Steven T. Whitten, Ph.D. - Related publications

2000 Johns Hopkins University, Baltimore, MD 
General Biophysics, Biochemistry
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Campos LA, Sadqi M, Muñoz V. Lessons about Protein Folding and Binding from Archetypal Folds. Accounts of Chemical Research. PMID 32914959 DOI: 10.1021/acs.accounts.0c00322   
2020 Heilmann N, Wolf M, Kozlowska M, Sedghamiz E, Setzler J, Brieg M, Wenzel W. Sampling of the conformational landscape of small proteins with Monte Carlo methods. Scientific Reports. 10: 18211. PMID 33097750 DOI: 10.1038/s41598-020-75239-7   
2020 Skolnick J, Gao M. The role of local versus nonlocal physicochemical restraints in determining protein native structure. Current Opinion in Structural Biology. 68: 1-8. PMID 33129066 DOI: 10.1016/   
2020 Subramanian S, Golla H, Divakar K, Kannan A, De Sancho D, Naganathan AN. Slow Folding of a Helical Protein: Large Barriers, Strong Internal Friction, or a Shallow, Bumpy Landscape? The Journal of Physical Chemistry. B. PMID 32955882 DOI: 10.1021/acs.jpcb.0c05976   
2020 Mukhopadhyay S. The Dynamism of Intrinsically Disordered Proteins: Binding-Induced Folding, Amyloid Formation, and Phase Separation. The Journal of Physical Chemistry. B. PMID 33108190 DOI: 10.1021/acs.jpcb.0c07598   
2020 Yagi-Utsumi M, Chandak MS, Yanaka S, Hiranyakorn M, Nakamura T, Kato K, Kuwajima K. Residual Structure of Unfolded Ubiquitin as Revealed by Hydrogen/Deuterium-Exchange 2D NMR. Biophysical Journal. PMID 33142107 DOI: 10.1016/j.bpj.2020.10.003   
2020 Di Lena P, Baldi P. Fold recognition by scoring protein maps using the congruence coefficient. Bioinformatics (Oxford, England). PMID 32976564 DOI: 10.1093/bioinformatics/btaa833   
2020 Chen X, Rajasekaran N, Liu K, Kaiser CM. Synthesis runs counter to directional folding of a nascent protein domain. Nature Communications. 11: 5096. PMID 33037221 DOI: 10.1038/s41467-020-18921-8   
2020 Henry L, Panman MR, Isaksson L, Claesson E, Kosheleva I, Henning R, Westenhoff S, Berntsson O. Real-time tracking of protein unfolding with time-resolved x-ray solution scattering. Structural Dynamics (Melville, N.Y.). 7: 054702. PMID 32984436 DOI: 10.1063/4.0000013   
2020 Bozovic O, Zanobini C, Gulzar A, Jankovic B, Buhrke D, Post M, Wolf S, Stock G, Hamm P. Real-time observation of ligand-induced allosteric transitions in a PDZ domain. Proceedings of the National Academy of Sciences of the United States of America. PMID 33020277 DOI: 10.1073/pnas.2012999117   
2020 Yan Z, Wang J. Funneled energy landscape unifies principles of protein binding and evolution. Proceedings of the National Academy of Sciences of the United States of America. PMID 33067388 DOI: 10.1073/pnas.2013822117   
2020 Zhang P, Wang D, Yang W, Marszalek PE. Piecewise All-Atom Steered Molecular Dynamics Simulations Reveal Key Secondary Structures in the Luciferase Mechanical Unfolding Pathway. Biophysical Journal. PMID 33130123 DOI: 10.1016/j.bpj.2020.10.023   
2020 Nandi T, Desai A, Ainavarapu SRK. The unfolding transition state of ubiquitin with charged residues has higher energy than that with hydrophobic residues. Physical Chemistry Chemical Physics : Pccp. PMID 33026000 DOI: 10.1039/d0cp03876h   
