Courtesy - Internet Archive...Courtesy Courtesy Created Date 20120829220815Z ...
Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and...
Transcript of Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and...
![Page 1: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/1.jpg)
����������������
����� �������� �������� 1
Courtesy of Wenqing Xu et al. and RCSBProtein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited. Used with permission.
Source: Barabási, Albert-László, Natali Gulbahce, et al."Network Medicine: A Network-based Approach to Human Disease."Nature Reviews Genetics 12, no. 1 (2011): 56-68.
![Page 2: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/2.jpg)
• L12�P�r�rp��t�u���r��tp�r�����rpt�rtp��� �rpt�rtp��&�tb�p�������&����� ��u�������
• L13�P�tp����u���bp�r�����rpt�rtp��� • L14�P�tp����u���bp�r������r�p��u����� • L1S�P�u����t��t��r�p(�N�rw�py��� • L16�P�tp�r����r�r�p��u���N�rw�py��� • L17�P�&�tbtr�r���N�rw�py���������
2
![Page 3: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/3.jpg)
L��rtp��12�
r�rp��t�u���r��bp�r�����rpt�rtp��
4�
3
![Page 4: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/4.jpg)
.��. �.���
������
4
![Page 5: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/5.jpg)
5
© Cold Spring Harbor Laboratory Press. All rights reserved. This content is excluded from our CreativeCommons license. For more information, see http://ocw.mit.edu/help/faq-fair-use/.
Source: Pavletich, Nikola P., Kristen A. Chambers and Carl O. Pabo. "The DNA-binding Domain of p53
Contains the Four Conserved Regions and the Major Mutation Hot Spots." Genes & Development 7, no.
12b (1993): 2556-64.
5
![Page 6: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/6.jpg)
© American Association for the Advancement of Science. All rights reserved. This content is excludedfrom our Creative Commons license. For more information, see http://ocw.mit.edu/help/faq-fair-use/.
Source: Cho, Yunje, Svetlana Gorina, et al. "Crystal Structure of a p53 Tumor Suppressor-DNA
Complex: Understanding Tumorigenic Mutations." Science 265, no. 5170 (1994): 346-55.
6
![Page 7: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/7.jpg)
�
��
��
��
��
��
htb://www/p��r/�p�/b�r
XPp�(�873434� ���tu���N�t�84323� E���rp������p����b(�8S22� �����P�r�r��N�t�8S6� H(rp���8S2� N�trp���t�3p��u���843� F�r�p�t�3p��u���837� E���rp���&p(�r�����p�bh(�834� ���tu������t�p����832� Orh�p�823�
7
![Page 8: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/8.jpg)
XPp�(�����N�t�
© Project Crystal. All rights reserved. This content is excluded from our CreativeCommons license. For more information, see http://ocw.mit.edu/help/faq-fair-use/.
8
![Page 9: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/9.jpg)
�
N�t�
htb://www/t����p��r/�p�/�
9
© Jens Meller. All rights reserved. This content is excluded from our CreativeCommons license. For more information, see http://ocw.mit.edu/help/faq-fair-use/.
Courtesy of Kjaergaard on wikipedia. Courtesy of MartinSaunders on wikipedia.
Photograph in the public domain. Photograph in the public domain.
9
![Page 10: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/10.jpg)
�rpt�rtp���p������p������r��r��pp���
• B�rh��p(�r�����p�bh(�����N�t���b������� ��tbtr�u�����t�rh����r�� ���rh���rpt�rtp�� 8�p��rpt�rtp����rh�r�r��r���p���w�rh� �yb�p�t��r�����r�/�
10
![Page 11: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/11.jpg)
tp����u����rpt�rtp��
• &�����(�u���r��rh����tbtr�u������h��������� �t���r�pbp�u���XPp�(�����N�t���r��
• A�y�(�r�b�������tp����rtp���
11
![Page 12: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/12.jpg)
�
Challenges of Structural Bioinformaticscourtesy of Russ Altman & Jonathan Dugan
in Structural Bioinformatics, Philip E. Bourne & Helge Weissig, editors
1/ �rpt�rtp�����r���p����r������p�P����ur��bb�(��rp��������p�rht�� 2/ ���p�h��b����������u�t�t�/�� ��r�� 3/ �rpt�rtp�������r�pt�����r(�bh(������������trr���w�(�rh�r�p����r��
��tb�� ��u��� 4/ Htt���p�/���tbtr�p���r�pt�����r���rpt�rtp��8p��t�����u���p�/�
���p����r�����p��p�p(���3�p��r� S/ Eyb�p�t��r����rpt�rtp�����r���p���tb�pt��r�������tb��r�� 6/ tp�r�����p���r������r�pt���t��rpt�rtp��t�(�h�p��p�p(������t���p�
��bt�������������r��h�p��r������ut(� 7/ W�����ur�y��w�tt�h��r�tr���t����p������������t��tb�pr��r�
bp�r����� 3/ �rpt�rtp���r�����(�t�p�rh��t��r�b�pr�����p�r���b�pr���t���wh����P�
����tr�(����rp��y(�
12
![Page 13: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/13.jpg)
t����b��r���t�r�p����t�p���r�������� bp�t�p(���������p(��r�pu�p(� �rpt�rtp�����bh��h��������r�r�� �h��r�������t�p��
13
Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission.
