed with Two Zinc Ions and Tylenol (4'-Hydroxyacetanilide)
Classification: Hormone
Source: Synthetic Based on the Human (Homo Sapiens) Sequence
PDB ID: 1TYL

In this project, we picked a hetero compound, extracted the protein from it and then performed some tasks suck as minimizing the energy and overlaying the minimized hetero with unminimized hetero. Measuerments such as Steric Energies, Non-1,4 VDW, etc. were taken for comparison of the protein before and after minimization. Throughout this project, we performed different tasks such as graphing the extracted hetero compound and changing the looks of it by choosing a different style, such as CPK, Ball & Stick.

Figure 1: The Extracted Hetero Compound:

Table 1: Energy Comparison of Tylenol Before & After Minimization

Before Minimization of 1TYL

After Minimization of 1TYL

Stretch = 64.3321

Bend = 1041.1645

Stretch-Bend = 1.5421

Torsion = 9.9476

Non-1, 4 VDW = -0.5543

1,4 VDW = 40.8931

Dipole/Dipole = 1.0035

Total = 1158.3286

Stretch = 0.2915

Bend = 9.0268

Stretch-Bend = 0.101

Torsion = -7.2595

Non-1, 4 VDW = -0.2518

1,4 VDW = 3.0299

Dipole/Dipole = 0.8314

Total = 5.7695

Table 2. Overlay of the Hetero Compound

Extracted Steric Energy of 1TYL	Minimized Steric Energy

In order to make the understanding of the overlay easier (below), I changed the colors of the minimized Steric Energy to distinguish the overlay.

In the overlaying of the tylenol (before and after minimization), the color of the minimized hetero was changed on purpose then it would be easier for viewer to see the overlay. The five pair that was selected overlapped almost exactly on top of the other pair.

Primary Bibliographic Citation

PDB ID	Authors	Journal Name	Title	Volume No	First Page	Publication Year
1GUJ	J.L.Whittingham, D.J.Scott, K.Chance, A.Wilson, J.Finch, J.Brange, G.G.Dodson	To be Published	Insulin at Ph2: Structural Analysis of the Conditions Promoting Insulin Fibre Formation	n/a	n/a	n/a
1HSK	T.E.Benson, M.S.Harris, G.H.Choi, J.I.Cialdella, J.T.Herberg, J.P.Martin Jr., E.T.Baldwin	Biochemistry	A Structural Variation for Murb: X-Ray Crystal Structure of Staphylococcus Aureus Udp-N-Acetylenolpyruvylglucosamine Reductase (Murb)	40	2340	2001
1MBB	W.J.Lees, T.E.Benson, J.M.Hogle, C.T.Walsh	Biochemistry	(E)-enolbutyryl-UDP-N-acetylglucosamine as a mechanistic probe of UDP-N-acetylenolpyruvylglucosamine reductase (MurB).	35	1342	1996
1MBT	T.E.Benson, C.T.Walsh, J.M.Hogle	Structure	The structure of the substrate-free form of MurB, an essential enzyme for the synthesis of bacterial cell walls.	4	47	1996
1TYL	G.D.Smith, E.Ciszak	Proc Natl cad Sci U S A	The structure of a complex of hexameric insulin and 4'-hydroxyacetanilide.	91	8851	1994
1TYM	G.D.Smith, E.Ciszak	Proc Natl Acad Sci U S A	The structure of a complex of hexameric insulin and 4'-hydroxyacetanilide.	91	8851	1994
1UXY	T.E.Benson, C.T.Walsh, J.M.Hogle	Biochemistry	X-ray crystal structures of the S229A mutant and wild-type MurB in the presence of the substrate enolpyruvyl-UDP-N-acetylglucosamine at 1.8-A resolution.	36	806	1997
2MBR	T.E.Benson, C.T.Walsh, J.M.Hogle	Biochemistry	X-ray crystal structures of the S229A mutant and wild-type MurB in the presence of the substrate enolpyruvyl-UDP-N-acetylglucosamine at 1.8-A resolution.	36	806	1997

