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Fernández A, Scott LR. Advanced Modeling Reconciles Counterintuitive Decisions in Lead Optimization. Trends Biotechnol 2017; 35:490-497. [DOI: 10.1016/j.tibtech.2016.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 11/24/2016] [Accepted: 12/07/2016] [Indexed: 12/21/2022]
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2
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Fernández A. Water promotes the sealing of nanoscale packing defects in folding proteins. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:202101. [PMID: 24769440 DOI: 10.1088/0953-8984/26/20/202101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A net dipole moment is shown to arise from a non-Debye component of water polarization created by nanoscale packing defects on the protein surface. Accordingly, the protein electrostatic field exerts a torque on the induced dipole, locally impeding the nucleation of ice at the protein-water interface. We evaluate the solvent orientation steering (SOS) as the reversible work needed to align the induced dipoles with the Debye electrostatic field and computed the SOS for the variable interface of a folding protein. The minimization of the SOS is shown to drive protein folding as evidenced by the entrainment of the total free energy by the SOS energy along trajectories that approach a Debye limit state where no torque arises. This result suggests that the minimization of anomalous water polarization at the interface promotes the sealing of packing defects, thereby maintaining structural integrity and committing the protein chain to fold.
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Affiliation(s)
- Ariel Fernández
- Instituto Argentino de Matemática, National Research Council (CONICET), Saavedra 15, Buenos Aires 1083, Argentina. Collegium Basilea, Institute for Advanced Study, Hochstrasse 51, CH 4053 Basel, Switzerland
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3
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Fernández A. The principle of minimal episteric distortion of the water matrix and its steering role in protein folding. J Chem Phys 2013; 139:085101. [DOI: 10.1063/1.4818874] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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4
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Fernández A, Fraser C, Scott LR. Purposely engineered drug–target mismatches for entropy-based drug optimization. Trends Biotechnol 2012; 30:1-7. [DOI: 10.1016/j.tibtech.2011.07.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 07/13/2011] [Accepted: 07/13/2011] [Indexed: 12/11/2022]
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5
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Folding and wrapping soluble proteins exploring the molecular basis of cooperativity and aggregation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009. [PMID: 19186252 DOI: 10.1016/s0079-6603(08)00602-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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6
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Fernández A, Crespo A. Protein wrapping: a molecular marker for association, aggregation and drug design. Chem Soc Rev 2008; 37:2373-82. [PMID: 18949110 DOI: 10.1039/b804150b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In this tutorial review we survey the concept of protein wrapping from a physico-chemical perspective. Wrapping is introduced as an indicator of the packing quality of protein structure. Thus, while a well-wrapped protein is sustainable in isolation, a poorly wrapped protein is reliant on binding partnerships to maintain its structural integrity. At a local level, wrapping is indicative of the extent of solvent exposure of the amide-carbonyl hydrogen bonds of the protein backbone. Poorly wrapped hydrogen bonds, the so-called dehydrons, are shown to represent structural vulnerabilities. These singularities are sticky, hence promoters of protein associations. We also focus on severely under-wrapped protein structures that belong to an order/disorder twilight. Such proteins are shown to be prone to aggregate. Finally, we survey the recent exploitation of dehydrons as targetable features to promote specificity in drug-based cancer therapy. Dehydrons prove to be valuable targets to reduce side effects and enhance drug safety.
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Affiliation(s)
- Ariel Fernández
- Department of Bioengineering, Rice University, Houston, TX 77005, USA.
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7
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Kouza M, Hu CK, Li MS. New force replica exchange method and protein folding pathways probed by force-clamp technique. J Chem Phys 2008; 128:045103. [DOI: 10.1063/1.2822272] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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8
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Carr JM, Wales DJ. Global optimization and folding pathways of selected alpha-helical proteins. J Chem Phys 2007; 123:234901. [PMID: 16392943 DOI: 10.1063/1.2135783] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The results of basin-hopping global optimization simulations are presented for four small, alpha-helical proteins described by a coarse-grained potential. A step-taking scheme that incorporates the local conformational preferences extracted from a large number of high-resolution protein structures is compared with an unbiased scheme. In addition, the discrete path sampling method is used to investigate the folding of one of the proteins, namely, the villin headpiece subdomain. Folding times from kinetic Monte Carlo simulations and iterative calculations based on a Markovian first-step analysis for the resulting stationary-point database are in good mutual agreement, but differ significantly from the experimental values, probably because the native state is not the global free energy minimum for the potential employed.