2020 Nagpal S, Luong TDN, Sadqi M, Muñoz V. Downhill (Un)Folding Coupled to Binding as a Mechanism for Engineering Broadband Protein Conformational Transducers. Acs Synthetic Biology. 9: 2427-2439. PMID 32822536 DOI: 10.1021/acssynbio.0c00190   
2020 Sánchez Rodríguez F, Simpkin AJ, Davies OR, Keegan RM, Rigden DJ. Helical ensembles outperform ideal helices in molecular replacement. Acta Crystallographica. Section D, Structural Biology. 76: 962-970. PMID 33021498 DOI: 10.1107/S205979832001133X   
2020 Cai K, Zheng X, Hou Y, Chen F, Yan G, Zhuang D. Deciphering the structural preference encoded in amide-I vibrations of lysine dipeptide in gas phase and in aqueous solution. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 247: 119066. PMID 33091736 DOI: 10.1016/j.saa.2020.119066   
2020 Chashmniam S, Teixeria JMC, Paniagua JC, Pons M. A methionine chemical shift based order parameter characterizing global protein dynamics. Chembiochem : a European Journal of Chemical Biology. PMID 33166021 DOI: 10.1002/cbic.202000701   
2020 Zohib M, Maheshwari D, Pal RK, Freitag-Pohl S, Biswal BK, Pohl E, Arora A. Crystal structure of the GDP-bound GTPase domain of Rab5a from Leishmania donovani. Acta Crystallographica. Section F, Structural Biology Communications. 76: 544-556. PMID 33135673 DOI: 10.1107/S2053230X20013722   
2020 Hinostroza F, Neely A, Araya-Duran I, Marabolí V, Canan J, Rojas M, Aguayo D, Latorre R, González-Nilo FD, Cárdenas AM. Dynamin-2 R465W mutation induces long range perturbation in highly ordered oligomeric structures. Scientific Reports. 10: 18151. PMID 33097808 DOI: 10.1038/s41598-020-75216-0   
2020 Fujino Y, Miyagawa T, Torii M, Inoue M, Fujii Y, Okanishi H, Kanai Y, Masui R. Structural changes induced by ligand-binding drastically increase the thermostability of the Ser/Thr protein kinase TpkD from Thermus thermophilus HB8. Febs Letters. PMID 33159808 DOI: 10.1002/1873-3468.13996   
2020 Wingert B, Krieger J, Li H, Bahar I. Adaptability and specificity: how do proteins balance opposing needs to achieve function? Current Opinion in Structural Biology. 67: 25-32. PMID 33053463 DOI: 10.1016/   
2020 Sonar P, Bellucci L, Mossa A, Heidarsson PO, Kragelund BB, Cecconi C. Effects of Ligand Binding on the Energy Landscape of Acyl-CoA-Binding Protein. Biophysical Journal. PMID 33080224 DOI: 10.1016/j.bpj.2020.09.016   
2020 Mendelman N, Zerbetto M, Buck M, Meirovitch E. Conformational Entropy from Mobile Bond Vectors in Proteins: A Viewpoint that Unifies NMR-Relaxation-Theory and Molecular-Dynamics-Simulation Approaches. The Journal of Physical Chemistry. B. PMID 32981310 DOI: 10.1021/acs.jpcb.0c05846   
2020 Tang WS, Fawzi NL, Mittal J. Refining All-Atom Protein Force Fields for Polar-Rich, Prion-like, Low-Complexity Intrinsically Disordered Proteins. The Journal of Physical Chemistry. B. PMID 33078950 DOI: 10.1021/acs.jpcb.0c07545   
2020 Neira JL, Rizzuti B, Jiménez-Alesanco A, Palomino-Schätzlein M, Abián O, Velázquez-Campoy A, Iovanna JL. A Phosphorylation-Induced Switch in the Nuclear Localization Sequence of the Intrinsically Disordered NUPR1 Hampers Binding to Importin. Biomolecules. 10. PMID 32933064 DOI: 10.3390/biom10091313   
