Visualization of transient encounter complexes in protein–protein association

Electrostatics of nanosystems: Application to microtubules and the ribosome

Baker, N., Sept, D., Joseph, S., Holst, M., & McCammon, J. A. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.181342398 · Cited by 7,125

Principles of protein-protein interactions

Jones, S., & Thornton, J. M. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.1.13 · Cited by 2,684

Structure and Mechanism in Protein Science

Fersht, A. (2017) · WORLD SCIENTIFIC eBooks · doi:10.1142/10574 · Cited by 2,053

Structural chemistry and molecular biology

Rich, A. S., Davidson, N., & Pauling, L. C. (1968) · Medical Entomology and Zoology · Cited by 1,693

SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions

Laskowski, R. A. (1995) · Journal of Molecular Graphics · doi:10.1016/0263-7855(95)00073-9 · Cited by 1,005

Using Xplor–NIH for NMR molecular structure determination

Schwieters, C. D., Kuszewski, J. J., & Clore, G. M. (2005) · Progress in Nuclear Magnetic Resonance Spectroscopy · doi:10.1016/j.pnmrs.2005.10.001 · Cited by 774

Rapid, electrostatically assisted association of proteins

Schreiber, G., & Fersht, A. R. (1996) · Nature Structural Biology · doi:10.1038/nsb0596-427 · Cited by 560

Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2

Nilges, M., Gronenborn, A. M., Brünger, A. T., & Clore, G. M. (1988) · Protein Engineering Design and Selection · doi:10.1093/protein/2.1.27 · Cited by 534

Detecting transient intermediates in macromolecular binding by paramagnetic NMR

Iwahara, J., & Clore, G. M. (2006) · Nature · doi:10.1038/nature04673 · Cited by 374

Ensemble Approach for NMR Structure Refinement against1H Paramagnetic Relaxation Enhancement Data Arising from a Flexible Paramagnetic Group Attached to a Macromolecule

Iwahara, J., Schwieters, C. D., & Clore, G. M. (2004) · Journal of the American Chemical Society · doi:10.1021/ja031580d · Cited by 328

Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy

Gruene, T., Cho, M., Karyagina, I., Kim, H., Grosse, C., Giller, K., Zweckstetter, M., & Becker, S. (2011) · Journal of Biomolecular NMR · doi:10.1007/s10858-011-9471-y · Cited by 22

Downhill binding energy surface of the barnase–barstar complex

Wang, L., Siu, S. W. I., Gu, W., & Helms, V. (2010) · Biopolymers · doi:10.1002/bip.21507 · Cited by 23

Dissecting subsecond cadherin bound states reveals an efficient way for cells to achieve ultrafast probing of their environment

Pierrès, A., Prakasam, A., Touchard, D., Benoliel, A., Bongrand, P., & Leckband, D. E. (2007) · FEBS Letters · doi:10.1016/j.febslet.2007.03.077 · Cited by 22

Structural Basis of Efficient Electron Transport between Photosynthetic Membrane Proteins and Plastocyanin in Spinach Revealed Using Nuclear Magnetic Resonance

Ueda, T., Nomoto, N., Koga, M., Ogasa, H., Ogawa, Y., Matsumoto, M., Stampoulis, P., Sode, K., Terasawa, H., & Shimada, I. (2012) · The Plant Cell · doi:10.1105/tpc.112.102517 · Cited by 22

Photoinitiated Singlet and Triplet Electron Transfer across a Redesigned [Myoglobin, Cytochromeb5] Interface

Nocek, J. M., Knutson, A. K., Peng, X., Co, N. P., & Hoffman, B. M. (2010) · Journal of the American Chemical Society · doi:10.1021/ja100499j · Cited by 21

Mobility of TOAC spin-labelled peptides binding to the Src SH3 domain studied by paramagnetic NMR

Lindfors, H. E., de Koning, P. E., Drijfhout, J. W., Venezia, B., & Ubbink, M. (2008) · Journal of Biomolecular NMR · doi:10.1007/s10858-008-9248-0 · Cited by 21

Subtle Dynamics of holo Glutamine Binding Protein Revealed with a Rigid Paramagnetic Probe

Liu, Z., Gong, Z., Guo, D., Zhang, W., & Tang, C. (2014) · Biochemistry · doi:10.1021/bi4015715 · Cited by 22

Noncovalent Spin Labeling of Riboswitch RNAs To Obtain Long-Range Structural NMR Restraints