13
![Page 14: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/14.jpg)
������
u�r�r�� y��w�rh�� �t����
F��tp��11/13������p���r�������B�tt�
© Garland Science. All rights reserved. This content is excluded from our Creative Commons license. For more information,see http://ocw.mit.edu/help/faq-fair-use/.
Source: Figure 11.18 in Zvelebil, Marketa J., and Jeremy O. Baum. "Understanding Bioinformatics." Garland Science, 2008.
acids
14
![Page 15: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/15.jpg)
�htb://www/p��r/�p�/b�r
16�
Courtesy of RCSB Protein Data Bank. Used with permission.15
![Page 16: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/16.jpg)
17� Courtesy of RCSB Protein Data Bank. Used with permission.
16
![Page 17: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/17.jpg)
t���p�r�����rpt�rtp���
• p�b��u������t��r�� • y�(������p����r��� • ��r�p�������p����r���
17
![Page 19: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/19.jpg)
•� •� •� �
19
![Page 20: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/20.jpg)
20
![Page 21: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/21.jpg)
���� �
x� v� z� B�
H��h�p��t����t�B���pp��b����r��t�p��rh�pt���t�u���8p�����1P111�� htb://www/p��r/�p�/b�r/111/�r�u�111/��-b-��t��u�������t�����/L��y���P�rP�rpt�rtp��/���p����r��/hrt�
t�p���r����/� 21
![Page 22: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/22.jpg)
r�r�p�������p����r���
22
© source unknown. All rights reserved. This content is excluded from our Creative
Commons license. For more information, see http://ocw.mit.edu/help/faq-fair-use/.
22
![Page 23: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/23.jpg)
23
© Annual Reviews. All rights reserved. This content is excluded from our Creative Commonslicense. For more information, see http://ocw.mit.edu/help/faq-fair-use/.Source: Orengo, Christine A., and Janet M. Thornton. "Protein Families and their Evolution--AStructural Perspective." Annual Review Biochemistry 74 (2005): 867-900.
![Page 24: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/24.jpg)
&�tb�p�����rpt�rtp��� • N����r���� ���
��pp��b��������r�t�/� • Fp�bt��r�(����(����tr��r��t�
�r�t�:� • t���P�h���� • h��p(��r�t��
• ����t����t��t�r(�p����� r��(�rp���t�pt�u����
RMSD(a, b) = 1 n
aix − bix( )2 + aiy − biy( )
2 + aiz − biz( )2⎡
⎣⎢ ⎤ ⎦⎥
i=1
n
∑
© source unknown. All rights reserved. This content is excluded from our Creative
Commons license. For more information, see http://ocw.mit.edu/help/faq-fair-use/.
24
![Page 25: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/25.jpg)
V)�.����.��
25
![Page 26: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/26.jpg)
26
![Page 27: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/27.jpg)
�r�r����rpt�rtp���p�����p��u��t���t�� �����.�
I � Courtesy of Nature Publishing Group. Used with permission.
Source: Dill, Ken A., and Hue Sun Chan. "From Levinthal to Pathways to Funnels."
Nature Structural Biology 4, no. 1 (1997): 10-9.
