The Role of E27-K31 and E56-K10 Salt-Bridge Pairs in the Unfolding Mechanism of the B1 Domain of Protein G

Molecular dynamics simulations of the B1 fragment of protein G (56 residues) have been performed at 325, 350, 375, 400, 450 and 500 K for 10 ns. An analysis of its structural and energetic parameters has indicated that the unfolding process of the GB1 protein begins at 900 ps of a 500-K simulation. The unfolding process is initiated when hydrogen bonds in the hydrophobic core region are broken; it continues with the α-helix transformation into coils and turns and ends with the destruction of the β-hairpins. These unfolding events are consistent with the hybrid model of the protein folding/unfolding mechanism, which is a compromise between the hydrophobic core collapse model and the zipper model. Salt-bridge pairs were found to play an important role in the unfolding process by maintaining the integrity of the tertiary structure of the protein. The breaking (or disappearance) of the salt-bridge pairs E27–K31 (in the α-helix) and E56–K10 (connecting β4 and β1) has resulted in the destruction of secondary structures and indicates the beginning of the unfolding process. Our results also suggest that the unfolding process in this simulation was not a complete denaturation of the protein because some β-hairpins remained

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Role of a nonnative interaction in the folding of the protein G B1 domain as inferred from the conformational analysis of the α-helix fragment

Folding and Design ◽

10.1016/s1359-0278(97)00017-5 ◽

1997 ◽

Vol 2 (2) ◽

pp. 123-133 ◽

Cited By ~ 30

Author(s):

Francisco J Blanco ◽

Angel R Ortiz ◽

Luis Serrano

Keyword(s):

Conformational Analysis ◽

Protein G ◽

B1 Domain ◽

Α Helix

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Folding and Intrinsic Disorder of the Receptor Tyrosine Kinase KIT Insert Domain Seen by Conventional Molecular Dynamics Simulations

International Journal of Molecular Sciences ◽

10.3390/ijms22147375 ◽

2021 ◽

Vol 22 (14) ◽

pp. 7375

Author(s):

Julie Ledoux ◽

Alain Trouvé ◽

Luba Tchertanov

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Tertiary Structure ◽

Average Distance ◽

Intrinsic Disorder ◽

Accessible Surface Area ◽

Solvent Accessible Surface Area ◽

Hydrophobic Core ◽

Direct Evaluation ◽

Dynamics Simulations

The kinase insert domain (KID) of RTK KIT is the key recruitment region for downstream signalling proteins. KID, studied by molecular dynamics simulations as a cleaved polypeptide and as a native domain fused to KIT, showed intrinsic disorder represented by a set of heterogeneous conformations. The accurate atomistic models showed that the helical fold of KID is mainly sequence dependent. However, the reduced fold of the native KID suggests that its folding is allosterically controlled by the kinase domain. The tertiary structure of KID represents a compact array of highly variable α- and 310-helices linked by flexible loops playing a principal role in the conformational diversity. The helically folded KID retains a collapsed globule-like shape due to non-covalent interactions associated in a ternary hydrophobic core. The free energy landscapes constructed from first principles—the size, the measure of the average distance between the conformations, the amount of helices and the solvent-accessible surface area—describe the KID disorder through a collection of minima (wells), providing a direct evaluation of conformational ensembles. We found that the cleaved KID simulated with restricted N- and C-ends better reproduces the native KID than the isolated polypeptide. We suggest that a cyclic, generic KID would be best suited for future studies of KID f post-transduction effects.

