Predicted structures of homo-complex of H2A/H2A by AWSEM and AlphaFold2.

The structure of DHβE and Ls-AChBP complexed with DHβE.

Azadeh Shahsavar (141340)
Jette S. Kastrup (141346)
Elsebet Ø. Nielsen (141351)
Jesper L. Kristensen (141358)
Michael Gajhede (73263)
Thomas Balle (104765)

August 2012

(a) Structure of DHβE. (b) Cartoon diagram showing homopentameric Ls-...

Prediction of the conformation of the histones

Fasman, G.D.
Chou, P.Y.
Adler, A.J.

October 1976

The secondary structures of the histones, H1, H2A, H2B, H3, and H4 have been predicted utilizing the...

Sequence symmetry of hydrophobic residues explains the predictability of inverted histone-fold structure.

Haiqing Zhao (2937306)
Hao Wu (65943)
Alex Guseman (17743429)
Dulith Abeykoon (4916302)
Christina M. Camara (17743432)
Yamini Dalal (33140)
David Fushman (239364)
Garegin A. Papoian (691984)

January 2024

(A) Hydrophobic interactions (orange) dominate the formation of binding interface of H2A/H2B (colore...

Predicted structures of eukaryotic histone homodimer.

Haiqing Zhao (2937306)
Hao Wu (65943)
Alex Guseman (17743429)
Dulith Abeykoon (4916302)
Christina M. Camara (17743432)
Yamini Dalal (33140)
David Fushman (239364)
Garegin A. Papoian (691984)

January 2024

(A) AWSEM and AlphaFold2 predicted homodimer structures of H2A/H2A align well with the native hetero...

Supplemental RMSF analyses of the homo-complex structures of H2A/H2A predicted by AWSEM and AlphaFold2 show similar structural flexibilities.

Haiqing Zhao (2937306)
Hao Wu (65943)
Alex Guseman (17743429)
Dulith Abeykoon (4916302)
Christina M. Camara (17743432)
Yamini Dalal (33140)
David Fushman (239364)
Garegin A. Papoian (691984)

January 2024

The RMSF analysis of all-atom simulations exhibit similar atomic flexibilities of AWSEM- and AlphaFo...

Histone tails disfavor the formation of histone homodimer, yet stabilize the histone fold once formed.

Haiqing Zhao (2937306)
Hao Wu (65943)
Alex Guseman (17743429)
Dulith Abeykoon (4916302)
Christina M. Camara (17743432)
Yamini Dalal (33140)
David Fushman (239364)
Garegin A. Papoian (691984)

January 2024

(A) AWSEM-predicted trancated and full-sequence homodimer H2A/H2A are assessed by the maximum Qdimer...

AlphaFold2-predicted truncated and full-sequence homo-complex of H2B/H2B.

Haiqing Zhao (2937306)
Hao Wu (65943)
Alex Guseman (17743429)
Dulith Abeykoon (4916302)
Christina M. Camara (17743432)
Yamini Dalal (33140)
David Fushman (239364)
Garegin A. Papoian (691984)

January 2024

The two chains are colored by the same scheme which is the plDDT confidence score provided by AF2. B...

Environment of Thr/Asn108α and Ser/Pro124α in the structure of the human hemoglobin tetramer and of AHSP-alpha globin chain complex structure.

Maria Grazia Bisconte (697043)
Mercedes Caldora (697044)
Gennaro Musollino (697045)
Giovanna Cardiero (697046)
Angela Flagiello (21882)
Gaetana La Porta (697047)
Laura Lagona (697048)
Romeo Prezioso (697049)
Gabriele Qualtieri (697050)
Carlo Gaudiano (697051)
Emilia Medulla (697052)
Antonello Merlino (697053)
Piero Pucci (21884)
Giuseppina Lacerra (697054)

March 2015

A: Structural representation of the environment of Thr108α in the structure of the human h...

Histone heterodimers fold in MD simulations and NMR experiments, not monomers.

Haiqing Zhao (2937306)
Hao Wu (65943)
Alex Guseman (17743429)
Dulith Abeykoon (4916302)
Christina M. Camara (17743432)
Yamini Dalal (33140)
David Fushman (239364)
Garegin A. Papoian (691984)

January 2024

(A) Q values as a function of the annealing temperature are plotted for simulated histone monomers, ...

Chemical structures of MADAM, SOMADAM, SO2MADAM, NHMADAM and NHSOMADAM.

Fabienne Gourand (795483)
Nahid Amini (742999)
Zhisheng Jia (795484)
Sharon Stone-Elander (145935)
Denis Guilloteau (291116)
Louisa Barré (795485)
Christer Halldin (314522)

September 2015

Chemical structures of MADAM, SOMADAM, SO2MADAM, NHMADAM and NHSOMADAM.</p

AlphaFold predicts alpha-helical regions in the IDRs of Cno and Afadin.