Helmling, C., Bessi, I., Wacker, A., Schnorr, K. A., Jonker, H. R. A., Richter, C. P., Wagner, D., Kreibich, M., & Schwalbe, H. (2014) · ACS Chemical Biology · doi:10.1021/cb500050t · Cited by 22

Structural Analysis of Protein–RNA Complexes in Solution Using NMR Paramagnetic Relaxation Enhancements

Hennig, J., Warner, L., Simon, B., Geerlof, A., Mackereth, C. D., & Sattler, M. (2015) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2015.02.006 · Cited by 21

Deamidation disrupts native and transient contacts to weaken the interaction between UBC13 and RING-finger E3 ligases

Mohanty, P., Agrata, R., Habibullah, B. I., Arun, G. S., & Das, R. (2019) · eLife · doi:10.7554/elife.49223 · Cited by 21

Size is Important: Artificial Catalyst Mimics Behavior of Natural Enzymes

Chen, J., & Gridnev, I. D. (2020) · iScience · doi:10.1016/j.isci.2020.100960 · Cited by 21

The impact of window functions on NMR-based paramagnetic relaxation enhancement measurements in membrane proteins

Horn, W. D. V., Beel, A. J., Kang, C., & Sanders, C. R. (2009) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2009.08.022 · Cited by 22

Intramolecular domain–domain association/dissociation and phosphoryl transfer in the mannitol transporter of Escherichia coli are not coupled

Suh, J.-Y., Iwahara, J., & Clore, G. M. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0609103104 · Cited by 20

Measuring transverse relaxation in highly paramagnetic systems

Invernici, M., Trindade, I. B., Cantini, F., Louro, R. O., & Piccioli, M. (2020) · Journal of Biomolecular NMR · doi:10.1007/s10858-020-00334-w · Cited by 20

Preferential Interactions of a Crowder Protein with the Specific Binding Site of a Native Protein Complex

Xu, D., Qin, L.-Y., Gong, Z., Qin, S., Zhou, H., & Tang, C. (2022) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.1c03794 · Cited by 20

Seeing the invisible by paramagnetic and diamagnetic NMR

Clore, G. M. (2013) · Biochemical Society Transactions · doi:10.1042/bst20130232 · Cited by 20

Paramagnetic NMR Spectroscopy Is a Tool to Address Reactivity, Structure, and Protein–Protein Interactions of Metalloproteins: The Case of Iron–Sulfur Proteins

Piccioli, M. (2020) · Magnetochemistry · doi:10.3390/magnetochemistry6040046 · Cited by 20

NMR studies of weak protein–protein interactions

Lian, L. (2012) · Progress in Nuclear Magnetic Resonance Spectroscopy · doi:10.1016/j.pnmrs.2012.11.002 · Cited by 20

Are transient protein-protein interactions more dispensable?

Ghadie, M. A., & Xia, Y. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010013 · Cited by 19

NMR of paramagnetic metalloproteins in solution: Ubi venire, quo vadis?

Trindade, I. B., Coelho, A., Cantini, F., Piccioli, M., & Louro, R. O. (2022) · Journal of Inorganic Biochemistry · doi:10.1016/j.jinorgbio.2022.111871 · Cited by 19

NMR characterization of weak interactions between RhoGDI2 and fragment screening hits

Liu, J., Gao, J., Li, F., Ma, R., Wei, Q., Wang, A., Wu, J., & Ruan, K. (2016) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2016.10.003 · Cited by 18

Transient protein–protein complexes in base excision repair

Endutkin, A. V., Yudkina, A. V., Sidorenko, V. S., & Zharkov, D. O. (2018) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2018.1553741 · Cited by 19

The cytochrome c peroxidase and cytochrome c encounter complex: The other side of the story

Schilder, J. T., Löhr, F., Schwalbe, H., & Ubbink, M. (2014) · FEBS Letters · doi:10.1016/j.febslet.2014.03.055 · Cited by 17

Solution Structure of the IIAChitobiose-HPr Complex of the N,N′-Diacetylchitobiose Branch of the Escherichia coli Phosphotransferase System

Jung, Y., Cai, M., & Clore, G. M. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.371492 · Cited by 17

Measurement of the signs of methyl 13C chemical shift differences between interconverting ground and excited protein states by R 1ρ : an application to αB-crystallin

Baldwin, A. J., & Kay, L. E. (2012) · Journal of Biomolecular NMR · doi:10.1007/s10858-012-9617-6 · Cited by 17