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Affiliation(s)
- Joanne M Carr
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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9
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Abstract
Molecular therapy requires a careful control of specificity. The authors review the recent advances in this regard focusing on a novel marker for ligand-target interaction, the solvent-exposed hydrogen bond or dehydron. Dehydrons promote their own dehydration and are not conserved across homolog proteins. Thus, the so-called wrapping technology is geared at enhancing drug specificity and hinges on an analysis of interfacial dehydrons in target-ligand complexes to assess microenvironmental changes occurring on association. Dehydron differences across purported targets have been exploited to redesign drugs in order to enhance selectivity. Tested wrapping modifications to cancer drugs are reviewed. Distance matrices defined by comparing dehydron patterns across targets correlate strongly with pharmacologic distances. This fact suggests a broad applicability of the wrapping technology, ultimately leading to molecular therapies with tighter control of side effects.
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Affiliation(s)
- Ariel Fernández
- Karl F. Hasselman Chair in Engineering, Professor of BioEngineering, Rice University, Department of Bioengineering, Houston, TX 77005, USA.
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10
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Li MS, Kouza M, Hu CK. Refolding upon force quench and pathways of mechanical and thermal unfolding of ubiquitin. Biophys J 2006; 92:547-61. [PMID: 17071662 PMCID: PMC1751401 DOI: 10.1529/biophysj.106.087684] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The refolding from stretched initial conformations of ubiquitin (PDB ID: 1ubq) under the quenched force is studied using the C(alpha)-Gō model and the Langevin dynamics. It is shown that the refolding decouples the collapse and folding kinetics. The force-quench refolding-times scale as tau(F) approximately exp(f(q)Deltax(F)/k(B)T), where f(q) is the quench force and Deltax(F) approximately 0.96 nm is the location of the average transition state along the reaction coordinate given by the end-to-end distance. This value is close to Deltax(F) approximately 0.8 nm obtained from the force-clamp experiments. The mechanical and thermal unfolding pathways are studied and compared with the experimental and all-atom simulation results in detail. The sequencing of thermal unfolding was found to be markedly different from the mechanical one. It is found that fixing the N-terminus of ubiquitin changes its mechanical unfolding pathways much more drastically compared to the case when the C-end is anchored. We obtained the distance between the native state and the transition state Deltax(UF) approximately 0.24 nm, which is in reasonable agreement with the experimental data.
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Affiliation(s)
- Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
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11
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Mayewski S. A multibody, whole-residue potential for protein structures, with testing by Monte Carlo simulated annealing. Proteins 2006; 59:152-69. [PMID: 15723360 DOI: 10.1002/prot.20397] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A new multibody, whole-residue potential for protein tertiary structure is described. The potential is based on the local environment surrounding each main-chain alpha carbon (CA), defined as the set of all residues whose CA coordinates lie within a spherical volume of set radius in 3-dimensional (3D) space surrounding that position. It is shown that the relative positions of the CAs in these local environments belong to a set of preferred templates. The templates are derived by cluster analysis of the presently available database of over 3000 protein chains (750,000 residues) having not more than 30% sequence similarity. For each template is derived also a set of residue propensities for each topological position in the template. Using lookup tables of these derived templates, it is then possible to calculate an energy for any conformation of a given protein sequence. The application of the potential to ab initio protein tertiary structure prediction is evaluated by performing Monte Carlo simulated annealing on test protein sequences.
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Affiliation(s)
- Stefan Mayewski
- Max-Planck-Institut für Biochemie, 82152 Martinsried, Germany.
