iMechanica - Comments for "Journal Club Theme of April 2007: Analytical Modeling of Biomolecules"
https://imechanica.org/node/1171
Comments for "Journal Club Theme of April 2007: Analytical Modeling of Biomolecules"enThis is what I presumed.
https://imechanica.org/comment/19144#comment-19144
<a id="comment-19144"></a>
<p><em>In reply to <a href="https://imechanica.org/comment/2115#comment-2115">over billions of molecules per cell</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>This is what I presumed.</p>
</div></div></div><ul class="links inline"><li class="comment_forbidden first last"><span><a href="/user/login?destination=node/1171%23comment-form">Log in</a> or <a href="/user/register?destination=node/1171%23comment-form">register</a> to post comments</span></li>
</ul>Wed, 13 Jun 2012 15:15:34 +0000Ronald Peterscomment 19144 at https://imechanica.orgbiomechanics is one of our research areas
https://imechanica.org/comment/2586#comment-2586
<a id="comment-2586"></a>
<p><em>In reply to <a href="https://imechanica.org/comment/2585#comment-2585">how far do you plan to go in biomechanics?</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>Honglai,</p>
<p>We are interested in mechanics of biomolecules in general but more focused on simulations (instead of modeling in this jClub article). Specifically, we are looking at <a href="/node/92">mechanosensitive channels</a> at this moment and developing multiscale simulation protocols. This will be one of our main directions in the coming years. Of course, just like you, we are also and equally interested in materials for energy, nanomechanics, thin films, nanoindentation, and solid-fluid interactions. I am updating my department webpage and should post some new information soon. </p>
</div></div></div><ul class="links inline"><li class="comment_forbidden first last"><span><a href="/user/login?destination=node/1171%23comment-form">Log in</a> or <a href="/user/register?destination=node/1171%23comment-form">register</a> to post comments</span></li>
</ul>Mon, 30 Apr 2007 01:27:17 +0000Xi Chencomment 2586 at https://imechanica.orghow far do you plan to go in biomechanics?
https://imechanica.org/comment/2585#comment-2585
<a id="comment-2585"></a>
<p><em>In reply to <a href="https://imechanica.org/node/1171">Journal Club Theme of April 2007: Analytical Modeling of Biomolecules</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>Xi,<br />So, how far do you plan to go in biomechanics? Any particular research directions?</p>
</div></div></div><ul class="links inline"><li class="comment_forbidden first last"><span><a href="/user/login?destination=node/1171%23comment-form">Log in</a> or <a href="/user/register?destination=node/1171%23comment-form">register</a> to post comments</span></li>
</ul>Mon, 30 Apr 2007 01:05:46 +0000Henry Tancomment 2585 at https://imechanica.orgtime scales in life
https://imechanica.org/comment/2346#comment-2346
<a id="comment-2346"></a>
<p><em>In reply to <a href="https://imechanica.org/comment/2263#comment-2263">time scale in cells</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>Well I think that you have a very good point there and I also often think that science has a problem with scales. We look at something small and want to understand the bigger picture. Sometimes it is fruitful but often it leads to "wrong" conclusions. But there is really no alternative way to do science because if we dont understand the basics we can not understand the advanced......</p>
</div></div></div><ul class="links inline"><li class="comment_forbidden first last"><span><a href="/user/login?destination=node/1171%23comment-form">Log in</a> or <a href="/user/register?destination=node/1171%23comment-form">register</a> to post comments</span></li>
</ul>Tue, 17 Apr 2007 06:19:19 +0000Mikko Hellgrencomment 2346 at https://imechanica.orgYou are right
https://imechanica.org/comment/2264#comment-2264
<a id="comment-2264"></a>
<p><em>In reply to <a href="https://imechanica.org/comment/2263#comment-2263">time scale in cells</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>Michelle, you are absolutely right, processes in cell can take a longer time. I referred to mechanotransduction (which is more mechanics-related and closely related with protein channels discussed in the jClub) to illustrate that, even a ms (or even μs) process is too difficult to be followed by all-atom simulations. Like you said, length and time scale challenges present in almost every material mechanics problems, not just biomechanics.</p>