27
![Page 28: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/28.jpg)
t�r��u���E��p�(��t���tp�r����
Physicist StaEsEcian
28
![Page 29: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/29.jpg)
�
t�r��u���E��p�(��t���tp�r����
• t���p�r��bh(������t�p���� • Ebt�u����t�(�r��
�bbp�y�t�r���rtr�p�bp����r� ����u �r���t�p����
CH�MMM
Physicist StaEsEcian
29
![Page 30: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/30.jpg)
�
�
t�r��u���E��p�(��t���tp�r����
• t���p�r��bh(������t�p���� • t���p�r���r��pp�u���� • Ebt�u����t�(�r�� • N�������r��t���p�r����
�bbp�y�t�r���rtr�p�bp����r� �p������t��r�u�u���� ����u �r���t�p���� bp�b�pu���
CH�MMM
Physicist StaEsEcian
Rose2a
30
![Page 31: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/31.jpg)
CH�MMM�
�
t�r��u���E��p�(��t���tp�r����
• t���p�r���r��pp�u���� • N�������r��t���p�r����
�p������t��r�u�u���� bp�b�pu���
• t���p�r��bh(������t�p���� • Ebt�u����t�(�r��
�bbp�y�t�r���rtr�p�bp����r� ����u �r���t�p����
Physicist StaEsEcian
Rose2a
31
© source unknown. All rights reserved. This content is excluded from our Creative
Commons license. For more information, see http://ocw.mit.edu/help/faq-fair-use/.31
![Page 32: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/32.jpg)
CH�MMM�
M� �� �
t�r��u���E��p�(��t���tp�r����
• t���p�r��bh(������t�p���� • t���p�r���r��pp�u���� • Ebt�u����t�(�r�� • N�������r��t���p�r����
�bbp�y�t�r���rtr�p�bp����r� �p������t��r�u�u���� ����u �r���t�p���� bp�b�pu���
Physicist StaEsEcian
“Data don’t make any sense, we will have to resort to sta<s<cs
32
© source unknown. All rights reserved. This content is excluded
from our Creative Commons license. For more information, seehttp://ocw.mit.edu/help/faq-fair-use/.
Courtesy of http://vadlo.com/. Used with permission.
![Page 33: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/33.jpg)
�
&HAt���E��p�(�Ft��u���
htb://www/�h�pttrtr�p���/�p�/����y/bhb/ h��E��p�(�Ft��u�� �
© source unknown. All rights reserved. This content is excluded from our Creative
Commons license. For more information, see http://ocw.mit.edu/help/faq-fair-use/.
http://cbio.bmt.tue.nl/pumma/index.php/Theory/Potentials33
![Page 34: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/34.jpg)
�
&HAt���E��p�(�Ft��u����r������
htb://www/�h�pttrtr�p���/�p�/����y/bhb/ h��E��p�(�Ft��u��http://cbio.bmt.tue.nl/pumma/index.php/Theory/Potentials 34
![Page 35: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/35.jpg)
�
�
35
&HAt���E��p�(�Ft��u����r�����
H�pt�����t�p���� t���r���� ���t�rp(�
�
© C. R. Nave. All rights reserved. This content is excluded from
our Creative Commons license. For more information, seehttp://ocw.mit.edu/help/faq-fair-use/.
htb://www/�h�pttrtr�p���/�p�/����y/bhb/ h��E��p�(�Ft��u��http://cbio.bmt.tue.nl/pumma/index.php/Theory/Potentials
35
![Page 36: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/36.jpg)
�&HAt���E��p�(�Ft��u����r�����
htb://www/�h�pttrtr�p���/�p�/����y/bhb/ h��E��p�(�Ft��u��http://cbio.bmt.tue.nl/pumma/index.php/Theory/Potentials
36
![Page 37: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/37.jpg)
�
�������
&HAt���E��p�(�Ft��u���� ���Pr�����
N��Pr������r�pt�:� L����p��I�����
E���rp��r�u���
and
37
![Page 38: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/38.jpg)
�&HAt���E��p�(�Ft��u���� ���Pr�����
38
© source unknown. All rights reserved. This content is excluded from our Creative
Commons license. For more information, see http://ocw.mit.edu/help/faq-fair-use/.
![Page 39: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/39.jpg)
V)�.����.��
39
![Page 40: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/40.jpg)
�
t���t��E��p�(�Ft��u��� ���b����t�rp(� y����
X 40
![Page 41: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/41.jpg)
t���t��E��p�(�Ft��u��� t�r�t�p�:� ��������p�r���������wh��� r�����p�r�r��
41
Source: Kuszewski, John, Angela M. Gronenborn, et al. "Improvements and Extensions
in the Conformational Database Potential for the Refinement of NMR and X-ray Structures
of Proteins and Nucleic Acids." Journal of Magnetic Resonance 125, no. 1 (1997): 171-7.