Noah J. Gurley (16748634)
Rachel A. Szymanski (16748637)
Robert H. Dowen (16748640)
T. Amber Butcher (16748643)
Noboru Ishiyama (15146993)
Mark Peifer (257909)

August 2023

Images are from the predicted structures of Drosophila Cno and Human Afadin from the AlphaFold Prote...

Structures of (a) G-quartet, four guanines can hydrogen bond in a square arrangement to form a G-quartet.

Bidisha Sengupta (421592)
Biswapathik Pahari (421593)
Laura Blackmon (421594)
Pradeep K. Sengupta (421595)

June 2013

There are two hydrogen bonds on each side of the square; (b) i. Tetramolecular parallel, ii. Bimo...

Overall structure of the ecMenB: HNA-CoA complex.

Yueru Sun (407471)
Haigang Song (407472)
Jie Li (15030)
Yan Li (23143)
Ming Jiang (11433)
Jiahai Zhou (407473)
Zhihong Guo (404198)

April 2013

(A) The hexameric assembly of ecMenB:HNA-COA complex viewed along the 3-fold axis of the t...

Structure superimposition of modeled (cyan) and crystal (green) structure of Hb-Hp complex (a) as well as Hp (b) and Hb (c) structures.

Chanin Nantasenamat (407497)
Virapong Prachayasittikul (13700)
Leif Bulow (5652454)

April 2013

Structure superimposition of modeled (cyan) and crystal (green) structure of Hb-Hp complex (a) as...

Overview of the structures of KR01 HA and its complex with Fab0587.

Ki Joon Cho (527874)
Kwang W. Hong (527875)
Se-Ho Kim (527876)
Jong Hyeon Seok (436871)
Sella Kim (527877)
Ji-Hye Lee (285311)
Xavier Saelens (28372)
Kyung Hyun Kim (436874)

February 2014

(A) Structure of KR01 HA-Fab0587 complex. HA are colored in orange and light brown, H-chains are ...

The structure of DHβE and Ls-AChBP complexed with DHβE.

Azadeh Shahsavar (141340)
Jette S. Kastrup (141346)
Elsebet Ø. Nielsen (141351)
Jesper L. Kristensen (141358)
Michael Gajhede (73263)
Thomas Balle (104765)

August 2012

(a) Structure of DHβE. (b) Cartoon diagram showing homopentameric Ls-...

Prediction of the conformation of the histones

Fasman, G.D.
Chou, P.Y.
Adler, A.J.

October 1976

The secondary structures of the histones, H1, H2A, H2B, H3, and H4 have been predicted utilizing the...

Sequence symmetry of hydrophobic residues explains the predictability of inverted histone-fold structure.

Haiqing Zhao (2937306)
Hao Wu (65943)
Alex Guseman (17743429)
Dulith Abeykoon (4916302)
Christina M. Camara (17743432)
Yamini Dalal (33140)
David Fushman (239364)
Garegin A. Papoian (691984)

January 2024

(A) Hydrophobic interactions (orange) dominate the formation of binding interface of H2A/H2B (colore...

Predicted structures of eukaryotic histone homodimer.

Haiqing Zhao (2937306)
Hao Wu (65943)
Alex Guseman (17743429)
Dulith Abeykoon (4916302)
Christina M. Camara (17743432)
Yamini Dalal (33140)
David Fushman (239364)
Garegin A. Papoian (691984)

January 2024

(A) AWSEM and AlphaFold2 predicted homodimer structures of H2A/H2A align well with the native hetero...

Supplemental RMSF analyses of the homo-complex structures of H2A/H2A predicted by AWSEM and AlphaFold2 show similar structural flexibilities.

Haiqing Zhao (2937306)
Hao Wu (65943)
Alex Guseman (17743429)
Dulith Abeykoon (4916302)
Christina M. Camara (17743432)
Yamini Dalal (33140)
David Fushman (239364)
Garegin A. Papoian (691984)

January 2024

The RMSF analysis of all-atom simulations exhibit similar atomic flexibilities of AWSEM- and AlphaFo...

Histone tails disfavor the formation of histone homodimer, yet stabilize the histone fold once formed.

Haiqing Zhao (2937306)
Hao Wu (65943)
Alex Guseman (17743429)
Dulith Abeykoon (4916302)
Christina M. Camara (17743432)
Yamini Dalal (33140)
David Fushman (239364)
Garegin A. Papoian (691984)

January 2024

(A) AWSEM-predicted trancated and full-sequence homodimer H2A/H2A are assessed by the maximum Qdimer...

AlphaFold2-predicted truncated and full-sequence homo-complex of H2B/H2B.

Haiqing Zhao (2937306)
Hao Wu (65943)
Alex Guseman (17743429)
Dulith Abeykoon (4916302)
Christina M. Camara (17743432)
Yamini Dalal (33140)
David Fushman (239364)
Garegin A. Papoian (691984)

January 2024

The two chains are colored by the same scheme which is the plDDT confidence score provided by AF2. B...