</div></div></div><ul class="links inline"><li class="comment_forbidden first last"><span><a href="/user/login?destination=node/1171%23comment-form">Log in</a> or <a href="/user/register?destination=node/1171%23comment-form">register</a> to post comments</span></li>
</ul>Wed, 11 Apr 2007 16:30:10 +0000Xi Chencomment 2264 at https://imechanica.orgtime scale in cells
https://imechanica.org/comment/2263#comment-2263
<a id="comment-2263"></a>
<p><em>In reply to <a href="https://imechanica.org/comment/2193#comment-2193">even more expensive for time scale</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>Time scales for physiological processes in cells can take more than ms, and in many cases much closer to s. There's then yet another huge leap towards thinking about biology and disease -- in humans we have to try and understand how processes taking place in cells on second-type time scales relate to diseases that appear in years. A similar problem exists in length-scales: a cell is tens of microns; a person is (usually!) several meters in size. </p>
<p>I applaud the advances in biomechanics at molecular length- and time-scales but hope that these advances are kept in the perspective of the larger picture. To actually use our understanding of molecular process to affect healthcare there's a large leap in scale, and this leap is not irrelevant in considering healthcare as at least one good reason for studying biomechanics (aside from basic understanding of the universe and the meaning of life, of course!) </p>
</div></div></div><ul class="links inline"><li class="comment_forbidden first last"><span><a href="/user/login?destination=node/1171%23comment-form">Log in</a> or <a href="/user/register?destination=node/1171%23comment-form">register</a> to post comments</span></li>
</ul>Wed, 11 Apr 2007 14:20:43 +0000MichelleLOyencomment 2263 at https://imechanica.orgMD Simulations
https://imechanica.org/comment/2221#comment-2221
<a id="comment-2221"></a>
<p><em>In reply to <a href="https://imechanica.org/comment/2193#comment-2193">even more expensive for time scale</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>I think that the ultimate test for dynamical processes in biomolecules is simulation of the folding process going from a random coil state to a native (folded) state. Several papers have shown that through MD simulations one can simulate the folding of small peptides with less than about 30 amino acids. But since most enzymes is typically much larger and that the folding process in general on the time scale of ms compared to only ns for large systems in MD we still have a long way to go.</p>
</div></div></div><ul class="links inline"><li class="comment_forbidden first last"><span><a href="/user/login?destination=node/1171%23comment-form">Log in</a> or <a href="/user/register?destination=node/1171%23comment-form">register</a> to post comments</span></li>
</ul>Mon, 09 Apr 2007 14:04:25 +0000Mikko Hellgrencomment 2221 at https://imechanica.orgeven more expensive for time scale
https://imechanica.org/comment/2193#comment-2193
<a id="comment-2193"></a>
<p><em>In reply to <a href="https://imechanica.org/comment/2192#comment-2192">all-atom simulations</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>Since typical processes occuring in the cell, such as mechanotransduction, can take several ms, all-atom simulations are simply impossible without some biased tricks.</p>
</div></div></div><ul class="links inline"><li class="comment_forbidden first last"><span><a href="/user/login?destination=node/1171%23comment-form">Log in</a> or <a href="/user/register?destination=node/1171%23comment-form">register</a> to post comments</span></li>
</ul>Sat, 07 Apr 2007 04:31:02 +0000Xi Chencomment 2193 at https://imechanica.orgall-atom simulations
https://imechanica.org/comment/2192#comment-2192
<a id="comment-2192"></a>
<p><em>In reply to <a href="https://imechanica.org/comment/2115#comment-2115">over billions of molecules per cell</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>Thanks for the information.</p>
<p>I can understand now that all-atom simulations of the conformational changes of proteins can be prohibitively expensive.</p>
</div></div></div><ul class="links inline"><li class="comment_forbidden first last"><span><a href="/user/login?destination=node/1171%23comment-form">Log in</a> or <a href="/user/register?destination=node/1171%23comment-form">register</a> to post comments</span></li>
