Folding Studies on a Knotted Protein

Mallam, Anna L.; Jackson, Sophie

doi:10.1016/j.jmb.2004.12.055

Cited by 119 publications

(185 citation statements)

References 46 publications

Supporting

Mentioning

170

Contrasting

Unclassified

Order By: Relevance

“…The free energy of denaturation for HBc (ΔG D−N of ∼32 kcal/mol) accords well with values reported for similarly sized oligomers (3,40). Our data support the dimerization interface being at least partially intact in I (thus shielding the disulfide from reductants) but not in D.…”

Section: Resultssupporting

confidence: 90%

“…}, R is the gas constant, and T is the temperature in K) (37,40). The free energy of denaturation for HBc (ΔG D−N of ∼32 kcal/mol) accords well with values reported for similarly sized oligomers (3,40).…”

Section: Resultssupporting

confidence: 83%

“…The transition 2 [GdmCl] 50% value was dependent on protein concentration, suggesting dimer-to-monomer dissociation occurs in this transition (37,40) (Fig. 3).…”

Section: Discussionmentioning

confidence: 93%

See 2 more Smart Citations

Thermodynamic origins of protein folding, allostery, and capsid formation in the human hepatitis B virus core protein

Alexander

Jürgens

Shepherd

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Significance Hepatitis B virus (HBV) is a major pathogen, yet no fully effective therapies exist. HBc is the multifunctional, capsid-forming protein essential for HBV replication. HBc structural plasticity is reportedly functionally important. We analyzed the folding mechanism of HBc using a multidisciplinary approach, including microscale thermophoresis and ion mobility spectrometry–mass spectrometry. HBc folds in a 3-state transition with a dimeric, helical intermediate. We found evidence of a strained native ensemble wherein the energy landscapes for folding, allostery, and capsid formation are linked. Mutations thermodynamically trapped HBc in conformations unable to form capsids, suggesting chemical chaperones could elicit similar, potentially antiviral, effects.

show abstract

Section: Resultssupporting

confidence: 90%

Section: Resultssupporting

confidence: 83%

See 1 more Smart Citation

Thermodynamic origins of protein folding, allostery, and capsid formation in the human hepatitis B virus core protein

Alexander

Jürgens

Shepherd

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…Previous investigations on the folding mechanisms of a few knotted proteins established that these proteins have complex multistep folding pathways with slow kinetics rather than the simple two-state mechanisms that are commonly seen for small, fast-folding, single-domain proteins (6)(7)(8)(9)(10)(11). Despite experimental and computational work over the last 10 years (12)(13)(14)(15)(16)(17), the folding mechanisms of knotted proteins remain poorly understood compared with those described for small model systems that have been studied in great detail (18)(19)(20)(21)(22)(23).…”

Section: Introductionmentioning

confidence: 99%

Characterization of the Folding of a 5 2 -Knotted Protein Using Engineered Single-Tryptophan Variants

Zhang

Jackson

2016

Biophysical Journal

Self Cite

View full text Add to dashboard Cite

An increasing number of proteins that contain topological knots have been identified over the past two decades; however, their folding mechanisms are still not well understood. UCH-L1 has a 5 2 -knotted topology. Here, we constructed a series of variants that contain a single tryptophan at different locations along the polypeptide chain. A study of the thermodynamic properties of the variants shows that the structure of UCH-L1 is remarkably tolerant to incorporation of bulky tryptophan side chains. Comprehensive kinetic studies of the variants reveal that they fold via parallel pathways on which there are two intermediate states very similar to wild-type UCH-L1. The structures of the intermediate states do not change significantly with mutation and therefore occupy local minima on the energy landscape that have relatively narrow basins. The kinetic studies also establish that there are considerably more tertiary interactions in the intermediate states than results from previous NMR studies suggested. The two intermediates differ from each other in the extent to which tertiary interactions between the highly stable central b-sheet and flanking a-helices and loop regions are formed. There is strong evidence that these states are aggregation prone. The transition states from both I 1 and I 2 to the native state are plastic and change with mutation and denaturant concentration. Previous studies indicated that the threading event that creates the 5 2 knot occurs during these steps, suggesting that there is a broad energy barrier consistent with the chain undergoing some searching of conformational space as the threading takes place.

show abstract

“…S1]. It has been shown experimentally that both these proteins unfold spontaneously and reversibly on addition of chemical denaturant (8)(9)(10)(11) and they are able to fold even when additional domains are attached to one or both termini (12). In very recent experimental work (13), based on analysis of the effect of mutations in the knotted region of the protein, a folding model for YibK was also proposed.…”

mentioning

confidence: 99%

Dodging the crisis of folding proteins with knots

Sułkowska

Sułkowski

Onuchic

2009

Proc. Natl. Acad. Sci. U.S.A.

168

217

View full text Add to dashboard Cite

Proteins with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. A mechanism is suggested for folding of these proteins, such as YibK and YbeA, that involves an intermediate configuration with a slipknot. It elucidates the role of topological barriers and backtracking during the folding event. It also illustrates that native contacts are sufficient to guarantee folding in Ϸ1-2% of the simulations, and how slipknot intermediates are needed to reduce the topological bottlenecks. As expected, simulations of proteins with similar structure but with knot removed fold much more efficiently, clearly demonstrating the origin of these topological barriers. Although these studies are based on a simple coarse-grained model, they are already able to extract some of the underlying principles governing folding in such complex topologies. molecular dynamics ͉ slipknots ͉ backtracking ͉ topological barriers D uring the past 2 decades, a joint theoretical and experimental effort has largely advanced the quantitative understanding of the protein folding mechanism. Most small-and intermediate-size proteins live on a minimally frustrated funnel-like energy landscape, which allows fast and robust folding (1-3). Because proteins have been able to solve the energy problem, the final challenge is the structural complexity of the protein folding motifs. Most proteins avoid complex topologies, but recent discoveries have shown that some proteins are actually able to fold into nontrivial topologies where the main chain folds into a knotted conformation (4-6). Although these ''knotted'' folding motifs have been observed, we still have to face the challenging question of how the protein overcomes the kinetic barrier associated with the search of the knotted conformation. We suggest a possible mechanism where the knot formation is preceded by a conformation called a ''slipknot.'' A slipknot is topologically similar to a knot, except that an internal knot is effectively undone as the pathway of the backbone folds back on itself. The fact that such slipknots have already been observed in some protein final structures (7) adds support to this suggestion.This folding mechanism is explored in the context of the two most experimentally investigated knotted families of proteins, Haemophilus influenzae YibK and Escherichia coli YbeA, which are homodimeric ␣/␤-knot methyltransferases (MTases). A schematic representation of these proteins is shown in Fig. 1, [see also supporting information (SI) Fig. S1]. It has been shown experimentally that both these proteins unfold spontaneously and reversibly on addition of chemical denaturant (8-11) and they are able to fold even when additional domains are attached to one or both termini (12). In very recent experimental work (13), based on analysis of the effect of mutations in the knotted region of the protein, a folding model for YibK was also proposed. In this model the threading of the polypeptide chain and fo...

show abstract

Folding Studies on a Knotted Protein

Cited by 119 publications

References 46 publications

Thermodynamic origins of protein folding, allostery, and capsid formation in the human hepatitis B virus core protein

Thermodynamic origins of protein folding, allostery, and capsid formation in the human hepatitis B virus core protein

Characterization of the Folding of a 5 2 -Knotted Protein Using Engineered Single-Tryptophan Variants

Dodging the crisis of folding proteins with knots

Contact Info

Product

Resources

About