2020 Muthuramalingam M, Whittier SK, Lovell S, Battaile KP, Tachiyama S, Johnson DK, Picking WL, Picking WD. The Structures of SctK and SctD from Pseudomonas aeruginosa Reveal the Interface of the Type III Secretion System Basal Body and Sorting Platform. Journal of Molecular Biology. PMID 33122003 DOI: 10.1016/j.jmb.2020.10.027   
2020 Oroz J, Félix SS, Cabrita EJ, Laurents DV. Structural transitions in Orb2 prion-like domain relevant for functional aggregation in memory consolidation. The Journal of Biological Chemistry. PMID 33093173 DOI: 10.1074/jbc.RA120.015211   
2020 Pang Y, Liu B. SelfAT-Fold: protein fold recognition based on residue-based and motif-based self-attention networks. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 33090951 DOI: 10.1109/TCBB.2020.3031888   
2020 Kumawat A, Chakrabarty S. Protonation-Induced Dynamic Allostery in PDZ Domain: Evidence of Perturbation-Independent Universal Response Network. The Journal of Physical Chemistry Letters. 9026-9031. PMID 33043672 DOI: 10.1021/acs.jpclett.0c02885   
2020 Fenner K, Redgate A, Brancaleon L. A 200 nanoseconds all-atom simulation of the pH-dependent EF loop transition in bovine β-lactoglobulin. The role of the orientation of the E89 side chain. Journal of Biomolecular Structure & Dynamics. 1-16. PMID 32909899 DOI: 10.1080/07391102.2020.1817785   
2020 Clark JJ, Orban ZJ, Carlson HA. Predicting binding sites from unbound versus bound protein structures. Scientific Reports. 10: 15856. PMID 32985584 DOI: 10.1038/s41598-020-72906-7   
2020 Smith LJ, van Gunsteren WF, Hansen N. On the Use of Side-Chain NMR Relaxation Data to Derive Structural and Dynamical Information on Proteins: A Case Study using Hen Lysozyme. Chembiochem : a European Journal of Chemical Biology. PMID 33146424 DOI: 10.1002/cbic.202000674   
2020 Kamalesh D, Nair A, Sreeshma J, Arundhathi PS, Sudandiradoss C. Statistical and molecular dynamics (MD) simulation approach to investigate the role of intrinsically disordered regions of shikimate dehydrogenase in microorganisms surviving at different temperatures. Extremophiles : Life Under Extreme Conditions. PMID 32975630 DOI: 10.1007/s00792-020-01198-6   
2020 Singh R, Deshmukh S, Kumar A, Goyal VD, Makde RD. Crystal structure of XCC3289 from Xanthomonas campestris: homology with the N-terminal substrate-binding domain of Lon peptidase. Acta Crystallographica. Section F, Structural Biology Communications. 76: 488-494. PMID 33006577 DOI: 10.1107/S2053230X20011875   
2020 Zong Z, Hao A, Xing P. Supramolecular secondary helical structures in solid-state -protected amino acids. Nanoscale. 12: 20610-20620. PMID 33090165 DOI: 10.1039/d0nr05259k   
2020 Wang X, Unarta IC, Cheung PP, Huang X. Elucidating molecular mechanisms of functional conformational changes of proteins via Markov state models. Current Opinion in Structural Biology. 67: 69-77. PMID 33126140 DOI: 10.1016/   
2020 Shityakov S, Fischer A, Su KP, Hussein AA, Dandekar T, Broscheit J. Novel Approach for Characterizing Propofol Binding Affinities to Serum Albumins from Different Species. Acs Omega. 5: 25543-25551. PMID 33073080 DOI: 10.1021/acsomega.0c01295   
2020 Romero JA, Nawrocka EK, Shchukina A, Blanco FJ, Diercks T, Kazimierczuk K. Non-Stationary Complementary Non-Uniform Sampling (NOSCO NUS) for Fast Acquisition of Serial 2D NMR Titration Data. Angewandte Chemie (International Ed. in English). PMID 32852098 DOI: 10.1002/anie.202009479   