Courtesy of Elsevier, Inc., http://www.sciencedirect.com. Used with permission.
![Page 42: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/42.jpg)
Fp�bt���(��t��r�r���
Etb�p�����b�r��u������p�(�
Courtesy of Steven Combs (PDF). Used with permission.
42
![Page 43: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/43.jpg)
Courtesy of Jeffrey J Gray (PDF). Used with permission.
43
![Page 44: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/44.jpg)
p�p(���t���p�r��bh(�����r�p��w�
44
Courtesy of Jeffrey J Gray (PDF) . Used with permission.
Courtesy of Steven Combs (PDF). Used with permission.
44
![Page 45: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/45.jpg)
Courtesy of Steven Combs (PDF). Used with permission.
45
![Page 46: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/46.jpg)
tp�t�p���tt���p�r�u����
46
© Wiley-Liss. All rights reserved. This content is excluded from our Creative Commons
license. For more information, see http://ocw.mit.edu/help/faq-fair-use/.
Source: Mendes, Joaquim, António M. Baptista, et al. "Improved Modeling of Side‐chains
in Proteins with Rotamer-based Methods: A Flexible Rotamer Model." Proteins: Structure,
Function, and Bioinformatics 37, no. 4 (1999): 530-43.Courtesy of Jane S. Richardson. License: CC-BY.
46
![Page 47: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/47.jpg)
����p�u������p�p(�h�p��t�p�rh��bh(�����r��
47
![Page 48: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/48.jpg)
48
![Page 49: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/49.jpg)
���p�u������p�p(�h�p��t�p�rh��bh(�����r�� ���(�t�p�rh���r�u�u�����
Etb�p��������tu��� solv RefΔGi = Δ Gi −∑ fi ( )rij Vj
Eyb�p�t��r���(� ��r�pt����� ���p�u���� �t��p�tb� wh���tt��(�
��r�p��u����t� �p�tb�t����p��r� �p�tb����t��yb����/�
8Fp�t�rp���t�p� �yb�p�t��r���
j i≠
V��tt���t�� ����hr�p����
t��r����P ��b�����r� tt��u���t�p��
49
![Page 50: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/50.jpg)
Courtesy of Jeffrey J Gray (PDF). Used with permission.
50
![Page 51: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/51.jpg)
�ttt�p(�
• tp�r�����rpt�rtp�����t����������r�����(� • Eyb�p�t��r���r��h��bt�����p������rp���r�����r� �rpt�rtp���
• &�tbtr�u�����t�rh�����������r����r�pbp�r� ����rp���r��
• w��t�����bbp���h��:�bh(�����������r�u�u����
51
![Page 52: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/52.jpg)
Wh�r�w�p��rh��y�(���tb�� ��u�����t� rh���r�u�u�����bbp���h-�
© source unknown. All rights reserved. This content is excluded from our Creative
Commons license. For more information, see http://ocw.mit.edu/help/faq-fair-use/.
52
Courtesy of http://vadlo.com/. Used with permission.
![Page 53: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/53.jpg)
Wh�r�w�p��rh��y�(���tb�� ��u�����t� rh���r�u�u�����bbp���h-�
• F�y������t�rp(�
• t���p�r��p�r�t�p��
• �r�u�u����b�r��u��� Fp�bt���(��t��r�r���
Etb�p�����b�r��u������p�(�
53
Source: Kuszewski, John, Angela M. Gronenborn, et al."Improvements and Extensions in the Conformational
Database Potential for the Refinement of NMR and X-ray
Structures of Proteinsand NucleicAcids." Journal of
Magnetic Resonance 125, no. 1 (1997): 171-7.
53
Courtesy of Elsevier, Inc., http://www.sciencedirect.com.Used with permission.
![Page 54: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/54.jpg)
A�rh�t�hr��yb�p�t��r:� Wh��h��rpt�rtp��t�r�h�������bt����-�
rQVFL�AtttAtEV��rY tNLrLQY�t���LQ�rLt tALutFEN�LAtu�Ft AAt��YtrtH AFE��rrV Q �t�FtV�LrEAAtN HFttLuLE AtAFuH�L A AALA&FFAtE�A N��
Courtesy of RCSB Protein Data Bank. Used with permission.
