Showing papers on "Contact order published in 2022"
TL;DR: In this article , the authors examined whether self-entangled states occur in long-time-scale, physics-based all-atom simulations of protein folding and found they do indeed form, estimate they can persist for weeks, and some have characteristics similar to the native state.
Abstract: Several mechanisms intrinsic to a protein’s primary structure are known to cause monomeric protein misfolding. Coarse-grained simulations, in which multiple atoms are represented by a single interaction site, have predicted a novel mechanism of misfolding exists involving off-pathway, non-covalent lasso entanglements, which are distinct from protein knots and slip knots. These misfolded states can be long-lived kinetic traps, and in some cases are structurally similar to the native state according to those simulations. Here, we examine whether such misfolded states occur in long-time-scale, physics-based all-atom simulations of protein folding. We find they do indeed form, estimate they can persist for weeks, and some have characteristics similar to the native state. Digestion patterns from Limited Proteolysis Mass Spectrometry are consistent with the presence of changes in entanglement in these proteins. These results indicate monomeric proteins can exhibit subpopulations of misfolded, self-entangled states that can explain long-timescale changes in protein structure and function in vivo. One-Sentence Summary Entangled misfolded states form in physics-based all-atom simulations of protein folding and have characteristics similar to the native state.
4 citations
TL;DR: This work analyzed the folding of thousands of natural Ankyrin repeat proteins and found that a multiplicity of folding mechanisms are possible and it is shown that the global stability and cooperativity of the repeating arrays can be predicted from simple sequence scores.
Abstract: Significance Protein sequences change over evolutionary times. The fixation of these changes is coupled to the protein’s capability to properly explore conformational space and perform biological functions. Repeat proteins are privileged systems to understand the relations between evolution and folding, due to their conserved structure and functional diversity. Here, we use the evolutionary record of natural sequences to model and analyze the folding mechanisms of thousands of proteins. The proposed model successfully reproduces folding experiments using only sequence information as input. We performed large-scale predictions of folding mechanisms in the most abundant repeat-protein family, identifying higher-order features such as domain emergence, stability, and cooperativity of repeat arrays.
3 citations
TL;DR: Zhang et al. as mentioned in this paper developed a novel approach, protein structure fingerprint, to expose the comprehensive local folding variations, and then construct folding conformations for an entire protein, which can be simultaneously apprehended at a glance within PFVM.
Abstract: The revelation of protein folding is a challenging subject in both discovery and description. Except for acquirement of accurate 3D structure in protein stable state, another big hurdle is how to discover structural flexibility for protein innate character. Even if a huge number of flexible conformations are known, difficulty is how to represent these conformations. A novel approach, protein structure fingerprint, has been developed to expose the comprehensive local folding variations, and then construct folding conformations for entire protein. The backbone of five amino acid residues was identified as a universal folden, and then a set of Protein Folding Shape Code (PFSC) was derived for completely covering folding space in alphabetic description. Sequentially, a database was created to collect all possible folding shapes of local folding variations for all permutation of five amino acids. Successively, Protein Folding Variation Matrix (PFVM) assembled all possible local folding variations along sequence for a protein, which possesses several prominent features. First, it showed the fluctuation with certain folding patterns along sequence which revealed how the protein folding was related the order of amino acids in sequence. Second, all folding variations for an entire protein can be simultaneously apprehended at a glance within PFVM. Third, all conformations can be determined by local folding variations from PFVM, so total number of conformations is no longer ambiguous for any protein. Finally, the most possible folding conformation and its 3D structure can be acquired according PFVM for protein structure prediction. Therefore, the protein structure fingerprint approach provides a significant means for investigation of protein folding problem.
1 citations
TL;DR: The results indicate that the free-energy landscape of small globule proteins have general Bactrian camel shape, and large contact order of the native state produces a high barrier dominate at low forces.
