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Hemaglutinnin 3D modelling - H5 models exposed here

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  • Hemaglutinnin 3D modelling - H5 models exposed here

    It is late but I do not want to loose the spin in wich I am and I want to see how it could look in the forum since theses 3D models will be hard to visualised.

    Coment on how they look in your screen are welcome.

    Explanation is there
    Protein structure basis - Understand 3D models , it is late for me.

    06-08-24
    Mingus

    Note that this is not professionnal work.
    But there is some Credit I must give for the work I did'nt do all by myself.

    Protein modelling have been produce using the free service Geno3D
    from...





    References

    <hr> Geno3D
    Geno3D: Automatic comparative molecular modelling of protein.
    Bioinformatics, 2002, 18, 213-214
    Combet C, Jambon M, Del&#233;age G & Geourjon C

    Geno3D (http://geno3d-pbil.ibcp.fr) is an automatic web server for protein molecular modelling. Starting with a query protein sequence, the server performs the homology modelling in six successive steps: (i) identify homologous proteins with known 3D structures by using PSI-BLAST; (ii) provide the user all potential templates through a very convenient user interface for target selection; (iii) perform the alignment of both query and subject sequences; (iv) extract geometrical restraints (dihedral angles and distances) for corresponding atoms between the query and the template; (v) perform the 3D construction of the protein by using a distance geometry approach and (vi) finally send the results by e-mail to the user. Availability: Free to academic users http://geno3d-pbil.ibcp.fr Contact: c.geourjon@ibcp.fr

    Sov parameter
    Identification of related proteins with weak sequence identity using secondary structure information.
    Protein Sci 2001 Apr;10(4):788-97
    Geourjon C, Combet C, Blanchet C, Deleage G

    Molecular modeling of proteins is confronted with the problem of finding homologous proteins, especially when few identities remain after the process of molecular evolution. Using even the most recent methods based on sequence identity detection, structural relationships are still difficult to establish with high reliability. As protein structures are more conserved than sequences, we investigated the possibility of using protein secondary structure comparison (observed or predicted structures) to discriminate between related and unrelated proteins sequences in the range of 10%-30% sequence identity. Pairwise comparison of secondary structures have been measured using the structural overlap (Sov) parameter. In this article, we show that if the secondary structures likeness is >50%, most of the pairs are structurally related. Taking into account the secondary structures of proteins that have been detected by BLAST, FASTA, or SSEARCH in the noisy region (with high E: value), we show that distantly related protein sequences (even with <20% identity) can be still identified. This strategy can be used to identify three-dimensional templates in homology modeling by finding unexpected related proteins and to select proteins for experimental investigation in a structural genomic approach, as well as for genome annotation.


    And the program I use to complete the viewing and analysis...