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12
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Abstract
The small alpha/beta protein ubiquitin has been used as a model system for experimental and computational studies on protein folding for many years. Here, we present a comprehensive phi-value analysis and characterize the structure and energetics of the transition state ensemble (TSE). Twenty-seven non-disruptive mutations are made throughout the structure and a range of phi-values from zero to one are observed. The values cluster such that medium and high values and found only in the N-terminal region of the protein, whilst the C-terminal region has consistently low phi-values. In the TSE, the main alpha-helix appears to be fully formed (two phi-values which specifically probe helical structure are one) and the helix is stabilized by packing against the first beta-turn, which is partially structured. In striking comparison, the phi-values in the C-terminal region are all very low, suggesting that this region of the protein is largely unstructured in the TSE. Data are consistent with a nucleation-condensation mechanism in which there is a highly polarized folding nucleus comprising the first beta-hairpin and the alpha-helix. Data presented from the protein engineering study and phi-value analysis are compared with results from other experimental studies and also computational studies.
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Affiliation(s)
- Heather M Went
- Chemistry Department, Centre for Protein Engineering, Lensfield Road, Cambridge CB2 1EW, UK
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Fernández A. Oncogenic mutations and packing defects in protein structure. J Biomol Struct Dyn 2003; 21:9-14. [PMID: 12854955 DOI: 10.1080/07391102.2003.10506901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Oncogenic mutations in expressed proteins are of primary interest to understand tumor formation but their structural consequences bearing on protein function are not clearly understood. In this contribution I report on two illustrative examples, p21ras and p57, revealing that such mutations have an effect on specific structural deficiencies in the packing of the protein structure, i. e., on backbone hydrogen bonds insufficiently shielded from water attack. These structural deficiencies in the wild type are typically "corrected intermolecularly" by protein complexation or protein-ligand association. However, in the oncogenic mutants, these binding signals are partially or completely suppressed: the mutated residues properly wrap or desolvate the hydrogen bonds intramolecularly. Thus, the interactivity of the proteins becomes impaired: their binding affinity decreases sharply, as there is no thermodynamic benefit from removing water surrounding properly desolvated hydrogen bonds. The results, specialized for p21ras and p53, reveal how oncogenic mutations determine a hindrance to GAP-induced hydrolysis (p21) and decrease binding affinity for DNA (p53). Furthermore, the oncogenic potential of mutations in residues not directly engaged in the interface electrostatics is assessed. The results suggest that a high sensitivity of structural defects to genetic accident might be a necessary condition to establish the existence of a proto-oncogene, an angle that merits a systematic study.
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Affiliation(s)
- Ariel Fernández
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA.
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14
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Despa F, Fernández A, Berry RS, Levy Y, Jortner J. Interbasin motion approach to dynamics of conformationally constrained peptides. J Chem Phys 2003. [DOI: 10.1063/1.1554393] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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15
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Fernández A, Kardos J, Goto Y. Protein folding: could hydrophobic collapse be coupled with hydrogen-bond formation? FEBS Lett 2003; 536:187-92. [PMID: 12586361 DOI: 10.1016/s0014-5793(03)00056-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A judicious examination of an exhaustive PDB sample of soluble globular proteins of moderate size (N<102) reveals a commensurable relationship between hydrophobic surface burial and number of backbone hydrogen bonds. An analysis of 50,000 conformations along the longest all-atom MD trajectory allows us to infer that not only the hydrophobic collapse is concurrent with the formation of backbone amide-carbonyl hydrogen bonds, they are also dynamically coupled processes. In statistical terms, hydrophobic clustering of the side chains is inevitably conducive to backbone burial and the latter process becomes thermodynamically too costly and kinetically unfeasible without amide-carbonyl hydrogen-bond formation. Furthermore, the desolvation of most hydrogen bonds is exhaustive along the pathway, implying that such bonds guide the collapse process.
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Affiliation(s)
- Ariel Fernández
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA.