</ul>Sat, 07 Apr 2007 04:23:20 +0000Henry Tancomment 2192 at https://imechanica.orgbeing more quantitative
https://imechanica.org/comment/2187#comment-2187
<a id="comment-2187"></a>
<p><em>In reply to <a href="https://imechanica.org/comment/2179#comment-2179">RE: unsolved problems on coarse-graining of proteins?</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>While most coarse-grained models of proteins can give reliable information about directionality of motion (such as structural transition), but not about the magnitude of motion. It's usually straightforward to correlate known structural transitions to a set of normal modes (which are collective basis vectors). It's much more difficult to predict structural transitions based on a single structure; e.g., what happens after an ATPase binds ATP. In other words, the work that you mentioned is quite nice but not yet predictive. For more quantitative coarse-graining attempts, you may want to refer to <a href="http://www.chem.utah.edu/faculty/voth/">Greg Voth</a>'s work.</p>
</div></div></div><ul class="links inline"><li class="comment_forbidden first last"><span><a href="/user/login?destination=node/1171%23comment-form">Log in</a> or <a href="/user/register?destination=node/1171%23comment-form">register</a> to post comments</span></li>
</ul>Fri, 06 Apr 2007 22:43:01 +0000Xi Chencomment 2187 at https://imechanica.orgRE: unsolved problems on coarse-graining of proteins?
https://imechanica.org/comment/2179#comment-2179
<a id="comment-2179"></a>
<p><em>In reply to <a href="https://imechanica.org/comment/2074#comment-2074">Thank you Kilho</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>Hi, Chen. I am very thankful to your reply to my comments. You said that coarse-graining of proteins is still at infant stage and there are still many unsolved problems. As far as I guess, the coarse-graining of proteins is attributed to the fact that the native topology (represented by contact map - map indicates the native contact) plays a role in protein dynamics. That is, in general, the stiffness matrix for proteins based on native contacts becomes sparse matrix that leads to possibility of coarse-graining. I think that that is why further model reduction from Tirion's coarse-grained model is possible.</p>
<p>I have simple question for you: You said that "there are many unsolved problems". Can you give some example on your comment? To my best knowledge, the challenging problem is to understand protein dynamics and/or mechanics for large protein complexes that I am still working on. Especially, I am working on protein dynamics of large protein complex (e.g. GroEL-GroES) by using various model reduction methods. Also, I am working on coarse-grained model for mechanics of protein crystals.</p>
<p>Anyway, I would like to hear from you about some examples of unsolved problems in coarse-graining of proteins, and your opinion for further directions on protein modelings. Thank you again for your reply.</p>
</div></div></div><ul class="links inline"><li class="comment_forbidden first last"><span><a href="/user/login?destination=node/1171%23comment-form">Log in</a> or <a href="/user/register?destination=node/1171%23comment-form">register</a> to post comments</span></li>
</ul>Fri, 06 Apr 2007 15:12:08 +0000Kilho Eomcomment 2179 at https://imechanica.orgover billions of molecules per cell
https://imechanica.org/comment/2115#comment-2115
<a id="comment-2115"></a>
<p><em>In reply to <a href="https://imechanica.org/comment/2077#comment-2077">how many atoms in a cell?</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>Honglai,</p>
<p> The actual number varies a lot because the cell size can be very different. On average a protein can contain millions of molecules, and a cell can easily contain over billions of molecules. See <a href="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.199" target="_blank">here</a> for a rough estimation.</p>
</div></div></div><ul class="links inline"><li class="comment_forbidden first last"><span><a href="/user/login?destination=node/1171%23comment-form">Log in</a> or <a href="/user/register?destination=node/1171%23comment-form">register</a> to post comments</span></li>
</ul>Sun, 01 Apr 2007 23:55:38 +0000Xi Chencomment 2115 at https://imechanica.orghow many atoms in a cell?