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Models of cooperativity in protein folding

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.1995.0046 ◽

1995 ◽

Vol 348 (1323) ◽

pp. 61-70 ◽

Cited By ~ 76

Keyword(s):

Protein Folding ◽

Molten Globule ◽

Core Collapse ◽

Hydrophobic Core ◽

Model Studies ◽

Helix Formation ◽

Collapse Model ◽

Folding Pathways ◽

State Behaviour ◽

Denatured States

What is the basis for the two-state cooperativity of protein folding? Since the 1950s, three main models have been put forward. 1. In ‘helix-coil’ theory, cooperativity is due to local interactions among near neighbours in the sequence. Helix-coil cooperativity is probably not the principal basis for the folding of globular proteins because it is not two-state, the forces are weak, it does not account for sheet proteins, and there is no evidence that helix formation precedes the formation of a hydrophobic core in the folding pathways. 2. In the ‘sidechain packing’ model, cooperativity is attributed to the jigsaw-puzzle-like complementary fits of sidechains. This too is probably not the basis of folding cooperativity because exact models and experiments on homopolymers with sidechains give no evidence that sidechain freezing is two-state, sidechain complementarities in proteins are only weak trends, and the molten globule model predicted by this model is far more native-like than experiments indicate. 3. In the ‘hydrophobic core collapse’ model, cooperativity is due to the assembly of non-polar residues into a good core. Exact model studies show that this model gives two-state behaviour for some sequences of hydrophobic and polar monomers. It is based on strong forces. There is considerable experimental evidence for the kinetics this model predicts: the development of hydrophobic clusters and cores is concurrent with secondary structure formation. It predicts compact denatured states with sizes and degrees of disorder that are in reasonable agreement with experiments.

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Structure, interdomain dynamics and pH-dependent autoactivation of pro-rhodesain, the main lysosomal cysteine protease from African trypanosomes

10.1101/2020.11.10.363747 ◽

2020 ◽

Author(s):

Patrick Johé ◽

Elmar Jaenicke ◽

Hannes Neuweiler ◽

Tanja Schirmeister ◽

Christian Kersten ◽

...

Keyword(s):

Crystal Structure ◽

Cysteine Protease ◽

Cathepsin L ◽

Salt Bridge ◽

Correlation Spectroscopy ◽

African Trypanosomes ◽

Lysosomal Cysteine Protease ◽

Control Switch ◽

Α Helix ◽

Dynamics Simulations

AbstractRhodesain is the lysosomal cathepsin L-like cysteine protease of T. brucei rhodesiense, the causative agent of Human African Trypanosomiasis. The enzyme is essential for the proliferation and pathogenicity of the parasite as well as its ability to overcome the blood-brain barrier of the host. Lysosomal cathepsins are expressed as zymogens with an inactivating pro-domain that is cleaved under acidic conditions. A structure of the uncleaved maturation intermediate from a trypanosomal cathepsin L-like protease is currently not available. We thus established the heterologous expression of T. brucei rhodesiense pro-rhodesain in E. coli and determined its crystal structure. The trypanosomal pro-domain differs from non-parasitic pro-cathepsins by a unique, extended α-helix that blocks the active site and whose interactions resemble that of the antiprotozoal inhibitor K11777. Interdomain dynamics between pro- and core protease domain as observed by photoinduced electron transfer fluorescence correlation spectroscopy increase at low pH, where pro-rhodesain also undergoes autocleavage. Using the crystal structure, molecular dynamics simulations and mutagenesis, we identify a conserved interdomain salt bridge that prevents premature intramolecular cleavage at higher pH values and may thus present a control switch for the observed pH-sensitivity of pro-enzyme cleavage in (trypanosomal) CathL-like proteases.

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Fast pressure-jump all-atom simulations and experiments reveal site-specific protein dehydration-folding dynamics

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1814927116 ◽

2019 ◽

Vol 116 (12) ◽

pp. 5356-5361 ◽

Cited By ~ 1

Author(s):

Maxim B. Prigozhin ◽

Yi Zhang ◽

Klaus Schulten ◽

Martin Gruebele ◽

Taras V. Pogorelov

Keyword(s):