54
htb://www/p��r/�p�/b�r/�t����/2ph3�r���p�S11/tb�
� htb://www/p��r/�p�/b�r/�t����/1btb�r���p�S11/tb��54
![Page 55: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/55.jpg)
p�/�
• H�w���t���(�t�t������p�(�tt��u����r�� ���u��t��h-�– L�ru�����tt�������t�rh���rpt�rtp������rh����pp��r� ���/�
– Wh��h��h�t���h�p��rh����w�p�b�r��u������p�(-�– Wh�r����(�t�rh��y�h�bb�������bp��u��-�
Courtesy of RCSB Protein Data Bank. Used with permission.
55
![Page 56: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/56.jpg)
p�/�
• rt������t�rh���rpt�rtp������rh����pp��r����:� – N����r����r�pt����������h�������t�pt�u���� r�t�p������t��u���b�r��u���
• rt�r�t�p��rpt�rtp��������(��bbp�y�t�r�:� – N����r��p� ���r��yr��������������h����� p�r/�
Courtesy of RCSB Protein Data Bank. Used with permission.
56
![Page 57: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/57.jpg)
hp�������8t����p������u����
rQVFL�AtttAtEV��rY tNLrLQY�t���LQ�rLt tALutFEN�LAtu�Ft AAt��YtrtH AFE��rrV Q �t�FtV�LrEAAtN HFttLuLE AtAFuH�L A AALA&FFAtE�A N��
Courtesy of RCSB Protein Data Bank.Used with permission.
57
![Page 58: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/58.jpg)
Orh�p�bp����u���bp�r��t�� �������p(��rpt�rtp��
rQVFL�AtttAtEV��rY tNLrLQY�t���LQ�rLt tALutFEN�LAtu�Ft AAt��YtrtH AFE��rrV Q �t�FtV�LrEAAtN HFttLuLE AtAFuH�L A AALA&FFAtE�A N��
��t�����rpt�rtp��
��p���3t��rpt�rtp��
58
Courtesy of RCSB Protein Data Bank.Used with permission.
58
![Page 59: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/59.jpg)
��t��h��r�p(�
�NrVA&�1�p�����������14S1� Courtesy of U.S. Department of the Army Ballistic Research Report. In the public domain.
59
© The estate of the authors. All rights reserved.
This content is excluded from our Creative
Commons license. For more information, see
http://ocw.mit.edu/help/faq-fair-use/.
Source: Pauling, Linus, Robert B. Corey, and Herman R.Branson. "The Structure of Proteins: Two Hydrogen-bonded Helical Configurations of the Polypeptide
Chain." Proceedings of the National Academy ofSciences 37, no. 4 (1951): 205-211.
![Page 60: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/60.jpg)
64�
��t��h��r�p(�
• t�b�p�t������� • ��(������hr�wh�����(�������r�������y�� • tp�������r(���r���t�h�p��w�py�������u��� �yb�p�t��r�����r��
• t����p�b�bu���r����� • ��y�t����h(�p�����r�����
60
© The estate of the authors. All rights reserved.
This content is excluded from our Creative
Commons license. For more information, see
http://ocw.mit.edu/help/faq-fair-use/.
Source: Pauling, Linus, Robert B. Corey, and Herman R.Branson. "The Structure of Proteins: Two Hydrogen-bonded Helical Configurations of the Polypeptide
Chain." Proceedings of the National Academy ofSciences 37, no. 4 (1951): 205-211.
![Page 61: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/61.jpg)
Source: Ramachandran, G. N., C. T. Ramakrishnan, et al. "Stereochemistry of Polypeptide
Chain Configurations." Journal of Molecular Biology 7, no. 1 (1963): 95-9.
© source unknown. All rights reserved. This content is excluded
from our Creative Commons license. For more information,
see http://ocw.mit.edu/help/faq-fair-use/.
61
Courtesy of Elsevier, Inc., http://www.sciencedirect.com. Used with permission.
![Page 62: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/62.jpg)
B��bh(������I�tp����V��tt��7��r��t��2����p�h�1467��t�����121�13S�
62
![Page 63: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/63.jpg)
© source unknown. All rights reserved. This content is excluded from our Creative
Commons license. For more information, see http://ocw.mit.edu/help/faq-fair-use/.
