MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data.
نویسندگان
چکیده
MERA (Maximum Entropy Ramachandran map Analysis from NMR data) is a new webserver that generates residue-by-residue Ramachandran map distributions for disordered proteins or disordered regions in proteins on the basis of experimental NMR parameters. As input data, the program currently utilizes up to 12 different parameters. These include three different types of short-range NOEs, three types of backbone chemical shifts ((15)N, (13)C(α), and (13)C'), six types of J couplings ((3)JHNHα, (3)JC'C', (3)JC'Hα, (1)JHαCα, (2)JCαN and (1)JCαN), as well as the (15)N-relaxation derived J(0) spectral density. The Ramachandran map distributions are reported in terms of populations of their 15° × 15° voxels, and an adjustable maximum entropy weight factor is available to ensure that the obtained distributions will not deviate more from a newly derived coil library distribution than required to account for the experimental data. MERA output includes the agreement between each input parameter and its distribution-derived value. As an application, we demonstrate performance of the program for several residues in the intrinsically disordered protein α-synuclein, as well as for several static and dynamic residues in the folded protein GB3.
منابع مشابه
Quantitative Residue-Specific Protein Backbone Torsion Angle Dynamics from Concerted Measurement of J Couplings
Three-bond JC′C′ and JHNHα couplings in peptides and proteins are functions of the intervening backbone torsion angle φ. In well-ordered regions, JHNHα is tightly correlated with JC′C′, but the presence of large φ angle fluctuations differentially affects the two types of couplings. Assuming the φ angles follow a Gaussian distribution, the width of this distribution can be extracted from JC′C′ ...
متن کاملQuantitative residue-specific protein backbone torsion angle dynamics from concerted measurement of 3J couplings.
Three-bond (3)J(C'C') and (3)J(HNHα) couplings in peptides and proteins are functions of the intervening backbone torsion angle ϕ. In well-ordered regions, (3)J(HNHα) is tightly correlated with (3)J(C'C'), but the presence of large ϕ angle fluctuations differentially affects the two types of couplings. Assuming the ϕ angles follow a Gaussian distribution, the width of this distribution can be e...
متن کاملFluctuations of backbone torsion angles obtained from NMR-determined structures and their prediction.
Protein molecules exhibit varying degrees of flexibility throughout their three-dimensional structures. Protein structural flexibility is often characterized by fluctuations in the Cartesian coordinate space. On the other hand, the protein backbone can be mostly defined by two torsion angles ϕ and ψ only. We introduce a new flexibility descriptor, backbone torsion-angle fluctuation derived from...
متن کاملA self-consistent description of the conformational behavior of chemically denatured proteins from NMR and small angle scattering.
Characterization of the conformational properties of unfolded proteins is essential for understanding the mechanisms of protein folding and misfolding. This information is also fundamental to determining the relationship between flexibility and function in the highly diverse families of intrinsically disordered proteins. Here we present a self-consistent model of conformational sampling of chem...
متن کاملTANGLE: Two-Level Support Vector Regression Approach for Protein Backbone Torsion Angle Prediction from Primary Sequences
Protein backbone torsion angles (Phi) and (Psi) involve two rotation angles rotating around the C(α)-N bond (Phi) and the C(α)-C bond (Psi). Due to the planarity of the linked rigid peptide bonds, these two angles can essentially determine the backbone geometry of proteins. Accordingly, the accurate prediction of protein backbone torsion angle from sequence information can assist the prediction...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Journal of biomolecular NMR
دوره 63 1 شماره
صفحات -
تاریخ انتشار 2015