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16
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Fernández A, Berry RS. Extent of hydrogen-bond protection in folded proteins: a constraint on packing architectures. Biophys J 2002; 83:2475-81. [PMID: 12414681 PMCID: PMC1302333 DOI: 10.1016/s0006-3495(02)75258-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Progressive structuring and ultimately exclusion of water by hydrophobes surrounding backbone hydrogen bonds turn the latter into guiding factors of protein folding. Here we demonstrate that an arrangement of five hydrophobes yields an optimal hydrogen-bond stabilization. This motif is shown to be nearly ubiquitous in native folds.
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Affiliation(s)
- Ariel Fernández
- Institute for Biophysical Dynamics, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.
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17
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Abstract
The effect of solvent structuring induced by molecular crowding is elucidated within a competitive situation involving protein folding and aggregation. Two patterned fragments of amyloidogenic proteins are chosen as study cases and analyzed by molecular dynamics with an implicit treatment of the solvent. The extent of crowding needed to induce aggregation is determined. The results constitute a first step to assess the relevance of in vivo environments in understanding fibrillogenesis. The approach is independently validated by satisfactorily reproducing the results of an all-atom explicit solvent trajectory.
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Affiliation(s)
- Ariel Fernández
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA.
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18
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Sosnick TR, Berry RS, Colubri A, Fernández A. Distinguishing foldable proteins from nonfolders: when and how do they differ? Proteins 2002; 49:15-23. [PMID: 12211012 DOI: 10.1002/prot.10193] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
When a denatured polypeptide is put into refolding conditions, it undergoes conformational changes on a variety of times scales. We set out here to distinguish the fast events that promote productive folding from other processes that may be generic to any non-folding polypeptide. We have apply an ab initio folding algorithm to model the folding of various proteins and their compositionally identical, random-sequence analogues. In the earliest stages, proteins and their scrambled-sequence counterparts undergo indistinguishable reductions in the extent to which they explore conformation space. For both polypeptides, an early contraction occurs but does not involve the formation of a distinct intermediate. Following this phase, however, the naturally-occurring sequences are distinguished by an increase in the formation of three-body correlations wherein a hydrophobic group desolvates and protects an intra-molecular hydrogen bond. These correlations are manifested in a mild but measurable reduction of the accessible configuration space beyond that of the random-sequence peptides, and portend the folding to the native structure. Hence, early events reflect a generic response of the denatured ensemble to a change in solvent condition, but the wild-type sequence develops additional correlations as its structure evolves that can reveal the protein's foldability.
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Affiliation(s)
- Tobin R Sosnick
- Department of Biochemistry and Molecular Biology and the Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, USA.
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19
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Fernández A. Desolvation shell of hydrogen bonds in folded proteins, protein complexes and folding pathways. FEBS Lett 2002; 527:166-70. [PMID: 12220654 DOI: 10.1016/s0014-5793(02)03204-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A few backbone hydrogen bonds (HBS) in native protein folds are poorly protected from water attack: their desolvation shell contains an inordinately low number of hydrophobic residues. Thus, an approach by solvent-structuring moieties of a binding partner should contribute significantly to enhance their stability. This effect represents an important factor in the site specificity inherent to protein binding, as inferred from a strong correlation between poorly desolvated HBs and binding sites. The desolvation shells were also examined in a dynamic context: except for a few singular under-protected bonds, the size of desolvation shells is preserved along the folding trajectory.
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Affiliation(s)
- Ariel Fernández
- Institute for Biophysical Dynamics, Cummings Life Science Center #439D, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.
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20
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Abstract
As proteins fold, a progressive structuring, immobilization and eventual exclusion of water surrounding backbone hydrogen bonds takes place. This process turns hydrogen bonds into major determinants of the folding pathway and compensates for the penalty of desolvation of the backbone polar groups. Taken as an average over all hydrogen bonds in a native fold, this extent of protection is found to be nearly ubiquitous. It is dynamically crucial, determining a constraint in the long-time limit behavior of coarse-grained ab initio simulations. Furthermore, an examination of one of the longest available (1micros) all-atom simulations with explicit solvent reveals that this average extent of protection is a constant of motion for the folding trajectory. We propose how such a stabilization is best achieved by clustering five hydrophobes around the backbone hydrogen bonds, an arrangement that yields the optimal stabilization. Our results support and clarify the view that hydrophobic surface burial should be commensurate with hydrogen-bond formation and enable us to define a basic desolvation motif inherent to structure and folding dynamics.