Estimating dispensable content in the human interactome

Ghadie, M. A., & Xia, Y. (2019) · Nature Communications · doi:10.1038/s41467-019-11180-2 · Cited by 16

Forces mediating protein–protein interactions: a computational study of p53 “approaching” MDM2

Dastidar, S. G., Madhumalar, A., Fuentes, G., Lane, D. P., & Verma, C. S. (2009) · Theoretical Chemistry Accounts · doi:10.1007/s00214-009-0682-1 · Cited by 17

Association of Cytochrome c with Membrane-Bound Cytochrome c Oxidase Proceeds Parallel to the Membrane Rather Than in Bulk Solution

Spaar, A., Flöck, D., & Helms, V. (2009) · Biophysical Journal · doi:10.1016/j.bpj.2008.11.052 · Cited by 17

On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures

Marín-López, M. A., Planas-Iglesias, J., Aguirre‐Plans, J., Bonet, J., Garcı́a-Garcı́a, J., Fernández‐Fuentes, N., & Oliva, B. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx616 · Cited by 16

Protein Interaction Energy Landscapes are Shaped by Functional and also Non-functional Partners

Schweke, H., Mucchielli, M.-H., Sacquin-Mora, S., Bei, W., & Lopes, A. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.12.047 · Cited by 15

The low-affinity complex of cytochrome c and its peroxidase

de Water, K. V., Sterckx, Y. G. ‐., & Volkov, A. N. (2015) · Nature Communications · doi:10.1038/ncomms8073 · Cited by 16

MD and NMR studies of α-bungarotoxin surface accessibility

Venditti, V., Bernini, A., Simone, A. D., Spiga, O., Prischi, F., & Niccolai, N. (2007) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2007.02.094 · Cited by 16

Network generation enhances interpretation of proteomics data sets by a combination of two-dimensional polyacrylamide gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry

Wang, X., Zhang, A., Sun, H. J., Wu, G., Sun, W., & Yan, G. (2012) · The Analyst · doi:10.1039/c2an35891c · Cited by 15

Proteomic tools for the analysis of transient interactions between metalloproteins

Martínez‐Fábregas, J., Rubio, S., Dı́az-Quintana, A., Díaz‐Moreno, I., & la Rosa, M. Á. D. (2011) · FEBS Journal · doi:10.1111/j.1742-4658.2011.08061.x · Cited by 15

Mapping Protein Conformational Energy Landscapes Using NMR and Molecular Simulation

Guerry, P., Mollica, L., & Blackledge, M. J. (2013) · ChemPhysChem · doi:10.1002/cphc.201300377 · Cited by 17

Protocol for analyzing protein ensemble structures from chemical cross-links using DynaXL

Gong, Z., Liu, Z., Xu, D., Ding, Y., Dong, M., & Tang, C. (2017) · Biophysics Reports · doi:10.1007/s41048-017-0044-9 · Cited by 15

Stable and rigid DTPA-like paramagnetic tags suitable for in vitro and in situ protein NMR analysis

Chen, J., Zhao, Y., Gong, Y.-J., Pan, B.-B., Wang, X., & Su, X. (2017) · Journal of Biomolecular NMR · doi:10.1007/s10858-017-0160-3 · Cited by 15

Docking and scoring: applications to drug discovery in the interactomics era

Grosdidier, S., & Fernández‐Recio, J. (2009) · Expert Opinion on Drug Discovery · doi:10.1517/17460440903002067 · Cited by 15

Protein-inhibitor interaction studies using NMR

Ishima, R. (2015) · Applications of NMR Spectroscopy · doi:10.2174/9781608059621115010007 · Cited by 13

Probing the Atomic Structure of Transient Protein Contacts by Paramagnetic Relaxation Enhancement Solution NMR

Venditti, V., & Fawzi, N. L. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7386-6_12 · Cited by 15

NMR Spectroscopy and Metal Ions in Life Sciences

Ravera, E., Takis, P. G., Fragai, M., Parigi, G., & Luchinat, C. (2018) · European Journal of Inorganic Chemistry · doi:10.1002/ejic.201800875 · Cited by 14

NMR Analysis of Apo Glutamine‐Binding Protein Exposes Challenges in the Study of Interdomain Dynamics

Kooshapur, H., Ma, J., Tjandra, N., & Bermejo, G. A. (2019) · Angewandte Chemie International Edition · doi:10.1002/anie.201911015 · Cited by 17

