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Natively Unstructured Loops Differ from Other Loops

Avner Schlessinger, Jinfeng Liu, Burkhard Rost
2007 PLoS Computational Biology  
Citation: Schlessinger A, Liu J, Rost B (2007) Natively unstructured loops differ from other loops. PLoS Comput Biol 3(7): e140.  ...  could predict natively unstructured regions.  ...  The work was supported by grants U54-GM074958-01 from the Protein Structure Initiative of the US National Institutes of Health to the Northeast Structural Genomics Consortium and 2R01-LM07329-01 from the  ... 
doi:10.1371/journal.pcbi.0030140 pmid:17658943 pmcid:PMC1924875 fatcat:zxnjdv65fbhl7cwtbv5nvp4qhe

Natively Unstructured Loops Differ from Other Loops

Avner Schlessinger, Jinfeng Liu, Burkhard Rost
2005 PLoS Computational Biology  
Citation: Schlessinger A, Liu J, Rost B (2007) Natively unstructured loops differ from other loops. PLoS Comput Biol 3(7): e140.  ...  could predict natively unstructured regions.  ...  The work was supported by grants U54-GM074958-01 from the Protein Structure Initiative of the US National Institutes of Health to the Northeast Structural Genomics Consortium and 2R01-LM07329-01 from the  ... 
doi:10.1371/journal.pcbi.0030140.eor fatcat:5r4bwlgegjfqplmc36oobheroy

Protein folding transition states probed by loop extension

I. E. Sanchez
2007 Protein Science  
We propose a new way to characterize protein folding transition states by (1) insertion of one or more residues into an unstructured protein loop, (2) measurement of the effect on protein folding kinetics  ...  and thermodynamics, and (3) analysis of the results in terms of a rate-equilibrium free energy relationship, a Loop . a Loop reports on the fraction of molecules that form the perturbed loop in the transition  ...  In this case, folding of the loop from the unfolded to the native state should have a free energy cost of purely entropic origin.  ... 
doi:10.1110/ps.073217708 pmid:18156472 pmcid:PMC2144597 fatcat:5knyfkeporgqthdrr4xxq5mnha

Order, Disorder, and Flexibility

Lilia M. Iakoucheva, A.Keith Dunker
2003 Structure  
These differences can The cases where the DisEMBL predictors disagree be utilized to predict intrinsic order and disorder from with each other suggest an area for further exploration. the amino acid sequence  ...  predictors) provides additional support to the Intrinsically unstructured proteins and regions, which hypothesis that both disorder and flexibility indeed have are also known as natively unfolded and intrinsically  ...  These differences can The cases where the DisEMBL predictors disagree be utilized to predict intrinsic order and disorder from with each other suggest an area for further exploration. the amino acid sequence  ... 
doi:10.1016/j.str.2003.10.009 pmid:14604521 fatcat:axeaqi64zrhptipi3vtzkafv3m

Supporting on-stack replacement in unstructured languages by loop reconstruction and extraction

Raphael Mosaner, David Leopoldseder, Manuel Rigger, Roland Schatz, Hanspeter Mössenböck
2019 Proceedings of the 16th ACM SIGPLAN International Conference on Managed Programming Languages and Runtimes - MPLR 2019  
Bytecode interpreters, however, represent control flow implicitly via unstructured jumps and thus do not exhibit the required high-level loop representation.  ...  OSR allows switching from interpreted to compiled code during the execution of this code.  ...  Other algorithms build on the work of Tarjan and add support for irreducible control flow [24, 26] , which slightly differ in the returned irreducible loops [20] .  ... 
doi:10.1145/3357390.3361030 dblp:conf/pppj/MosanerLRSM19 fatcat:cmh6jnctzzacrl4jdx5g7xpgp4

Identification of Formation of Initial Native Structure in Onconase from an Unfolded State

Robert F. Gahl, Robert E. Oswald, Harold A. Scheraga
2011 Biochemistry  
To identify the residues responsible for initial formation of structured intermediates, the transition from an ensemble of unstructured three-disulfide species, 3S U , to a single structured three-disulfide  ...  The time-dependence of formation of native-like structure was then followed by NMR spectroscopy after arresting the transition at different times by lowering the pH to 3 and then acquiring 1 H, 15 N -HSQC  ...  The des-[30-75] was separated from other 3S U species by RP-HPLC as described in the previous section.  ... 
doi:10.1021/bi201168d pmid:22142378 pmcid:PMC3254794 fatcat:lzbmbewibfd2dhxkna3ni6du4q

The Early Phase of β2m Aggregation: An Integrative Computational Study Framed on the D76N Mutant and the ΔN6 Variant

Rui J. S. Loureiro, Diogo Vila-Viçosa, Miguel Machuqueiro, Eugene I. Shakhnovich, Patrícia F. N. Faísca
2019 Biomolecules  
Results from extensive protein–protein docking simulations predict an essential role of the C- and N-terminal regions (both variants), as well as of the BC-loop (ΔN6 variant), DE-loop (both variants) and  ...  EF-loop (D76N mutant) in dimerization.  ...  The DE-loop and the EF-loop also exhibited significant deviations from their native positions (up to~9 Å for I 2 ) across the investigated pH values (SI Tables S2 and S3 ).  ... 
doi:10.3390/biom9080366 pmid:31416179 pmcid:PMC6722664 fatcat:t5phiectmbcxflhqi7tpzmp67i