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Affiliation(s)
- Ariel Fernández
- Institute for Biophysical Dynamics, The University of Chicago, 920E 58th Street Chicago, IL 60637, USA
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21
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Abstract
We generate ab initio folding pathways in two single-domain proteins, hyperthermophile variant of protein G domain (1gb4) and ubiquitin (1ubi), both presumed to be two-state folders. Both proteins are endowed with the same topology but, as shown in this work, rely to a different extent on large-scale context to find their native folds. First, we demonstrate a generic feature of two-state folders: A downsizing of structural fluctuations is achieved only when the protein reaches a stationary plateau maximizing the number of highly protected hydrogen bonds. This enables us to identify the folding nucleus and show that folding does not become expeditious until a topology is generated that is able to protect intramolecular hydrogen bonds from water attack. Pathway heterogeneity is shown to be dependent on the extent to which the protein relies on large-scale context to fold, rather than on contact order: Proteins that can only stabilize native secondary structure by packing it against scaffolding hydrophobic moieties are meant to have a heterogeneous transition-state ensemble if they are to become successful folders (otherwise, successful folding would be too fortuitous an event.) We estimate mutational Phi values as ensemble averages and deconvolute individual-route contributions to the averaged two-state kinetic picture. Our results find experimental corroboration in the well-studied chymotrypsin inhibitor (CI2), while leading to verifiable predictions for the other two study cases.
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Affiliation(s)
- Ariel Fernández
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA.
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22
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Abstract
A method is presented to identify hot mutational spots and predict the extent of surface burial at the transition state relative to the native fold in two-state folding proteins. The method is based on ab initio simulations of folding histories in which transitions between coarsely defined conformations and pairwise interactions are dependent on the solvent environments created by the chain. The highly conserved mammalian ubiquitin is adopted as a study case to make predictions. The evolution in time of the chain topology suggests a nucleation process with a critical point signaled by a sudden quenching of structural fluctuations. The occurrence of this nucleus is shown to be concurrent with a sudden escalation in the number of three-body correlations whereby hydrophobic units approach residue pairs engaged in amide-carbonyl hydrogen bonding. These correlations determine a pattern designed to structure the surrounding solvent, protecting intramolecular hydrogen bonds from water attack. Such correlations are shown to be required to stabilize the nucleus, with kinetic consequences for the folding process. Those nuclear residues that adopt the dual role of protecting and being protected while engaged in hydrogen bonds are predicted to be the hottest mutational spots. Some such residues are shown not to retain the same protecting role in the native fold. This kinetic treatment of folding nucleation is independently validated vis-a-vis a Phi-value analysis on chymotrypsin inhibitor 2, a protein for which extensive mutational data exists.
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Affiliation(s)
- Ariel Fernández
- Max-Planck-Institut für Biochemie, Martinsried (bei München), Germany and Instituto de Matemática, Universidad Nacional del Sur-CONICET, Bahia Blanca, Argentina.
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Fernández A. How do we probe ubiquitin's pathway heterogeneity? J Biomol Struct Dyn 2002; 19:949-60. [PMID: 12023798 DOI: 10.1080/07391102.2002.10506799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We identify folding pathways for ubiquitin and assess its extent of transition state (TS) heterogeneity using a kinetically controlled ab initio algorithm that generates a coarse-grained description of torsional dynamics. The algorithm computes the time evolution of backbone-motion constraints, finds optimized conformations within such constraints, evaluates local solvent environments, and rescales accordingly the energetic contributions to determine the transition to the next set of torsional constraints. Native and nonnative structural features are found in the TS ensemble determined from a pool of 72 successful runs whose final folds are within 4-5 A RMSD from native. Certain nonnative features at the TS are shown to be necessary to create a large-scale context that overrides local propensities. Such misfolds undergo a subsequent rearrangement on the downhill side of the energy profile. The effects of tunable bi-histidine metal-binding sites, point mutations, negative Phi-value mutations, and denaturant on kinetics are predicted.