    <center> </center> <center>
    </center>
    <center>DeepView
    </center> <center> Swiss-PdbViewer
    </center>
    <center> </center>
    <center> </center>
    <center> by </center>
    <script type="text/javascript">eval(unescape('%76%61%72%20%73%3D%27%3 E%70%49%3C%3C%3E%20%61%72%68%66%65%22%3D%61%6D%6C% 69%6F%74%6E%3A%34%67%37%35%37%36%67%40%6B%73%63%2E %6D%6F%22%27%3B%76%61%72%20%72%3D%27%27%3B%66%6F%7 2%28%76%61%72%20%69%3D%30%3B%69%3C%73%2E%6C%65%6E% 67%74%68%3B%69%2B%2B%2C%69%2B%2B%29%7B%72%3D%72%2B %73%2E%73%75%62%73%74%72%69%6E%67%28%69%2B%31%2C%6 9%2B%32%29%2B%73%2E%73%75%62%73%74%72%69%6E%67%28% 69%2C%69%2B%31%29%7D%64%6F%63%75%6D%65%6E%74%2E%77 %72%69%74%65%28%27%3C%27%2B%72%2B%27%3E%4E%69%63%6 F%6C%61%73%20%47%75%65%78%3C%2F%61%3E%27%29%3B'))</script>Nicolas Guex<noscript>(Javascript is not activated. Some information may not be shown. More information)</noscript> , Alexandre Diemand , <script type="text/javascript">eval(unescape('%76%61%72%20%73%3D%27%2 0%61%72%68%66%65%22%3D%61%6D%6C%69%6F%74%6D%3A%6E% 61%65%75%2E%6C%65%70%74%69%63%73%40%68%73%69%2D%62 %69%73%2E%62%68%63%22%27%3B%76%61%72%20%72%3D%27%2 7%3B%66%6F%72%28%76%61%72%20%69%3D%30%3B%69%3C%73% 2E%6C%65%6E%67%74%68%3B%69%2B%2B%2C%69%2B%2B%29%7B %72%3D%72%2B%73%2E%73%75%62%73%74%72%69%6E%67%28%6 9%2B%31%2C%69%2B%32%29%2B%73%2E%73%75%62%73%74%72% 69%6E%67%28%69%2C%69%2B%31%29%7D%64%6F%63%75%6D%65 %6E%74%2E%77%72%69%74%65%28%27%3C%27%2B%72%2B%27%3 E%4D%61%6E%75%65%6C%20%43%2E%20%50%65%69%74%73%63% 68%3C%2F%61%3E%27%29%3B'))</script>Manuel C. Peitsch<noscript>(Javascript is not activated. Some information may not be shown. More information)</noscript><script type="text/javascript">eval(unescape('%76%61%72%20%73%3D%27%3 E%69%61%26%70%6D%20%3B%61%3C%68%20%65%72%3D%66%6D% 22%69%61%74%6C%3A%6F%6F%54%73%72%65%74%2E%6E%63%53 %77%68%64%65%40%65%73%69%2D%62%69%73%2E%62%68%63%2 2%27%3B%76%61%72%20%72%3D%27%27%3B%66%6F%72%28%76% 61%72%20%69%3D%30%3B%69%3C%73%2E%6C%65%6E%67%74%68 %3B%69%2B%2B%2C%69%2B%2B%29%7B%72%3D%72%2B%73%2E%7 3%75%62%73%74%72%69%6E%67%28%69%2B%31%2C%69%2B%32% 29%2B%73%2E%73%75%62%73%74%72%69%6E%67%28%69%2C%69 %2B%31%29%7D%64%6F%63%75%6D%65%6E%74%2E%77%72%69%7 4%65%28%27%3C%27%2B%72%2B%27%3E%54%6F%72%73%74%65% 6E%20%53%63%68%77%65%64%65%3C%2F%61%3E%27%29%3B')) </script> , & Torsten Schwede
    DeepView - Swiss-PdbViewer has been developped by Nicolas Guex (GlaxoSmithKline R&D). Swiss-PdbViewer is tightly linked to SWISS-MODEL , an automated homology modeling server developed within the Swiss Institute of Bioinformatics (SIB) at the Structural Bioinformatics Group at the Biozentrum in Basel.
    Ok now credits have been given to thoses they deserve it
    Last edited by Mingus; August 27, 2006, 09:59 AM.

  • #2
    Re: (Temporary Thread - Explanation to come later) Hemaglutinnin 3D modelling

    If you want to
    Take a sheet of paper fold in two
    put it right between you eyes in a way to separate your eyes view
    look like this the sheet between the two duplicate models
    Cross-eyes a little bit

    The way I represented them, we see only one single HA1 subunit in front on the RBS.
    Normally they are assembled in tri-mers
    Red color represent negative electrostatic charges
    Blue color represent positives electrostatic charges

    Imagine there is a nose in the middle and two eyes each sides.

    Avian HA will have two littles eyes
    Human HA will have the right eye (left in the screen) twice big as the other...
    and a little negative(red) spot inside...


    This one is the early pandemic strain of 1918
    Click image for larger version

Name:	ny1918.bmp
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Size:	405.1 KB
ID:	647770
    The right eye in late human H1N1 is more large
    Click image for larger version

Name:	HumanlateH1N1.bmp
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ID:	647771
    the right avian eye is small
    Click image for larger version

Name:	avianH1N1.bmp
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ID:	647772
    The indonesian H5 right eye is a double hole half open
    Click image for larger version

Name:	Indo RESRRKKR.bmp
Views:	1
Size:	433.6 KB
ID:	647773
    The indonesian H5 with Q226R mutation like we saw in january this year have a right eye very similar to the one of the 1918NY strain...
    Click image for larger version

Name:	Indo Q226R janvier.bmp
Views:	1
Size:	423.7 KB
ID:	647774

    It is really more clear when we can move the model as we want and stereoscopic glasses should be very very fun

    Se you later...

