In order to understand retinal we calculated the dihedral angles around carbon axis IOC-12C, since two different carbon sequences 9C-10C-11C-12C and 10C-11C-12C-13C exist. We also calculated the distances between two specified carbon pairs. Those results are tabulated. Photon absorption changes the conformation of retinal conformation. This fact is confirmed from dihedral angle changes and distance changes of targeted of retinal carbon atoms. These matters are discussed in the present paper.Copyright Information: Copyright the autho

Kito, Masashi

Maddess, Ted

Nagai, Yoshinori

English

The Australian National University

ISSN 2187- 9516 ~ )[_ The Background of Instability in Employment among the Young People in Japan and the Career Education Challenge ···············Masabumi Tokoro ( 1 ) Retinal Location and Structure in Squid Rhodopsin ····································Yoshinori Nagai, Masashi Kito and Ted Maddess ( 19 ) )-~ r7'./:A · ~1.I.'./:Ai!JtJglZ"'('O)-{'./::'l-:t·y 1-~-l:::.":AI:-:H, ,"( · ·· ·· · ···*~JII:ll'J: ( 24 ) -t<7){t!! *-·» r/-r~~'./7717'./r~"A::ri..>.l:"'?\,'-c ·············· · ······ · ····· :tc~~1f. ( 36 ) ~ 5 IID~~o~~c~~t~f.+~iiJf~~lft11i ... ij:)( ······ ·············································· · ······································ ··········· ( 43 ) e~n~O)~•••m• c~oq ··················~~~m. P~•oo. E•~- < « > e~n~OJ~••~m•K~~~~¥~mfi······~~~oo. ~~~m. E•~- < ~ > Interactions between Dynein and Microtubules ····················· ············Yoshinori Nagai, Stephen Hyde and Hiroshi Wako ( 54 ) -MEMOIRS OF THE KOKUSHIKAN UNIVERSITY INFORMATION SCIENCE Paper No. 35 March, 2014 CONTENTS The Background of Instability in Employment among the Young People in Japan and the Career Education Challenge ......... ................................. MASABUMI TOKORO ( 1 Retinal Location and Structure in Squid Rhodopsin ..................... YOSHINORI NAGAI, MASASHI Krro and TED MADDESS ( 19) Note Internet Services for the Area of Trans-Sciences ................................. ........ YUTAKA HASEGAWA( 24 ) Other About a Thin Client System of NetBoot Type .......................................... KAZUTOSHI ADACHI ( 36 ) The Fifth Memorial Workshop for Kazuhide Mori on Computational Sciences Foreword .... ...... .. ........................ .... ... ............................ ( 43 ) Spontaneous Oscillatory Contraction in Skeletal Muscle ........................ SEINE SHINTANI, NAOAKI BEKKI and SH!N'ICHI lSHIWATA( 44) Model Analysis for Spontaneous Oscillatory Contraction in Skeletal Muscle ........................ NAOAKI BEKKI, SEINE SHINTANI and SHIN'ICHI lSHIW AT A ( 48 ) Interactions between Dynein and Microtubules ......... .. .......... YOSHINORI NAGAI, STEPHEN HYDE and HIROSHI W AKO ( 54 ) Paper Retinal Location and Structure in Squid Rhodopsin Yoshinori Nagai 1, Masashi Kito1, and Ted Maddess2 (Received II January 2014, Revised 15 January 2014) Abstract: In order to understand retinal we calculated the dihedral angles around carbon axis IOC-12C, since two difl'erent carbon sequences 9C-10C-11C-12C and 10C-11 C- 12C- 13C exist. We a lso calculated the distances be-tween two specified carbon pairs. Those results are tabulated. Photon absorption changes the conformation of retinal conformation. This fact is confirmed from dihedral angle changes and distance changes of targeted of retinal carbon atomsa. These matters are discussed in the present paper. 1. Introduction We have been studying squid rhodopsin. In particular we have concentrated on understanding the conformation of retinal in squid rhodopsin. We have used the PDB identification codes 2273, 2ZIY, 3AYM, and 3AYN found in the RCSB protein data bank (URL, www .rcsb.org/ pdb/ ). Squid retinal consist of twenty carbons (1C- 20C) as shown in Fig. 1 [1]. The squid retinal has the hexa-ring [1] that interacts with ring parts of amino acid residues (phenylalanine: Phe and tryp-tophan: Trp) in rhodopsin chain A, while the long chain residues of amino acids (arginine: Arg and isoleucine: Ile) are in chain B [2, 3]. The nearest atom contact of retinal to the atoms of the rhodopsin molecules was tabulated [2]. The retinal area in a rhodopsin molecule is estimated in an obscure way. The considered results are shown in references 2 and 3. Our investigations employed viewing procedures created RasMol or RasWin software. The resulting viewings yielded intuitive scope, but those pictures are not quan-titative ones [1 , 2, 3]. The wave--length of light absorbed is determined by which side of carbon is changed between cis-conformation and trans-conformation [4, 5, 6]. The utilized PDB data denote citations [7, 8, 9]. In section 2, we considered the retinal location within squid rhodopsin to look at what every retinal carbon is contacting with respect to the nearest atom of residue of the amino acids in squid 1 Faculty of Administration, Koksuhikan University, Tokyo 2 Eccels Institute for Neuroscience, Joh Curtin School of Medical Research, Australian National University, Canberra - 19 -Memoirs of the Kokushikan Univ. Information Science. No. 35 (2014) rhodopsin. Those facts can be seen from the references [2, 3], where we calculated the distances be-tween the retinal carbon and atoms in the amino acid residues of squid rhodopsin. In squid retinal, carbon eleven (1 1C) has the advantage for conformation change. Thus we have here calculated the dihedral angle around carbon pair axis 10C-12C. Dihedral angles less than n radi-ans imply that the triangle plane including 11 C is located on the upper side with respect to the other triangle plane. On the other hand , dihedral angles over n radian denote that the triangle plane in-cluding 11C is located on the lower side with respect to the other triangle plane. T herefore the di-hedral angle around 10C-12C line indicates whether the location of carbon 11C is upper or lower. There exist two kinds of the carbon axes for 1°C to 12C, namely, the carbon sequences 9C-IOC- 11 C-12C and 10C-11 C-12C-13C. We therefore give two dihedral angles for chain A or chain B of the PDB identification of squid rhodopsin. We also calculated carbon pairs to look at the cases of retinal taking the cis- or trans-conformation. If the retinal takes the trans-conformation, the distance be-tween 9C and 13C becomes longer than the distance is given by the cis-conformation. Section 4 is devoted to " Discussion", where we consider what conformation changes occur in squid retinal within squid rhodopsin. 2. Contact residues of rhodopsin for each carbon of retinal We have reported the contact atoms of the amino acid residues of squid rhodopsin to each reti-na l carbon [2]. The relevant contact amino acid residues are 112- 120, 187-209, 274, and 305 for chain A, and 69, 70, 129- 133, 187, 259-274, 305, and 319 for chain B [2] . We placed the data for those retinal twenty carbons for those amino acid residues in name.pdb fi les. We used RasMol software, to create the ball and stick representation of Fig. 2. The below figure is an example chai n A and chain B using PDB 2Z73. As seen from Fig. 2, It is difficult to image the retinal and amino acid residues of rhodopsin. Fig. 2 Ball and stick pictures for chain A and chain B of rhodopsin data from PDB 2Z73 - 20 -Retinal Location and Structure in Squid Rhodopsin We therefore searched for the nearest atom of amino acid residues to each carbon of squid retinal [2, 7]. Thus we know that the above amino acid residues of rhodopsin should be included with squid retinal to draw figures. We actually calculated the real distances to find what atoms of the amino acid residues contact each retina l carbon. We a lso quantified the mobility of t iC o f retinal. We therefore now calculate the dihedral angles and distances between specified pairs o f carbons . 3. Dihedral angles around axis JOC-12C and distances of carbon pairs We calculated the dihedral angles around the carbon axis that consisted of the carbon pair 10C and 12C. There are two kinds of dihedral angles for the same carbon pair using the two amino acid sequences 9C-1°C-11C-12C and 10C-11C-12C-13C. We refer to this dihedral angle as 0('°C-12C). One can see the relevant two triangle-planes from Fig. 3. We therefore use these two carbon sequences (9C_toc_ttC-'2C and IOC-"C-12C- 13C). The dihedral angles around carbon axis IOC-12C we are calculated using following formula. (IOC9C X fO""CT2C). (flCTOC X II CI2C) 0('°C- 12C ) = . • • . I 10C9C X 10C 12C II "C 10C X 11 C 12C I ('ICI2C X IICIOC). (13CI 2C X 13CIOC) O(IOC- 12C) = • • • I 11 CI2C X IICIOC II 13CI2C X 13CIOC I Were the vector denotes iCiC' =(!C_,.-iC.n iCy-iCy, iCz-iCz) and x indicates the vector product. The dihedral angles calculated are tabulated in T able I. In Table I, values of dihedral angles have radian units, i .e., n is 3. 14159265 ... and it is obvious that unit circle has the length 2n radian. If two vectors cross orthogonally , the dihedral angle is n / 2 or 3n/ 2 radian. In the case of the two triangle planes coexisting on a plane, the dihedral angle is n radian , in other words, the two triangle planes are opened on a flat plane. If dihedral angle is zero radian , the two triangle planes take a closed form . We can read Table I from these viewpoints. We can give a discussion in the next section about the obtained dihedral angles. We tabulate distances between specified carbon pairs of squid retinal to consider the move-ment of carbon 11 C. Quite small deviations were fou nd in carbon pair 9C-13C . Large distance changes were found in carbon pair 2°C- 18C. Electron movement is the order of 0.1 nm so that 0.4 I I I Fig. 3 Two carbon sequences (9C-10C-11C-12C and IOC-11C-12C-13C) of squid retinal - 21 -Memoirs of the Kokushikan Univ. Information Science. No . 35 (2014) Table I Dihedralangles for chain A and chain B of the PDB data 9C-10C-11C-12C IOC-11C-1lC-1lC PDB id chain A chain B chain A chain B 2Z73 3.139705 3 .099925 2.919768 2.427 132 2ZIY 3.038743 - 2.882382 -3AYM 2.59887 2.409588 1.222221 1.042949 3AYN 3.019744 3 .002237 0 .7108 11 0. 126709 Table II Calculated distances for specified carbon pairs to look at the movement of 11C 2Z73 2Z73 2ZIY 3AYM 3AYM 3AYN 3AYN Distances for paired carbons cahin A cahin B cahin A cahin A cahin B cahin A cahin B 9C-1 lC 4.666776 4.667803 4.609363 4.942753 4.795278 4.935296 4.973205 9C-20C 4.392748 4.37294 4.396047 5.33824 1 4.969198 5.152009 5.200158 19c-2oc 5.713856 5.699356 5.624375 5.655004 4.99673 6.625895 6.672787 19C- 1lC 5.72009 5.7355 14 5 .541339 5.620504 5.261216 6.273443 6 .309689 lOC-ISC 6.775899 6.8219 12 4. 887197 9 .31865 8.78693 6.396053 6.70284 nm is a relatively long distance. The average distance of alpha-carbons of the amino acid residues is 0.38 nm. The distance change can encompass bond rotation or carbon movement. 4. Discussion Here we discuss the results of Table I and Table II, in particular we can discuss dihedral angle changes and distance changes of carbon pairs. The unit of Table II is A since location atom is denoted by A unit. For Table I, Dihedral angles have values near n except for the 3A YM PDB data for the carbon sequence 9C-IOC-11C-12C. This means that for this case the two triangle planes have an open shape. Thus, this means 11 C is located on an expand plane. The PDB data 3AYM for this sequence takes a little bit closed but still open shape for both chains. In 3A YM, chain A of the carbon sequence 10C-11C-12C-13C takes a value near n / 2 = 1.5707 .. . so that the two triangle planes are almost orthogonal to each other. In the chain B of 3A YN the value of the dihedral angle is near 0. 127. This might indi-cate a closed shape for the two triangle planes, namely it is expected that conformation change has occurred from trans to cis . This implies that the distance between 2oc and 18C has become shorter. This fact can be seen from Table II. We can estimate distance changes of the carbon pairs . Large distance change implies rotation of the bond. With the rotation of the bond, the distance between carbon pairs becomes shorter or longer. If the retinal takes the trans-conformation, the distance between carbon pairs becomes lon-ger. As seen from Table II, big changes can be seen at carbon pair 2°C-18C . In this sense, the PDB data 3A YM takes the trans-conformation, namely a wavy line of carbons within the sequence 9C-IOC-11C-12C-13C is expected . The shape can be visualized using RasMol pictures, and the expecta-tion can be seen. In comparing the distances for carbon pair 2°C-18C, big distance changes ap--22-Retinal Location and Structure in Squid Rhodopsin peared. Thus we can conclude that rotation of the bonds 10C-11 C or 11C- 12C should have occurred. In other words, cis and trans conformation change occurrs by this rotation of the bond. Light ab-sorption should have occurred creating the retinal change of conformation [4-9]. References [I] Y. Nagai, K. Kito, H. Kagawa, T. Maddess, A quantum chemistry of retinal of squid rhodopsin, Mem. Kokushikan U Cent. fnj. Sci. 32 (2011) 20-31. [ 2 ] Y. Nagai, K. Kito, T. Maddess, Spacing between retinal and amino acid residues in squid rhodopsin , Mem. Kokushikan U Cent. lnf. Sci. 33 (2012) 1-7 . [ 3 ] Y. Nagai, K. Kito, T. Maddess, Atomic configuration around retinal in squid rhodopsin, Mem. Kokushikan U Cenl. !nf. Sci. 34 (2013) 1-8. [ 4] 0. P. Ernst* and F. J. Bartl, Active States of Rhodopsin, Chem. Bio. Chem. 3 (2002) 968- 974. [ 5 ] M. V. Altaisky, V. N. Gorbachev, and F. Pichierri, Coherent Signal Amplification in Rhodopsin Media, Physics of Particles and Nuclei Letters, 4 (2007) 150-153. [ 6] W. D. Hoff, K. H .H. Jung, and J. L. Spudich, Molecular mechanism of photosignaling by archaeal sensory rhodop-sins, Annu. Rev. Biophys. Biomol. Struct. 26 (1997) 223-258. [ 7] M. Murakami, T . Kouyama, Crystal structure of squid rhodopsin, Nature 453 (2008) 363-367. [ 8 ] M. Miyano, T . Shimamura, Crystal structure of squid rhodopsin with intracellularly extended cytoplasmic region, J. Bioi. Chem. 283 (2008) 17753-17756. [ 9] M. Murakami , T . Kouyama, Crystallographic Analysis o f the Primary Photochemical Reaction of Squid Rhodopsin, J. Mol. Bioi. 413 (2011) 61 5-627. - 23 -

Retinal location and structure in squid rhodopsin

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Retinal location and structure in squid rhodopsin

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