Pressure Drop ◽

Time Scale ◽

Tertiary Structure ◽

Specific Protein ◽

Pressure Jump ◽

Characteristic Time Scale ◽

Hydrophobic Core ◽

Pressure Drops ◽

Contact Formation ◽

Α Helix

As theory and experiment have shown, protein dehydration is a major contributor to protein folding. Dehydration upon folding can be characterized directly by all-atom simulations of fast pressure drops, which create desolvated pockets inside the nascent hydrophobic core. Here, we study pressure-drop refolding of three λ-repressor fragment (λ6–85) mutants computationally and experimentally. The three mutants report on tertiary structure formation via different fluorescent helix–helix contact pairs. All-atom simulations of pressure drops capture refolding and unfolding of all three mutants by a similar mechanism, thus validating the nonperturbative nature of the fluorescent contact probes. Analysis of simulated interprobe distances shows that the α-helix 1–3 pair distance displays a slower characteristic time scale than the 1–2 or 3–2 pair distance. To see whether slow packing of α-helices 1 and 3 is reflected in the rate-limiting folding step, fast pressure-drop relaxation experiments captured refolding on a millisecond time scale. These experiments reveal that refolding monitored by 1–3 contact formation indeed is much slower than when monitored by 1–2 or 3–2 contact formation. Unlike the case of the two-state folder [three–α-helix bundle (α3D)], whose drying and core formation proceed in concert, λ6–85repeatedly dries and rewets different local tertiary contacts before finally forming a solvent-excluded core, explaining the non–two-state behavior observed during refolding in molecular dynamics simulations. This work demonstrates that proteins can explore desolvated pockets and dry globular states numerous times before reaching the native conformation.

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Evidence of turn and salt bridge contributions to β-hairpin stability: MD simulations of C-terminal fragment from the B1 domain of protein G

Biophysical Chemistry ◽

10.1016/s0301-4622(02)00198-9 ◽

2002 ◽

Vol 101-102 ◽

pp. 187-201 ◽

Cited By ~ 40

Author(s):

Jerry Tsai ◽

Michael Levitt

Keyword(s):

Salt Bridge ◽

Md Simulations ◽

Protein G ◽

B1 Domain ◽

Terminal Fragment

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Mechanics and dynamics of B1 domain of protein G: Role of packing and surface hydrophobic residues

Protein Science ◽

10.1110/ps.8.1.147 ◽

2008 ◽

Vol 8 (1) ◽

pp. 147-160 ◽

Cited By ~ 33

Author(s):

Marc A. Ceruso ◽

Andrea Amadei ◽

Alfredo Di Nola

Keyword(s):

Protein G ◽

Hydrophobic Residues ◽

B1 Domain

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MOLECULAR DYNAMIC SIMULATION OF V176G MUTATION ASSOCIATED WITH GERSTMANN–STRÄUSSLER–SCHEINKER AT ELEVATED TEMPERATURE

Jurnal Teknologi ◽

10.11113/jt.v78.5200 ◽

2016 ◽

Vol 78 (2) ◽

Author(s):

Ashraf Fadhil Jomah ◽

Mohd Shahir Shamsir

Keyword(s):

Hydrogen Bonds ◽

Prion Protein ◽

Novel Mutation ◽

Solvent Accessibility ◽

Transmissible Spongiform Encephalopathy ◽

Salt Bridge ◽

Cellular Prion Protein ◽

Spongiform Encephalopathy ◽

Α Helix ◽

Dynamics Simulations

The transformation of cellular prion protein (PrPc) into pathogenic conformer (PrPSc) in transmissible spongiform encephalopathy is expedited by mutations in the prion protein. One recently reported novel mutation V176G is located in region of the protein known to cause Creutzfeldt-Jakob disease (CJD) but possess a unique neuropathological profile and spongiform alteration similar to Gerstmann–Sträussler–Scheinker syndrome (GSS). Using molecular dynamics simulations; the denaturation of the prion structure with V176G at 500K was studied to identify the dynamics in structural properties such as salt bridge, solvent accessibility, hydrogen bonds and hydrophobicity. The simulations revealed that the heat-induced unfolding caused destabilization of the native structure of PrP and affecting the β-sheet region of the structure more than the α-helix. Unique salt bridge formation suggests conformational orientation that may be attributed to the V176G mutation. The mutation effects showed an increased fluctuation of the H1 region, gain of hydrogen bonds between H3 and H2 which may be part of the oligomerization pathway and determine the features of the PrPSc assemblies.

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