https://imechanica.org/comment/2077#comment-2077
<a id="comment-2077"></a>
<p><em>In reply to <a href="https://imechanica.org/comment/2075#comment-2075">The biomolecules cannot be placed in an isolated system</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>Xi,</p>
<p>how many atoms in a cell? Counted in molecules, what is the number?</p>
</div></div></div><ul class="links inline"><li class="comment_forbidden first last"><span><a href="/user/login?destination=node/1171%23comment-form">Log in</a> or <a href="/user/register?destination=node/1171%23comment-form">register</a> to post comments</span></li>
</ul>Sun, 01 Apr 2007 15:36:04 +0000Henry Tancomment 2077 at https://imechanica.orgThe biomolecules cannot be placed in an isolated system
https://imechanica.org/comment/2075#comment-2075
<a id="comment-2075"></a>
<p><em>In reply to <a href="https://imechanica.org/comment/2069#comment-2069">temperature effects in DNA, RNA and proteins</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>Thank you Honglai. All components discussed here must be embedded within a cell and its surrounding environment and thus it is usually assumed the system temperature is a constant. In MD simulation that would be to put the entire system in a "water bath" with a constant temperature. The thermal fluctuation can, of course, influence the system equilibrium and dynamics (especially those from the solvent molecules). This is discussed in Mahadevan and Schulten's work. </p>
</div></div></div><ul class="links inline"><li class="comment_forbidden first last"><span><a href="/user/login?destination=node/1171%23comment-form">Log in</a> or <a href="/user/register?destination=node/1171%23comment-form">register</a> to post comments</span></li>
</ul>Sun, 01 Apr 2007 14:21:15 +0000Xi Chencomment 2075 at https://imechanica.orgThank you Kilho
https://imechanica.org/comment/2074#comment-2074
<a id="comment-2074"></a>
<p><em>In reply to <a href="https://imechanica.org/comment/2072#comment-2072">further model reductions on protein structures</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>Since the journal club could only include 3-5 papers for discussion, I only chose the most representative (and more pioneering) papers in this area (based on my humble and limited knowledge). I am aware of the three NMA/ENM papers you mentioned, which are more or less follow-ups on this topic. The papers you listed will be important for the readers to further understand the topic. </p>
<p>For coarse graining of proteins though, I feel it is more computational than analytical; plus, comparing with coarse graining of lipid, the coarse graining of protein is still at its infant stage and there are still many unsolved problems. Moreover our group is also doing research in this area. Overall I leave this topic out of this issue of journal club but I welcome discussion on this topic; or you may consider to include that in the theme of a future issue of journal club.</p>
</div></div></div><ul class="links inline"><li class="comment_forbidden first last"><span><a href="/user/login?destination=node/1171%23comment-form">Log in</a> or <a href="/user/register?destination=node/1171%23comment-form">register</a> to post comments</span></li>
</ul>Sun, 01 Apr 2007 13:48:59 +0000Xi Chencomment 2074 at https://imechanica.orgfurther model reductions on protein structures
https://imechanica.org/comment/2072#comment-2072
<a id="comment-2072"></a>