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Affiliation(s)
- Ariel Fernández
- Instituto de Matemática, UNS-CONICET, Bahiá Blanca, Argentina.
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24
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Abstract
A coarse-grained simulation accessing relevant folding timescales for beta-lactoglobulin was corroborated experimentally and reveals a dynamic role for nonnative structures dictated by local propensity vis-á-vis the large-scale context. This picture prompts us to shift focus, leaving aside the hierarchical vs. nonhierarchical controversy.
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Affiliation(s)
- Ariel Fernández
- Institute for Biophysical Dynamics, Cummings Life Science Center #439D, The University of Chicago, Chicago, IL 60637, USA.
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Colubri A, Fernández A. Pathway diversity and concertedness in protein folding: an ab-initio approach. J Biomol Struct Dyn 2002; 19:739-64. [PMID: 11922833 DOI: 10.1080/07391102.2002.10506782] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Making use of an ab-initio folding simulator, we generate in vitro pathways leading to the native fold in moderate size single- domain proteins. The assessment of pathway diversity is not biased by any a priori information on the native fold. We focus on two study cases, hyperthermophile variant of protein G domain (1gb4) and ubiquitin (1ubi), with the same topology but different context dependence in their native folds. We demonstrate that a quenching of structural fluctuations is achieved once the proteins find a stationary plateau maximizing the number of highly protected hydrogen bonds. This enables us to identify the folding nucleus and show that folding does not become expeditious until a concerted event takes place generating a topology able to prevent water attack on a maximal number of hydrogen bonds. This result is consistent with the standard nucleation mechanism postulated for two-state folders. Pathway diversity is correlated with the extent of conflict between local structural propensity and large-scale context, rather than with contact order: In highly context-dependent proteins, the success of folding cannot rely on a single fortuitous event in which local propensity is overruled by large-scale effects. We predict mutational Pi values on individual pathways, compute ensemble averages and predict extent of surface burial and percentage of hydrogen bonding on each component of the transition state ensemble, thus deconvoluting individual folding-route contributions to the averaged two-state kinetic picture. Our predicted kinetic isotopic effects find experimental support and lead to further probes. Finally, the molecular redesign potentiality of the method, aimed at increasing folding expediency, is explored.
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Affiliation(s)
- Andrés Colubri
- Instituto de Matemática, Universidad Nacional del Sur, Consejo Nacional de Investigaciones Científicas y Técnicas, 8000 Bahía Blanca, Argentina
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26
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Fernández A. Protein design from in silico dynamic information: the emergence of the 'turn-dock-lock' motif. Protein Eng Des Sel 2002; 15:1-6. [PMID: 11842231 DOI: 10.1093/protein/15.1.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A protein design methodology based on ab initio folding simulations is described and illustrated. First, the time evolution of the chain topology is generated to identify a collapse-triggering nucleus. Then, a minimal spliced sequence of nuclear residues is created and systematically mutated in silico until it can sustain a stable conformation retaining the original nucleus topology. The mutations introduce a structural compensation for the deletions and eventually lead to the recovery of the native fold motif beyond topological identity. For ubiquitin, the systematically modified sequence is predicted to be a resilient folder, since it is 92% homologous to the hyperthermophile variant of B1-domain in streptococcal protein G. The methodology enabling us to identify the nucleus is independently validated vis-á-vis site-directed mutagenesis experiments on chymotrypsin inhibitor (CI2).
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Affiliation(s)
- Ariel Fernández
- Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz, 82152 Martinsried (bei München), Germany.
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27
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Fernández A. Cooperative walks in a cubic lattice: Protein folding as a many-body problem. J Chem Phys 2001. [DOI: 10.1063/1.1405447] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Fernández A, Appignanesi GA, Colubri A. Finding the collapse-inducing nucleus in a folding protein. J Chem Phys 2001. [DOI: 10.1063/1.1368134] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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