Proteomic Identification Network Analysis of Haptoglobin as a Key Regulator Associated with Liver Fibrosis

Zhang, A., Sun, H. J., Sun, W., Yuan, Y., & Wang, X. (2012) · Applied Biochemistry and Biotechnology · doi:10.1007/s12010-012-0001-5 · Cited by 14

Opposing Intermolecular Tuning of Ca2+ Affinity for Calmodulin by Neurogranin and CaMKII Peptides

Zhang, P., Tripathi, S., Trinh, H., & Cheung, M. S. (2017) · Biophysical Journal · doi:10.1016/j.bpj.2017.01.020 · Cited by 14

Extensive Sampling of the Cavity of the GroEL Nanomachine by Protein Substrates Probed by Paramagnetic Relaxation Enhancement

Wälti, M. A., Libich, D. S., & Clore, G. M. (2018) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.8b01586 · Cited by 14

A spatiotemporal characterization of the effect of p53 phosphorylation on its interaction with MDM2

ElSawy, K. M., Sim, A. Y. L., Lane, D. P., Verma, C. S., & Caves, L. S. D. (2015) · Cell Cycle · doi:10.4161/15384101.2014.989043 · Cited by 14

Weak self‐association of human growth hormone investigated by nitrogen‐15 NMR relaxation

Jensen, M. R., Kristensen, S. M., Keeler, C., Christensen, H. E. M., Hodsdon, M. E., & Led, J. J. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22039 · Cited by 14

Measurement of rate constants for homodimer subunit exchange using double electron–electron resonance and paramagnetic relaxation enhancements

Yang, Y., Ramelot, T. A., Ni, S., McCarrick, R. M., & Kennedy, M. A. (2012) · Journal of Biomolecular NMR · doi:10.1007/s10858-012-9685-7 · Cited by 15

Protein docking using an ensemble of spin labels optimized by intra-molecular paramagnetic relaxation enhancement

Schilder, J. T., Liu, W.-M., Kumar, P., Overhand, M., Huber, M., & Ubbink, M. (2015) · Physical Chemistry Chemical Physics · doi:10.1039/c5cp03781f · Cited by 14

Poisson–Boltzmann for oppositely charged bodies: an explicit derivation

Paillusson, F., Barbi, M., & Victor, J. (2009) · Molecular Physics · doi:10.1080/00268970902893156 · Cited by 13

Detection and characterization of nonspecific, sparsely populated binding modes in the early stages of complexation

Cardone, A., Bornstein, A., Pant, H. C., Brady, M. C., Sriram, R. D., & Hassan, S. A. (2015) · Journal of Computational Chemistry · doi:10.1002/jcc.23883 · Cited by 13

smFRET studies of the ‘encounter’ complexes and subsequent intermediate states that regulate the selectivity of ligand binding

Kinz-Thompson, C. D., & Gonzalez, R. L. (2014) · FEBS Letters · doi:10.1016/j.febslet.2014.07.013 · Cited by 12

Phase formation during air annealing of Ti-Ni-Ti laminate

Marchenko, E. S., Yasenchuk, Y. F., Baigonakova, G. A., Gunther, S., Yuzhakov, M. M., Zenkin, S., Potekaev, A. I., & Максимович, Д. К. (2020) · Surface and Coatings Technology · doi:10.1016/j.surfcoat.2020.125543 · Cited by 13

Structural fluctuations and mechanical stabilities of the metamorphic protein RfaH

Seifi, B., Aina, A., & Wallin, S. (2020) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26014 · Cited by 13

Impact of spin label rigidity on extent and accuracy of distance information from PRE data

Schnorr, K. A., Gophane, D. B., Helmling, C., Çetiner, E. C., Pasemann, K., Fürtig, B., Wacker, A., Qureshi, N. S., Gränz, M., Barthelmes, D., et al. (2017) · Journal of Biomolecular NMR · doi:10.1007/s10858-017-0114-9 · Cited by 13

Transient protein encounters characterized by paramagnetic NMR

de Water, K. V., van Nuland, N. A. J., & Volkov, A. N. (2014) · Chemical Science · doi:10.1039/c4sc01232a · Cited by 12

Force spectroscopy of barnase–barstar single molecule interaction

Sekatskii, S. K., Favre, M., Dietler, G., Mikhailov, A. G., Klinov, D. V., Lukash, S. V., & Deyev, S. M. (2010) · Journal of Molecular Recognition · doi:10.1002/jmr.1030 · Cited by 12