63
![Page 64: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/64.jpg)
• A���tr�����r�u�u���� ��r��tp�t�rh���t������r� �t�y��w���rpt�rtp���
• t� �����bp�b����r(�� t�p�h���y�t�pt�u���
• &pt���pt����r��bp����r� h�������p�������
© American Chemical Society. All rights reserved. This content is excludedfrom our Creative Commons license. For more information, seehttp://ocw.mit.edu/help/faq-fair-use/.
64
Source: Chou, Peter Y., and Gerald D. Fasman. "Conformational Parameters
for Amino Acidsin Helical, β-sheet, and Random Coil Regions Calculated from
Proteins." Biochemistry 13, no. 2 (1974): 211-22.
![Page 65: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/65.jpg)
�
• Helix Nucleaton/��L���r����t�r�p���t�t�tp��tr��t���y� p����t���w�rh���h��h�bp�b����r(�t�p�t�pt����h������/�����
• h�p���p���b������������t�p�A�b�����H���wh��h�w��y�(� �t����r������t�p� (p��A����tp������u�(�wh��h��p�� �������p���h���y�rp��y�p�/�
• Helix Terminaton/��Eyr����rh��h����������t��r���� �o�� ��p��u����t�u��r�pt���r���r(�r�rp�b�bu����w�rh���w� �p�p����h�������bp�b����r(����p��/���
• tp�������r����tp����rh����bh��h���y/�
65
![Page 66: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/66.jpg)
t61%����tp��(�
66
![Page 67: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/67.jpg)
• Obu�����p������:� – &h�br�p�12��t��p���r�������B�tt�h��������r������ ����p�bu����t��tpp��r�����p�rht��
67
![Page 68: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/68.jpg)
Orh�p�bp����u���bp�r��t�� �������p(��rpt�rtp��
rQVFL�AtttAtEV��rY tNLrLQY�t���LQ�rLt tALutFEN�LAtu�Ft AAt��YtrtH AFE��rrV Q �t�FtV�LrEAAtN HFttLuLE AtAFuH�L A AALA&FFAtE�A N��
��t�����rpt�rtp��
��p���3t��rpt�rtp��
Courtesy of RCSB Protein Data Bank.Used with permission.
68
![Page 69: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/69.jpg)
�����.�
��p���3t��rpt�rtp��
&�tbtr�u�����tp�r����F�������
r��bp����b����w�����ur��p�����������r�pu����rpt�rtp�/� rQVFL�AtttAtEV��rY tNLrLQY�t���LQ�rLt tALutFEN�LAtu�Ft AAt��YtrtH AFE��rrV Q �t�FtV�LrEAAtN HFttLuLE AtAFuH�L A AALA&FFAtE�A N��
Courtesy of RCSB Protein Data Bank.Used with permission.
Courtesy of Nature Publishing Group. Used with permission.Source: Dill, Ken A. and Hue Sun Chan. "From Levinthal to Pathways to Funnels."
Nature Structural Biology 4, no. 1 (1997): 10-9.
69
![Page 70: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/70.jpg)
�r�u�u������p�/�th(�����r��
© source unknown. All rights reserved. This content is excluded from our Creative
Commons license. For more information, see http://ocw.mit.edu/help/faq-fair-use/.
70
Courtesy of http://vadlo.com/. Used with permission.
![Page 71: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/71.jpg)
�r�u�u������p�/�th(�����r��
M� �� • L�p�p�����p�p(rh����w��
y��w��r�tr��y��u��� �rpt�rtp����t�bp�r��������� b�bu����r��rt�����r�pu��� t������
• t� ���t�������y��w�����P r�����b�r��u���
D��.. �� • tONu �&HEA �� • O��(�t���bh(������t�p���/� • F����bp�r�����r(���tt��u���
rh�����p�rp��bp������
71
![Page 72: Lecture 12: Introduction to Protein Structure; Structure ......Courtesy of Wenqing Xu et al. and RCSB Protein Data Bank. Used with permission. Courtesy of Macmillan Publishers Limited.](https://reader033.fdocuments.us/reader033/viewer/2022041801/5e515a48b0e0283b762cd407/html5/thumbnails/72.jpg)
MIT OpenCourseWarehttp://ocw.mit.edu
7.91J / 20.490J / 20.390J / 7.36J / 6.802J / 6.874J / HST.506J Foundations of Computational and Systems BiologySpring 2014
For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms.