The DOI matches its Crossref record; 26 of the 26 references it cites were found in a registry or an index.
Visualization of transient encounter complexes in protein–protein association
Abstract
Kinetic data on a number of protein-protein associations have provided evidence for the initial formation of a pre-equilibrium encounter complex that subsequently relaxes to the final stereospecific complex. Site-directed mutagenesis and brownian dynamics simulations have suggested that the rate of association can be modulated by perturbations in charge distribution outside the direct interaction surfaces. Furthermore, rate enhancement through non-specific binding may occur by either a reduction in dimensionality or the presence of a short-range, non-specific attractive potential. Here, using paramagnetic relaxation enhancement, we directly demonstrate the existence and visualize the distribution of an ensemble of transient, non-specific encounter complexes under equilibrium conditions for a relatively weak protein-protein complex between the amino-terminal domain of enzyme I and the phosphocarrier protein HPr. Neither the stereospecific complex alone nor any single alternative conformation can account fully for the intermolecular paramagnetic relaxation enhancement data. Restrained rigid-body simulated annealing refinement against the paramagnetic relaxation enhancement data enables us to obtain an atomic probability distribution map of the non-specific encounter complex ensemble that qualitatively correlates with the electrostatic surface potentials on the interacting proteins. Qualitatively similar results are presented for two other protein-protein complexes.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“In all cases, the broad spatial distribution of PRE effects likely reflects the dynamic binding with multiple low-affinity interactions that are reflected by the paramagnetic effects (52).”
From Client binding shifts the populations of dynamic Hsp90 conformations through an allosteric network (2021) · cites this paper as [52]
Citations
Cites
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
Self-citationRapid, electrostatically assisted association of proteins
Schreiber, G., & Fersht, A. R. (1996) · Nature Structural Biology · doi:10.1038/nsb0596-427 · Cited by 560
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
Self-citationDetecting transient intermediates in macromolecular binding by paramagnetic NMR
Iwahara, J., & Clore, G. M. (2006) · Nature · doi:10.1038/nature04673 · Cited by 374
Self-citationIwahara, J., Schwieters, C. D., & Clore, G. M. (2004) · Journal of the American Chemical Society · doi:10.1021/ja031580d · Cited by 328
Self-citationRational design of faster associating and tighter binding protein complexes.
Schreiber, G., Selzer, T., & Albeck, S. (2000) · Nature Structural Biology · doi:10.1038/76744 · Cited by 299
Brownian Dynamics of Cytochrome c and Cytochrome c Peroxidase Association
Northrup, S. H., Boles, J. O., & Reynolds, J. C. L. (1988) · Science · doi:10.1126/science.2838904 · Cited by 289
Kuszewski, J. J., Gronenborn, A. M., & Clore, G. M. (1999) · Journal of the American Chemical Society · doi:10.1021/ja9843730 · Cited by 238
Self-citationIdentification of Protein Surfaces by NMR Measurements with a Paramagnetic Gd(III) Chelate
Pintacuda, G., & Otting, G. (2001) · Journal of the American Chemical Society · doi:10.1021/ja016985h · Cited by 216
Gronenborn, A. M., Clore, G. M., Garrett, D. S., Seok, Y., & Peterkofsky, A. (1999) · Nature Structural Biology · doi:10.1038/5854 · Cited by 212
Self-citationVijayakumar, M., Wong, K.-Y., Schreiber, G., Fersht, A. R., Szabó, A., & Zhou, H. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.1747 · Cited by 199
Biomolecular diffusional association
Gabdoulline, R. R., & Wade, R. C. (2002) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(02)00311-1 · Cited by 180
Donaldson, L. W., Skrynnikov, N. R., Choy, W., Muhandiram, D. R., Sarkar, B., Forman-Kay, J. D., & Kay, L. E. (2001) · Journal of the American Chemical Society · doi:10.1021/ja011241p · Cited by 175
Assessing the Quality of Solution Nuclear Magnetic Resonance Structures by Complete Cross-Validation
Brünger, A. T., Clore, G. M., Gronenborn, A. M., Saffrich, R., & Nilges, M. (1993) · Science · doi:10.1126/science.8332897 · Cited by 146
Self-citationDiffusional Encounter of Barnase and Barstar
Spaar, A., Dammer, C., Gabdoulline, R. R., Wade, R. C., & Helms, V. (2005) · Biophysical Journal · doi:10.1529/biophysj.105.075507 · Cited by 125
Ebright, Y. W., Chen, Y., Pendergrast, P. S., & Ebright, R. H. (1992) · Biochemistry · doi:10.1021/bi00159a004 · Cited by 109
Characterization of Nonspecific Protein−DNA Interactions by 1H Paramagnetic Relaxation Enhancement
Iwahara, J., Schwieters, C. D., & Clore, G. M. (2004) · Journal of the American Chemical Society · doi:10.1021/ja046246b · Cited by 79
Self-citationEnhancement of Association Rates by Nonspecific Binding to DNA and Cell Membranes
Zhou, H., & Szabó, A. (2004) · Physical Review Letters · doi:10.1103/physrevlett.93.178101 · Cited by 68
Cornilescu, G., Lee, B. R., Cornilescu, C. C., Wang, G., Peterkofsky, A., & Clore, G. M. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m207314200 · Cited by 66
Self-citationReweighted atomic densities to represent ensembles of NMR structures*
Schwieters, C. D., & Clore, G. M. (2002) · Journal of Biomolecular NMR · doi:10.1023/a:1019875223132 · Cited by 63
Self-citationWilliams, D. C., Cai, M., Suh, J.-Y., Peterkofsky, A., & Clore, G. M. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m501986200 · Cited by 59
Self-citation
Cited by
Sorted by citations
Reaching for high-hanging fruit in drug discovery at protein–protein interfaces
Wells, J. A., & McClendon, C. L. (2007) · Nature · doi:10.1038/nature06526 · Cited by 2,002
Mechanism of coupled folding and binding of an intrinsically disordered protein
Sugase, K., Dyson, H. J., & Wright, P. E. (2007) · Nature · doi:10.1038/nature05858 · Cited by 1,071
Conicella, A. E., Zerze, G. H., Mittal, J., & Fawzi, N. L. (2016) · Structure · doi:10.1016/j.str.2016.07.007 · Cited by 881
Csermely, P., Palotai, R., & Nussinov, R. (2010) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2010.04.009 · Cited by 821
Clore, G. M., & Iwahara, J. (2009) · Chemical Reviews · doi:10.1021/cr900033p · Cited by 800
Self-citation
Metadata
- Authors
- Tang, C., Iwahara, J., & Clore, G. M.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Clore, G. Marius
- Venue
- Nature
- Published
- 2006-10-15
- Volume
- 444
- Issue
- 7117
- Pages
- 383-386
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2063810968
- Cited by
- 406
- References
- 26
- Citations by year
- 2026: 5 · 2025: 6 · 2024: 5 · 2023: 9 · 2022: 14 · 2021: 10 · 2020: 16 · 2019: 19 · 2018: 15 · 2017: 15 · 2016: 23 · 2015: 28 · 2014: 22 · 2013: 32 · 2012: 30
- FWCI
- 12.09
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Institutes of Health
- National Institute of Diabetes and Digestive and Kidney Diseases
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Diffusion and Search Dynamics
- Physical Sciences › Chemistry › Spectroscopy › Advanced NMR Techniques and Applications
- Keywords
- protein-protein interaction, non-specific binding, paramagnetic relaxation enhancement, surface electrostatic potential
- MeSH terms
- Bacterial Proteins, Enzymes, Kinetics, Models, Molecular, Phosphoenolpyruvate Sugar Phosphotransferase System, Protein Binding, Protein Conformation, Nuclear Magnetic Resonance, Biomolecular, Multiprotein Complexes, Static Electricity
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