<p><em>In reply to <a href="https://imechanica.org/node/1171">Journal Club Theme of April 2007: Analytical Modeling of Biomolecules</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>Probably, it may be good to include Bahar's paper on protein modeling. First, we may consider her paper published in J. Mol. Biol. in 2003: <a href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-49KGR41-G&_user=10&_coverDate=10%2F10%2F2003&_alid=557375070&_rdoc=1&_fmt=summary&_orig=search&_cdi=6899&_sort=d&_docanchor=&view=c&_ct=1&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=dd906912036aa39dc84208df16ec02a8">Xu, C., Tobi, D., and Bahar, I., <em>J. Mol. Biol.</em>, <strong>333</strong>, 153-168 (2003)</a>. In her work, it was shown that conformation transition from T form (tense conformation: ligand-unbound state) to R form (relaxed conformation: ligand-bound state) was induced by purely elastic forces (entropic forces). That is, the conformational transitions are related to low-frequency normal modes responsible for entropic forces (thermal fluctuations). For understanding conformational transition by using NMA, one may also consider the following papers:</p>
<p><a href="http://www.biophysj.org/cgi/content/abstract/88/5/3109">Zheng, W., Brooks, B.R., <em>Biophys. J.</em>, <strong>88</strong>, 3109-3117 (2005)</a><br /><a href="http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=PRLTAO000094000007078102000001&idtype=cvips&gifs=yes">Ikeguchi, M., Ueno, J., Sato, M., Kidera, A., <em>Phys. Rev. Lett.</em>, 078102 (2005)</a></p>
<p>Moreover, in recent year, there was an issue on further coarse-graining on protein structures. In Bahar's recent work, it was shown that collective motion of large proteins can be represented by small number of degrees of freedom. Specifically, in her work, the structure (~10^4 residues) of GroEL-GroES complex can be represented by only 30 nodal points. For details, you may refer to her paper: <a href="http://www.ccbb.pitt.edu/Professor_Websites/bahar/b13.pdf">Chennubbhotla, C., and Bahar, I., <em>Lecture Notes in Computer Science, </em><strong>3909</strong>, 379-393 (2006)</a>. Further, I also provided a method of coarse-graining of protein structures. For details, you may look at the paper: <a href="http://www3.interscience.wiley.com/cgi-bin/abstract/114131990/ABSTRACT?CRETRY=1&SRETRY=0">Eom, K., Baek, S.-C., Ahn, J.-H., Na, S., <em>J. Comput. Chem.</em>, in press, doi: 10.1002/jcc.20672</a>.</p>
</div></div></div><ul class="links inline"><li class="comment_forbidden first last"><span><a href="/user/login?destination=node/1171%23comment-form">Log in</a> or <a href="/user/register?destination=node/1171%23comment-form">register</a> to post comments</span></li>
</ul>Sun, 01 Apr 2007 06:32:16 +0000Kilho Eomcomment 2072 at https://imechanica.orgtemperature effects in DNA, RNA and proteins
https://imechanica.org/comment/2069#comment-2069
<a id="comment-2069"></a>
<p><em>In reply to <a href="https://imechanica.org/node/1171">Journal Club Theme of April 2007: Analytical Modeling of Biomolecules</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>Dear Xi,</p>
<p>I finished reading the papers you suggested. Thanks for providing very good references for this interesting topic. I would like to say something, although I know nothing about biomechanics.</p>
<p>How to analyze the temperature effects for DNA, RNA and proteins? How was the temperature of DNA, RNA, or proteins, calculated in the previous molecular dynamics analyses?</p>
<p>As discussed before (<a href="/node/1064">http://imechanica.org/node/1064</a>), temperature, as well as other thermodynamic concepts such as entropy and the 2nd law of thermodynamics, will become confusing at the molecular scale.</p>
<p>The challenge is that, the temperature fluctuation will <strong>affect greatly the functioning</strong> of DNA, RNA, and proteins. It is a very important issue that we just cannot ignore.</p>
</div></div></div><ul class="links inline"><li class="comment_forbidden first last"><span><a href="/user/login?destination=node/1171%23comment-form">Log in</a> or <a href="/user/register?destination=node/1171%23comment-form">register</a> to post comments</span></li>
</ul>Sun, 01 Apr 2007 02:28:34 +0000Henry Tancomment 2069 at https://imechanica.orgError | iMechanica