Natively unstructured regions in proteins identified from contact predictions

Avner Schlessinger, Marco Punta, Burkhard Rost
2007 Computer applications in the biosciences : CABIOS  
By computing the difference between predictions based on specific contacts (approach introduced here) and those based on generic potentials (realized in other methods), we might identify unstructured regions  ...  Low propensity for the formation of internal residue contacts has been previously used to predict natively unstructured regions.  ...  Genomics Consortium (U54-GM074958) and by the grant U54-GM072980 from the NIH.  ... 
doi:10.1093/bioinformatics/btm349 pmid:17709338 fatcat:32bjhx6xc5hhtokx3tukqom7ma

A Stevedore's Protein Knot

Daniel Bölinger, Joanna I. Sułkowska, Hsiao-Ping Hsu, Leonid A. Mirny, Mehran Kardar, José N. Onuchic, Peter Virnau, William Taylor
2010 PLoS Computational Biology  
To unravel this enigma, we performed folding simulations with a structure-based coarse-grained model and uncovered a possible mechanism by which the knot forms in a single loop flip.  ...  The proposed mechanism differs from mechanisms suggested before as it involves the flipping of a large loop over a mostly folded structure rather than folding via mostly unstructured knotted intermediates  ...  The flipping of a loop over a mostly folded structure constitutes a new scenario in the folding of knotted proteins which differs, e.g., from the folding of knots via partially unstructured knotted intermediates  ... 
doi:10.1371/journal.pcbi.1000731 pmid:20369018 pmcid:PMC2848546 fatcat:zmp35qarpvcgll55ohzggbkene

An Automated Approach to Segregate and Identify Functional or Disordered Loop Regions in Protein Structures using their Ramachandran Maps

Mattaparthi V.S. Kumar, Rajaram Swaminathan
2010 Biophysical Journal  
) and strands (MSRP < 64) stand effectively demarcated from the loop regions (MSRP > 130).  ...  The above results validate use of MSRP parameter as a tool to identify & investigate functionally active loops and unstructured regions in protein structures.  ... 
doi:10.1016/j.bpj.2009.12.2471 fatcat:323k3btq7vgmjkzzjqeakcganm

Controlling the Heterodimerisation of the Phytosulfokine Receptor 1 (PSKR1) via Island Loop Modulation

João Victor de Souza, Matthew Kondal, Piotr Zaborniak, Ryland Cairns, Agnieszka K. Bronowska
2021 International Journal of Molecular Sciences  
In this work, we used atomistic molecular dynamics (MD) simulations and free energy calculations to elucidate how the PSKR1 island domain (ID) loop forms and binds PSK.  ...  The binding of PSK to its cognate receptor, PSKR1, is modulated by the formation of a binding site located between a leucine-rich repeat (LRR) domain of PSKR1 and the loop located in the receptor's island  ...  The island loop conformation for state B is different from the native PSK-PSK1-SERK1 configuration.  ... 
doi:10.3390/ijms22041806 pmid:33670396 pmcid:PMC7918699 fatcat:b6fhc5rwt5evjc6c4wo3irxpqi

The effect of surface tethering on the folding of the src-SH3 protein domain

Zhuoyun Zhuang, Andrew I Jewett, Patricia Soto, Joan-Emma Shea
2009 Physical Biology  
We suggest locations on the protein at which tethering could be performed in single molecule experiments so as to leave the folding mechanism unaltered from the bulk.  ...  Our simulations reveal that tethering in a structured part of the transition state can dramatically alter the folding mechanism, while tethering in an unstructured part leaves the folding mechanism unaltered  ...  Each folding event was initiated from a different denatured state generated at high temperature (800 K). Simulations were terminated when 75% of the native contacts are formed.  ... 
doi:10.1088/1478-3975/6/1/015004 pmid:19208934 fatcat:wcknob6j5rfippnbyiezo6k43i

Thermophilic Adaptation of Protein Complexes Inferred from Proteomic Homology Modeling

Igor N. Berezovsky, Bin-Guang Ma, Alexander Goncearenco
2010 Biophysical Journal  
) and strands (MSRP < 64) stand effectively demarcated from the loop regions (MSRP > 130).  ...  The above results validate use of MSRP parameter as a tool to identify & investigate functionally active loops and unstructured regions in protein structures.  ... 
doi:10.1016/j.bpj.2009.12.2473 fatcat:eg4owvepuzd2xbro4kf7yixt4y

Protein-Protein Docking Using a Brownian Dynamics Simulations Approach

Xuan-Yu Meng, Hong-Xing Zhang, Mihaly Mezei, Meng Cui
2010 Biophysical Journal  
) and strands (MSRP < 64) stand effectively demarcated from the loop regions (MSRP > 130).  ...  The above results validate use of MSRP parameter as a tool to identify & investigate functionally active loops and unstructured regions in protein structures.  ... 
doi:10.1016/j.bpj.2009.12.2474 fatcat:u4hpwsfirvcxncudib5zjbzyjq

Origins of Thermophilicity in Endoglucanases

Ragothaman M. Yennamalli, Jeffrey D. Wolt, Taner Z. Sen
2010 Biophysical Journal  
) and strands (MSRP < 64) stand effectively demarcated from the loop regions (MSRP > 130).  ...  The above results validate use of MSRP parameter as a tool to identify & investigate functionally active loops and unstructured regions in protein structures.  ... 
doi:10.1016/j.bpj.2009.12.2472 fatcat:idqc2n2djff4jdozsefmahdjhu
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