Utilization of paramagnetic relaxation enhancements for structural analysis of actin-binding proteins in complex with actin

Huang, S., Umemoto, R., Tamura, Y., Kofuku, Y., Uyeda, T. Q. P., Nishida, N., & Shimada, I. (2016) · Scientific Reports · doi:10.1038/srep33690 · Cited by 12

Unbiased Atomistic Insight into the Mechanisms and Solvent Role for Globular Protein Dimer Dissociation

Brotzakis, Z. F., & Bolhuis, P. G. (2019) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.8b10005 · Cited by 12

Subunit interactions as mediated by “non-interface” residues in living cells for multiple homo-oligomeric proteins

Fu, X., Wang, Y., Song, X., Shi, X., Shao, H., Liu, Y., Zhang, M., & Chang, Z. (2019) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2019.03.004 · Cited by 12

Transition path dynamics in the binding of intrinsically disordered proteins: A simulation study

Ozmaian, M., & Makarov, D. E. (2019) · The Journal of Chemical Physics · doi:10.1063/1.5129150 · Cited by 12

The Photocatalyzed Thiol‐ene reaction: A New Tag to Yield Fast, Selective and reversible Paramagnetic Tagging of Proteins

Denis, M., Softley, C. A., Giuntini, S., Gentili, M., Ravera, E., Parigi, G., Fragai, M., Popowicz, G. M., Sattler, M., Luchinat, C., et al. (2020) · ChemPhysChem · doi:10.1002/cphc.202000071 · Cited by 12

The identification of intermediate states of the electron-transfer proteins plastocyanin and cytochrome f diffusional encounters

Khruschev, S., Abaturova, A. M., Fedorov, V. A., Kovalenko, I. B., Riznichenko, G. Y., & Rubin, A. B. (2015) · BIOPHYSICS · doi:10.1134/s0006350915040156 · Cited by 12

Brownian-dynamics simulations of protein–protein interactions in the photosynthetic electron transport chain

Khruschev, S., Abaturova, A. M., Diakonova, A. N., Fedorov, V. A., Ustinin, D. M., Kovalenko, I. B., Riznichenko, G. Y., & Rubin, A. B. (2015) · BIOPHYSICS · doi:10.1134/s0006350915020086 · Cited by 12

KPFM and PFM of Biological Systems

Rodriguez, B. J., & Kalinin, S. V. (2011) · Springer series in surface sciences · doi:10.1007/978-3-642-22566-6_12 · Cited by 12

Hepatitis B surface antigen–antibody interactions studied by optical tweezers

Zhou, Z., Tang, B. H., Ngan, A. H. W., Dong, Z., & Wu, C.-B. (2012) · IET Nanobiotechnology · doi:10.1049/iet-nbt.2010.0023 · Cited by 12

Computational approaches to the interpretation of NMR data for studying protein dynamics

Markwick, P. R. L., & Nilges, M. (2011) · Chemical Physics · doi:10.1016/j.chemphys.2011.11.023 · Cited by 12

Relaxation-based NMR assignment: Spotlights on ligand binding sites in human CISD3

Grifagni, D., Silva, J. M., Cantini, F., Piccioli, M., & Banci, L. (2022) · Journal of Inorganic Biochemistry · doi:10.1016/j.jinorgbio.2022.112089 · Cited by 10

Cover and spacer insertions: Small nonhydrophobic accessories that assist protein oligomerization

Nishi, H., Koike, R., & Ota, M. (2011) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.23084 · Cited by 11

Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY

Shi, J., Nobrega, R. P., Schwantes, C. R., Kathuria, S. V., Bilsel, O., Matthews, C. R., Lane, T. J., & Pande, V. S. (2017) · Scientific Reports · doi:10.1038/srep44116 · Cited by 11

Potential Regulatory Role of Competitive Encounter Complexes in Paralogous Phosphotransferase Systems

Strickland, M., Kale, S., Strub, M., Schwieters, C. D., Liu, J., Peterkofsky, A., & Tjandra, N. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.04.040 · Cited by 11

Conformational Properties Relevant to the Amyloidogenicity of β2-Microglobulin Analyzed Using Pressure- and Salt-Dependent Chemical Shift Data

Sakurai, K., Maeno, A., Lee, Y., & Akasaka, K. (2019) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.8b11408 · Cited by 11