Abstract: Acylphosphatase (AcP) is a small protein with 98 amino acid residues that catalyzes the hydrolysis of carboxyl-phosphate bonds. AcP is a typical two-state protein with slow folding rate due to its relatively large contact order in the native structure. The mechanical properties and unfolding behavior of AcP has been studied by atomic force microscope. Here using stable magnetic tweezers, we measured the force-dependent folding rates within a force range 1-3 pN, and unfolding rates 15-40 pN. The obtained unfolding rates show different force sensitivities at forces below and above ∼27 pN, which determines a free-energy landscape with two energy barriers. Our results indicate that the free-energy landscape of small globule proteins have general Bactrian camel shape, and large contact order of the native state produces a high barrier dominate at low forces.
1 citations
TL;DR: Psi analysis as mentioned in this paper employs rationally inserted metal binding sites designed to probe pairwise contacts in the transition state ensemble (TSE) and consistently produces a considerably more structured and native-like TSE than traditional Phi analysis.
Abstract: The formation of the transition state ensemble (TSE) represents the rate-limiting step in protein folding. The TSE is the least populated state on the pathway, and its characterization remains a challenge. Properties of the TSE can be inferred from the effects on folding and unfolding rates for various perturbations. A difficulty remains on how to translate these kinetic effects to structural properties of the TSE. Several factors can obscure the translation of point mutations in the frequently used method, "mutational Phi analysis." We take a complementary approach in "Psi analysis," employing rationally inserted metal binding sites designed to probe pairwise contacts in the TSE. These contacts can be confidently identified and used to construct structural models of the TSE. The method has been applied to multiple proteins and consistently produces a considerably more structured and native-like TSE than Phi analysis. This difference has significant implications to our understanding of protein folding mechanisms. Here we describe the application of the method and discuss how it can be used to study other conformational transitions such as binding.
1 citations
TL;DR: In this article , the authors used single-molecule Förster resonance energy transfer to report on the folding of fluorescently labeled outer membrane protein G and measured the real-time insertion of a β-barrel membrane protein from an unfolded state.
Abstract: In comparison to globular proteins, the spontaneous folding and insertion of β-barrel membrane proteins are surprisingly slow, typically occurring on the order of minutes. Using single-molecule Förster resonance energy transfer to report on the folding of fluorescently labeled outer membrane protein G we measured the real-time insertion of a β-barrel membrane protein from an unfolded state. Folding events were rare and fast (<20 ms), occurring immediately upon arrival at the membrane. This combination of infrequent, but rapid, folding resolves this apparent dichotomy between slow ensemble kinetics and the typical timescales of biomolecular folding.
1 citations
11 Mar 2022
TL;DR: In this paper , the authors measured the force-dependent folding rates within a force range from 1 pN to 3 pN, and the unfolding rates from 15pN to 40pN, which determined a free energy landscape with two energy barriers.
Abstract: Acylphosphatase (AcP) is a small protein with 98 amino acid residues that catalyzes the hydrolysis of carboxyl-phosphate bonds. AcP is a typical two-state protein with slow folding rate due to its relatively large contact order in the native structure. The mechanical properties and unfolding behavior of AcP has been studied by atomic force microscope. But the folding and unfolding dynamics at low forces has not been reported. Here using stable magnetic tweezers, we measured the force-dependent folding rates within a force range from 1 pN to 3 pN, and unfolding rates from 15 pN to 40 pN. The obtained unfolding rates show different force sensitivities at forces below and above ~27 pN, which determines a free energy landscape with two energy barriers. Our results indicate that the free energy landscape of small globule proteins have general Bactrian camel shape, and large contact order of the native state produces a high barrier dominate at low forces.
16 Feb 2022
TL;DR: Zhang et al. as discussed by the authors proposed a protein structure fingerprint approach to expose the comprehensive local folding variations, and then construct folding conformations for entire protein. But the approach is not suitable for protein structure prediction.