The Structure of a Complex of Hexameric Insulin and 4'-Hydroxyacetanilide

Proceedings of the National Academy of Sciences

Volume 91, 8851-8855, Copyright © 1994 by National Academy of Sciences

GD Smith and E Ciszak

X-ray crystallographic studies have been carried out on human insulin crystals grown in the presence of 4'-hydroxyacetanilide (Tylenol) and show that this nontoxic phenolic derivative can induce the T R transition, producing a T₃R₃ hexamer. Two different crystals, grown under different conditions, are rhombohedral, space group R3, with cell constants a = 81.11, c = 37.97 and a = 80.88, c = 37.60 Å. The T₃R₃ hexamer is symmetric, resulting from the presence of a crystallographic threefold axis, and the asymmetric unit consists of a TR dimer. Data to a resolution of 1.9 Å were measured on a crystal from each of the two crystallizations and the structures have been refined to residuals of 0.168 and 0.173. The guest molecule is bound by the R-state monomer through the formation of two hydrogen bonds from the hydroxy group of Tylenol to the carbonyl oxygen and the nitrogen of A6 Cys and A11 Cys, respectively. Due to steric constraints of the phenolic binding site, the acetamide group of Tylenol is rotated 50 out of the plane of the phenyl group and the methyl group is cis; no hydrogen bonds exist between the acetamide group and the hexamer. Although the zinc ion, which is bound to the R-state trimer, has tetrahedral coordination in both structures, the T-state zinc is observed to have octahedral coordination in one structure but tetrahedral coordination in the other. The side chain of A10 Ile in the R-state monomer adopts a highenergy conformation as a result of close contact to a residue in an adjacent dimer and may explain in part the differences between therapeutic preparations of beef insulin, for which A10 is a Val residue, and human insulin.

This article has been cited by other articles:

Brader, M. L., Kaarsholm, N. C., Harnung, S. E., Dunn, M. F. (1997). Ligand Perturbation Effects on a Pseudotetrahedral Co(II)(His)3-Ligand Site. A MAGNETIC CIRCULAR DICHROISM STUDY OF THE Co(II)-SUBSTITUTED INSULIN HEXAMER. J. Biol. Chem. 272: 1088-1094

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X-ray Crystal Structures of the S229A Mutant and Wild-Type MurB in the Presence of the Substrate Enolpyruvyl-UDP-N-Acetylglucosamine at 1.8-Å Resolution

Biochemistry

Volume 36 (4), 806 -811 bi962221g S0006-2960(96)02221-0

Timothy E. Benson, Christopher T. Walsh,* and James M. Hogle

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115

Received: August 30, 1996

Abstract:

MurB catalyzes the second committed step in the synthesis of peptidoglycan, a key component of the bacterial cell wall. The crystal structures of both a S229A mutant and wild-type MurB in the presence of the substrate enolpyruvyl-UDP-N-acetylglucosamine were solved and refined at 1.8 Å resolution. The single point mutation of residue 229 from serine to alanine eliminated a hydroxyl group which has previously been proposed to play a critical role as a proton donor during the second half-reaction of MurB, namely, reoxidation of FADH₂ and reduction of the enolpyruvyl substrate. The mutation also resulted in the loss of the water molecule-hydrogen bonded to the serine hydroxyl in the wild-type structure changing the hydrogen-bonding network with in the active site. Comparison of the wild-type and S229A mutant structures confirms that the dramatic kinetic defect of an approximately 10⁷-fold decrease observed for the Ser 229 Ala mutant in the second half-reaction [Benson, T. E., Walsh, C. T., & Massey, V. (1997) Biochemistry 36, 796-805] is a direct result of the loss of the serine hydroxyl moiety rather than other nonspecific active-site changes or general structural defects.

Figure 2. Graphics of primary and secondary structure diagram from PDSum:

Figure 3. Graphic of ligand interaction plot from PDBSum:

Figure 4: Graphic of Tylenol (in Ball & Stick) with Amino Acids:

Figure 5: The CPK model of Tylenol with Amino Acids:

Figure 6: The CPK model of Tylenol with the Hetero compound:

All the information was obtained from the following websites on May of 2002:

http://falcon.sbuniv.edu/~ggray.wh.bol/imagegal/enz3ref.htm

Protein Data Bank

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