2020 Liu Q, He QT, Lyu X, Yang F, Zhu ZL, Xiao P, Yang Z, Zhang F, Yang ZY, Wang XY, Sun P, Wang QW, Qu CX, Gong Z, Lin JY, et al. DeSiphering receptor core-induced and ligand-dependent conformational changes in arrestin via genetic encoded trimethylsilyl H-NMR probe. Nature Communications. 11: 4857. PMID 32978402 DOI: 10.1038/s41467-020-18433-5   
2020 Kaur N, Sagar A, Sharma P, Ashish, Pati PK. Structural insights into rice SalTol QTL located SALT protein. Scientific Reports. 10: 16589. PMID 33024209 DOI: 10.1038/s41598-020-73517-y   
2020 Heller GT, Aprile FA, Michaels TCT, Limbocker R, Perni M, Ruggeri FS, Mannini B, Löhr T, Bonomi M, Camilloni C, De Simone A, Felli IC, Pierattelli R, Knowles TPJ, Dobson CM, et al. Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer's disease. Science Advances. 6. PMID 33148639 DOI: 10.1126/sciadv.abb5924   
2020 Bergues-Pupo AE, Lipowsky R, Vila Verde A. Unfolding mechanism and free energy landscape of single, stable, alpha helices at low pull speeds. Soft Matter. PMID 33030193 DOI: 10.1039/d0sm01166e   
2020 Sindhikara D, Wagner M, Gkeka P, Güssregen S, Tiwari G, Hessler G, Yapici E, Li Z, Evers A. Automated Design of Macrocycles for Therapeutic Applications: From Small Molecules to Peptides and Proteins. Journal of Medicinal Chemistry. PMID 33017535 DOI: 10.1021/acs.jmedchem.0c01500   
2020 Ou X, Xue B, Lao Y, Wutthinitikornkit Y, Tian R, Zou A, Yang L, Wang W, Cao Y, Li J. Structure and sequence features of mussel adhesive protein lead to its salt-tolerant adhesion ability. Science Advances. 6. PMID 32978166 DOI: 10.1126/sciadv.abb7620   
2020 Kumar S, Akabayov SR, Kessler N, Cohen LS, Solanki J, Naider F, Kay LE, Anglister J. The methyl C-edited/C-filtered transferred NOE for studying protein interactions with short linear motifs. Journal of Biomolecular Nmr. PMID 32997264 DOI: 10.1007/s10858-020-00340-y   
2020 Szabó G, Pénzes K, Torner B, Fagyas M, Tarr T, Soltész P, Kis G, Antal M, Kappelmayer J. Distinct and overlapping effects of β-glycoprotein I conformational variants in ligand interactions and functional assays. Journal of Immunological Methods. 112877. PMID 33031793 DOI: 10.1016/j.jim.2020.112877   
2020 Croll T, Diederichs K, Fischer F, Fyfe C, Gao Y, Horrell S, Joseph AP, Kandler L, Kippes O, Kirsten F, Müller K, Nolte K, Payne A, Reeves MG, Richardson J, et al. Making the invisible enemy visible. Biorxiv : the Preprint Server For Biology. PMID 33052340 DOI: 10.1101/2020.10.07.307546   
2020 Taidi L, Maurady A, Britel MR. Molecular docking study and molecular dynamic simulation of human cyclooxygenase-2 (COX-2) with selected eutypoids. Journal of Biomolecular Structure & Dynamics. 1-16. PMID 32990169 DOI: 10.1080/07391102.2020.1823884   
2020 Karlsson E, Paissoni C, Erkelens AM, Tehranizadeh ZA, Sorgenfrei FA, Andersson E, Ye W, Camilloni C, Jemth P. Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins. The Journal of Biological Chemistry. PMID 33067355 DOI: 10.1074/jbc.RA120.015645   
2020 Morales P, Bruix M, Jiménez MA. Structural Insights into β-arrestin/CB1 Receptor Interaction: NMR and CD Studies on Model Peptides. International Journal of Molecular Sciences. 21. PMID 33143110 DOI: 10.3390/ijms21218111