Environment of Thr/Asn108α and Ser/Pro124α in the structure of the human hemoglobin tetramer and of AHSP-alpha globin chain complex structure.

Maria Grazia Bisconte (697043)
Mercedes Caldora (697044)
Gennaro Musollino (697045)
Giovanna Cardiero (697046)
Angela Flagiello (21882)
Gaetana La Porta (697047)
Laura Lagona (697048)
Romeo Prezioso (697049)
Gabriele Qualtieri (697050)
Carlo Gaudiano (697051)
Emilia Medulla (697052)
Antonello Merlino (697053)
Piero Pucci (21884)
Giuseppina Lacerra (697054)

March 2015

A: Structural representation of the environment of Thr108α in the structure of the human h...

Histone heterodimers fold in MD simulations and NMR experiments, not monomers.

Haiqing Zhao (2937306)
Hao Wu (65943)
Alex Guseman (17743429)
Dulith Abeykoon (4916302)
Christina M. Camara (17743432)
Yamini Dalal (33140)
David Fushman (239364)
Garegin A. Papoian (691984)

January 2024

(A) Q values as a function of the annealing temperature are plotted for simulated histone monomers, ...

Chemical structures of MADAM, SOMADAM, SO2MADAM, NHMADAM and NHSOMADAM.

Fabienne Gourand (795483)
Nahid Amini (742999)
Zhisheng Jia (795484)
Sharon Stone-Elander (145935)
Denis Guilloteau (291116)
Louisa Barré (795485)
Christer Halldin (314522)

September 2015

Chemical structures of MADAM, SOMADAM, SO2MADAM, NHMADAM and NHSOMADAM.</p

AlphaFold predicts alpha-helical regions in the IDRs of Cno and Afadin.

Noah J. Gurley (16748634)
Rachel A. Szymanski (16748637)
Robert H. Dowen (16748640)
T. Amber Butcher (16748643)
Noboru Ishiyama (15146993)
Mark Peifer (257909)

August 2023

Images are from the predicted structures of Drosophila Cno and Human Afadin from the AlphaFold Prote...

Structures of (a) G-quartet, four guanines can hydrogen bond in a square arrangement to form a G-quartet.

Bidisha Sengupta (421592)
Biswapathik Pahari (421593)
Laura Blackmon (421594)
Pradeep K. Sengupta (421595)

June 2013

There are two hydrogen bonds on each side of the square; (b) i. Tetramolecular parallel, ii. Bimo...

Overall structure of the ecMenB: HNA-CoA complex.

Yueru Sun (407471)
Haigang Song (407472)
Jie Li (15030)
Yan Li (23143)
Ming Jiang (11433)
Jiahai Zhou (407473)
Zhihong Guo (404198)

April 2013

(A) The hexameric assembly of ecMenB:HNA-COA complex viewed along the 3-fold axis of the t...

Structure superimposition of modeled (cyan) and crystal (green) structure of Hb-Hp complex (a) as well as Hp (b) and Hb (c) structures.

Chanin Nantasenamat (407497)
Virapong Prachayasittikul (13700)
Leif Bulow (5652454)

April 2013

Structure superimposition of modeled (cyan) and crystal (green) structure of Hb-Hp complex (a) as...

Overview of the structures of KR01 HA and its complex with Fab0587.

Ki Joon Cho (527874)
Kwang W. Hong (527875)
Se-Ho Kim (527876)
Jong Hyeon Seok (436871)
Sella Kim (527877)
Ji-Hye Lee (285311)
Xavier Saelens (28372)
Kyung Hyun Kim (436874)

February 2014

(A) Structure of KR01 HA-Fab0587 complex. HA are colored in orange and light brown, H-chains are ...

The structure of DHβE and Ls-AChBP complexed with DHβE.

Azadeh Shahsavar (141340)
Jette S. Kastrup (141346)
Elsebet Ø. Nielsen (141351)
Jesper L. Kristensen (141358)
Michael Gajhede (73263)
Thomas Balle (104765)

August 2012

(a) Structure of DHβE. (b) Cartoon diagram showing homopentameric Ls-...

Prediction of the conformation of the histones

Fasman, G.D.
Chou, P.Y.
Adler, A.J.

October 1976

The secondary structures of the histones, H1, H2A, H2B, H3, and H4 have been predicted utilizing the...

Sequence symmetry of hydrophobic residues explains the predictability of inverted histone-fold structure.

Haiqing Zhao (2937306)
Hao Wu (65943)
Alex Guseman (17743429)
Dulith Abeykoon (4916302)
Christina M. Camara (17743432)
Yamini Dalal (33140)
David Fushman (239364)
Garegin A. Papoian (691984)

January 2024

(A) Hydrophobic interactions (orange) dominate the formation of binding interface of H2A/H2B (colore...

Predicted structures of homo-complex of H2A/H2A by AWSEM and AlphaFold2.

Abstract

Extracted data

Predicted structures of homo-complex of H2A/H2A by AWSEM and AlphaFold2.

Abstract

Extracted data

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