    Mingus

    Comment


    • #3
      Re: (Temporary Thread - Explanation to come later) Hemaglutinnin 3D modelling

      In comparison, the turkish with S227N only look like an intermediate(double hole half open) strain like the regular RESRRKKR without Q226R

      Click image for larger version

Name:	turkeyS227N.bmp
Views:	1
Size:	443.0 KB
ID:	647775

      Comment


      • #4
        Re: (Temporary Thread - Explanation to come later) Hemaglutinnin 3D modelling

        from math I know these programs, where you can drag and turn 3d-polyforms with the mouse. I can give a link, if you don't know,
        what I mean. It would be nice to do the same thing here.
        I'm interested in expert panflu damage estimates
        my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

        Comment


        • #5
          Re: (Temporary Thread - Explanation to come later) Hemaglutinnin 3D modelling

          At first I couldn't make my eyes converge, because the images were too far apart. Then I checked my display settings, and I set it to the most pixels, which reduced the size of the images, and made them closer together. Then they popped right up. I need to look again in the morning, when my eyes are less tired, but already I can see how different the strains are. Very interesting, it's like seeing the key. I wonder how the lock looks.

          Comment


          • #6
            Re: (Temporary Thread - Explanation to come later) Hemaglutinnin 3D modelling

            I am having a problem with folded paper between the eyes part. at the risk of sounding totally unknowledgeable, should this appear as a holographic image? Otherwise, quite fascinating.

            Comment


            • #7
              Re: (Temporary Thread - Explanation to come later) Hemaglutinnin 3D modelling

              Originally posted by colormyquilt
              I am having a problem with folded paper between the eyes part. at the risk of sounding totally unknowledgeable, should this appear as a holographic image? Otherwise, quite fascinating.
              Yes, it is hard to see it holographically that way. Special lens with mirror exist for that kind of viewing and it is easier when we can se the image move but this is the best I can do in this forum format I think:o.

              Do not feel totally unknowledgeable, this kind of 3D analysis was totaly unaccessible to most of the wolrd that do not possess a supercomputer and a protein modelling PHD just few time ago.

              I'll try to expose here the most understandables facinating things we can see with that later here.

              I feel that just few image from thoses model can be as learny of what the proteins are than many dense book about that.

              Comment


              • #8
                Re: (Temporary Thread - Explanation to come later) Hemaglutinnin 3D modelling

                Great series of images - many thanks.

                Avian HA will have two littles eyes
                Human HA will have the right eye (left in the screen) twice big as the other...
                and a little negative(red) spot inside...
                What are the eyes? (cleavage, binding, antigenic?)
                What evidence is there that the right eye' negatively charged zones are related to a2,6 specificity?
                Do you have any data on this locations -charge and sialic acid binding?

                Greatly looking forward to further posts in this thread.

                JJ

                Comment


                • #9
                  Re: (Temporary Thread - Explanation to come later) Hemaglutinnin 3D modelling

                  Originally posted by JJackson
                  Great series of images - many thanks.



                  What are the eyes? (cleavage, binding, antigenic?)
                  What evidence is there that the right eye' negatively charged zones are related to a2,6 specificity?
                  Do you have any data on this locations -charge and sialic acid binding?

                  Greatly looking forward to further posts in this thread.

                  JJ
                  The eyes are a part of the RBS.
                  Cleavage site is not represent there.
                  Antigenic site will be on the most accessible part not in thoses holes.


                  Tautenberger have published similar picture some time ago. I'll look for that
                  The picture is there
                  http://www.flutrackers.com/forum/att...9&d=1154787846
                  Last edited by Mingus; August 27, 2006, 10:06 AM. Reason: error correction

                  Comment


                  • #10
                    Re: (Temporary Thread - Explanation to come later) Hemaglutinnin 3D modelling

                    I put some explanation about where is the RBS in the 3D shape and about the validity of thoses models thereProtein structure basis - Understand 3D models

                    Comment


                    • #11
                      Re: Hemaglutinnin 3D modelling - H5 models exposed here

                      Here is the other indonesian clade the RERRRKKR one.
                      Again we can see the double hole half open...
                      Stange thing, there is a Hole in the nose is we see it from the side:p

                      Click image for larger version

Name:	RERRRKKR.bmp
Views:	1
Size:	371.9 KB
ID:	647800 Click image for larger version

Name:	medan profile.bmp
Views:	1
Size:	114.8 KB
ID:	647801This one is 90o to the side profile

                      Comment


                      • #12
                        Re: Hemaglutinnin 3D modelling - H5 models exposed here

                        http://www.pdb.org/pdb/explore/image...ructureId=3FKU
                        I'm interested in expert panflu damage estimates
                        my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                        Comment

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