Insights into Actin Polymerization and Nucleation Using a Coarse-Grained Model

Horan, B. G., Hall, A. R., & Vavylonis, D. (2020) · Biophysical Journal · doi:10.1016/j.bpj.2020.06.019 · Cited by 11

Intermolecular Interactions Drive Protein Adaptive and Coadaptive Evolution at Both Species and Population Levels

Peng, J., Svetec, N., & Zhao, L. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msab350 · Cited by 10

Fast cross-linking by DOPA2 promotes the capturing of a stereospecific protein complex over nonspecific encounter complexes

Wang, J.-H., Gong, Z., Xu, D., Liu, S.-Q., Tang, Y., Lei, X., Tang, C., & Dong, M. (2022) · Biophysics Reports · doi:10.52601/bpr.2022.220014 · Cited by 9

A New Method for Determining Structure Ensemble: Application to a RNA Binding Di-Domain Protein

Liu, W., Zhang, J., Fan, J., Tria, G., Grüber, G., & Yang, D. (2016) · Biophysical Journal · doi:10.1016/j.bpj.2016.04.009 · Cited by 10

Facilitated Protein Association via Engineered Target Search Pathways Visualized by Paramagnetic NMR Spectroscopy

An, S. Y., Kim, E., & Suh, J. (2018) · Structure · doi:10.1016/j.str.2018.04.009 · Cited by 10

NMR spectroscopy, excited states and relevance to problems in cell biology – transient pre-nucleation tetramerization of huntingtin and insights into Huntington's disease

Clore, G. M. (2022) · Journal of Cell Science · doi:10.1242/jcs.258695 · Cited by 9

Structures of Larger Proteins, Protein-Ligand, and Protein-DNA Complexes by Multidimensional Heteronuclear NMR

Clore, G. M., & Gronenborn, A. M. (2009) · Wiley eBooks · doi:10.1002/9780470034590.emrstm0542.pub2 · Cited by 10

Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery

Luo, S., Wohl, S., Zheng, W., & Yang, S. (2023) · Biomolecules · doi:10.3390/biom13030530 · Cited by 10

How Hydrophilic Proteins Form Nonspecific Complexes

Ulucan, Ö., & Helms, V. (2015) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5b05831 · Cited by 9

Identification of primary and secondary UBA footprints on the surface of ubiquitin in cell‐mimicking crowded solution

Munari, F., Bortot, A., Zanzoni, S., D’Onofrio, M., Fushman, D., & Assfalg, M. (2017) · FEBS Letters · doi:10.1002/1873-3468.12615 · Cited by 9

Reverse Binding Mode of Phosphotyrosine Peptides with SH2 Protein

Wang, R. Y., Leung, P. Y. M., Huang, F., Tang, Q., Kaneko, T., Huang, M. J., Li, Z., Li, S. S. ‐., Wang, Y., & Xia, J. (2018) · Biochemistry · doi:10.1021/acs.biochem.8b00677 · Cited by 9

Spatial Layouts of Low‐Entropy Hydration Shells Guide Protein Binding

Yang, L., Guo, S., Liao, C., Hou, C., Jiang, S., Li, J., Ma, X., Shi, L., Ye, L., & He, X. (2023) · Global Challenges · doi:10.1002/gch2.202300022 · Cited by 8

E9-Im9 Colicin DNase−Immunity Protein Biomolecular Association in Water: A Multiple-Copy and Accelerated Molecular Dynamics Simulation Study

Baron, R., Wong, S., de Oliveira, C. A. F., & McCammon, J. A. (2008) · The Journal of Physical Chemistry B · doi:10.1021/jp8061543 · Cited by 11

Effect of non-specific interactions on formation and stability of specific complexes

Osmanović, D., & Rabin, Y. (2016) · The Journal of Chemical Physics · doi:10.1063/1.4952981 · Cited by 9

Experimental Methods for Determination of Protein–Protein Interactions

Poluri, K. M., Gulati, K., & Sarkar, S. (2021) · Springer eBooks · doi:10.1007/978-981-16-1594-8_5 · Cited by 9

Using multiple quantum coherence to increase the 15N resolution in a three-dimensional TROSY HNCO experiment for accurate PRE and RDC measurements

Hu, K., Doucleff, M., & Clore, G. M. (2009) · Journal of Magnetic Resonance · doi:10.1016/j.jmr.2009.06.019 · Cited by 9