Abstract: The revelation of protein folding is a challenging subject in both discovery and description. Except acquirement of accurate 3D structure for protein stable state, another big hurdle is how to discover structural flexibility for protein innate character. Even if a huge number of flexible conformations are known, difficulty is how to describe these conformations. A novel approach, protein structure fingerprint, has been developed to expose the comprehensive local folding variations, and then construct folding conformations for entire protein. The backbone of 5 amino acid residues was identified as a universal folden, and then a set of Protein Folding Shape Code (PFSC) was derived for completely covering folding space in alphabetic description. Sequentially, a database was created to collect all possible folding shapes of local folding variations for all permutation of 5 amino acids. Successively, Protein Folding Variation Matrix (PFVM) assembled all possible local folding variations along sequence for a protein, which possesses several prominent features. First, it showed the fluctuation with certain folding patterns along sequence which revealed how the protein folding was related the order of amino acids in sequence. Second, all folding variations for an entire protein can be simultaneously apprehended at a glance within PFVM. Third, all conformations can be determined by local folding variations from PFVM, so total number of conformations is no longer ambiguous for any protein. Finally, the most possible folding conformation and its 3D structure can be acquired according PFVM for protein structure prediction. Therefore, the protein structure fingerprint approach provides a significant means for investigation of protein folding problem.
24 Feb 2022
TL;DR: In this article , a coarse-grained model for repeat-protein folding was proposed to investigate the folding of thousands of repeat-proteins, and a multiplicity of folding mechanisms are possible.
Abstract: Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure, folding and function. Here, we propose a scheme to map evolutionary information at the sequence level to a coarse-grained model for repeat-protein folding and use it to investigate the folding of thousands of repeat-proteins. We model the energetics by a combination of an inverse Potts model scheme with an explicit mechanistic model of duplications and deletions of repeats to calculate the evolutionary parameters of the system at single residue level. This is used to inform an Ising-like model that allows for the generation of folding curves, apparent domain emergence and occupation of intermediate states that are highly compatible with experimental data in specific case studies. We analyzed the folding of thousands of natural Ankyrin-repeat proteins and found that a multiplicity of folding mechanisms are possible. Fully cooperative all-or-none transition are obtained for arrays with enough sequence-similar elements and strong interactions between them, while non-cooperative element-by-element intermittent folding arose if the elements are dissimilar and the interactions between them are energetically weak. In between, we characterised nucleation-propagation and multi-domain folding mechanisms. Finally, we showed that stability and cooperativity of a repeat-array can be quantitatively predicted from a simple energy score, paving the way for guiding protein folding design with a co-evolutionary model.
TL;DR: In this paper , the effect of circular permutation on metalloproteins was investigated in both metal-free and metal-bound (holo) forms of azurin.
Abstract: Native topology is known to determine the folding kinetics and the energy landscape of proteins. Furthermore, the circular permutation (CP) of proteins alters the order of the secondary structure connectivity while retaining the three‐dimensional structure, making it an elegant and powerful approach to altering native topology. Previous studies elucidated the influence of CP in proteins with different folds such as Greek key β‐barrel, β‐sandwich, β‐α‐β, and all α‐Greek key. CP mainly affects the protein stability and unfolding kinetics, while folding kinetics remains mostly unaltered. However, the effect of CP on metalloproteins is yet to be elaborately studied. The active site of metalloproteins poses an additional complexity in studying protein folding. Here, we investigate a CP variant (cpN42) of azurin—in both metal‐free and metal‐bound (holo) forms. As observed earlier in other proteins, apo‐forms of wild‐type (WT) and cpN42 fold with similar rates. In contrast, zinc‐binding accelerates the folding of WT but decelerates the folding of cpN42. On zinc‐binding, the spontaneous folding rate of WT increases by >250 times that of cpN42, which is unprecedented and the highest for any CP to date. On the other hand, zinc‐binding reduces the spontaneous unfolding rate of cpN42 by ~100 times, making the WT and CP azurins unfold at similar rates. Our study demonstrates metal binding as a novel way to modulate the unfolding and folding rates of CPs compared to their WT counterparts. We hope our study increases the understanding of the effect of CP on the folding mechanism and energy landscape of metalloproteins.