Dual roles of electrostatic-steering and conformational dynamics in the binding of calcineurin’s intrinsically-disordered recognition domain to calmodulin

Sun, B., Cook, E. C., Creamer, T. P., & Kekenes-Huskey, P. M. (2018) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2018.07.027 · Cited by 8

Simplified geometric representations of protein structures identify complementary interaction interfaces

McCafferty, C. L., Marcotte, E. M., & Taylor, D. W. (2020) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26020 · Cited by 7

Self-adaptive multiscaling algorithm for efficient simulations of many-protein systems in crowded conditions

Hassan, S. A. (2018) · Physical Chemistry Chemical Physics · doi:10.1039/c8cp05517c · Cited by 8

MCMap─A Computational Tool for Mapping Energy Landscapes of Transient Protein–Protein Interactions

Foerster, J. M., Pöhner, I., & Ullmann, G. M. (2018) · ACS Omega · doi:10.1021/acsomega.8b00572 · Cited by 8

Comparison of distance information in [TOAC1, Glu(OMe)7, 18, 19] alamethicin F50/5 from paramagnetic relaxation enhancement measurements with data obtained from an X‐ray diffraction‐based model

Jose, R. A., Zotti, M. D., Peggion, C., Formaggio, F., Toniolo, C., & Borggraeve, W. M. D. (2011) · Journal of Peptide Science · doi:10.1002/psc.1354 · Cited by 7

Generating Accurate Contact Maps of Transient Long-Range Interactions in Intrinsically Disordered Proteins by Paramagnetic Relaxation Enhancement

Clore, G. M. (2013) · Biophysical Journal · doi:10.1016/j.bpj.2013.01.060 · Cited by 7

Development of R7BP inhibitors through cross-linking coupled mass spectrometry and integrated modeling

Adikaram, P. R., Zhang, J., Kittock, C. M., Pandey, M., Hassan, S. A., Lue, N., Wang, G., Guček, M., & Simonds, W. F. (2019) · Communications Biology · doi:10.1038/s42003-019-0585-1 · Cited by 7

Protein folding and surface interaction phase diagrams in vitro and in cells

Gruebele, M. (2021) · FEBS Letters · doi:10.1002/1873-3468.14058 · Cited by 7

PP2A is activated by cytochrome c upon formation of a diffuse encounter complex with SET/TAF-Iβ

Casado‐Combreras, M. Á., Rivero-Rodríguez, F., Elena‐Real, C. A., Molodenskiy, D. S., Dı́az-Quintana, A., Martinho, M., Gerbaud, G., González‐Arzola, K., Velázquez‐Campoy, A., Svergun, D. I., et al. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.07.009 · Cited by 7

HECT domain interaction with ubiquitin binding sites on Tsg101-UEV controls HIV-1 egress, maturation, and infectivity

Nyenhuis, D. A., Rajasekaran, R., Watanabe, S. M., Strub, M., Khan, M. B., Powell, M. D., Carter, C. A., & Tjandra, N. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.102901 · Cited by 7

Current Computational Methods for Protein-peptide Complex Structure Prediction

Yang, C., Xu, X., & Xiang, C. (2023) · Current Medicinal Chemistry · doi:10.2174/0109298673263447230920151524 · Cited by 7

Path to Collagenolysis

Prior, S. H., Byrne, T. S., Tokmina‐Roszyk, D., Fields, G. B., & Doren, S. R. V. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.703124 · Cited by 7

Brief encounters bolster contacts

Blundell, T. L., & Fernández‐Recio, J. (2006) · Nature · doi:10.1038/nature05306 · Cited by 46

Influence of Electrostatics on Protein-Protein Interactions of Photosynthetic Proteins

Förster, J. M. (2018) · EPub Bayreuth (University of Bayreuth) · doi:10.15495/epub_ubt_00003575

Replica exchange simulations of transient encounter complexes in protein–protein association

Kim, Y. C., Tang, C., Clore, G. M., & Hummer, G. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0802460105 · Cited by 104

Mechanistic details of a protein–protein association pathway revealed by paramagnetic relaxation enhancement titration measurements

Fawzi, N. L., Doucleff, M., Suh, J., & Clore, G. M. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909370107 · Cited by 85

Dynamics in photosynthetic transient complexes studied by paramagnetic NMR spectroscopy

Scanu, S. (2013) · Data Archiving and Networked Services (DANS)