Rama Reddy Goluguri

All Publications

• Transcriptional factors control their diffusion on DNA by modulating their dynamics Goluguri, R., Sadqi, M., Munoz, V. CELL PRESS. 2022: 457A

  View details for Web of Science ID 000759523003039

• Microsecond sub-domain motions and the folding and misfolding of the mouse prion protein ELIFE Goluguri, R., Sen, S., Udgaonkar, J. 2019; 8

  Abstract

  Protein aggregation appears to originate from partially unfolded conformations that are sampled through stochastic fluctuations of the native protein. It has been a challenge to characterize these fluctuations, under native like conditions. Here, the conformational dynamics of the full-length (23-231) mouse prion protein were studied under native conditions, using photoinduced electron transfer coupled to fluorescence correlation spectroscopy (PET-FCS). The slowest fluctuations could be associated with the folding of the unfolded state to an intermediate state, by the use of microsecond mixing experiments. The two faster fluctuations observed by PET-FCS, could be attributed to fluctuations within the native state ensemble. The addition of salt, which is known to initiate the aggregation of the protein, resulted in an enhancement in the time scale of fluctuations in the core of the protein. The results indicate the importance of native state dynamics in initiating the aggregation of proteins.

  View details for DOI 10.7554/eLife.44766

  View details for Web of Science ID 000467898100001

  View details for PubMedID 31025940

  View details for PubMedCentralID PMC6516828

• Ruggedness in the Free Energy Landscape Dictates Misfolding of the Prion Protein JOURNAL OF MOLECULAR BIOLOGY Moulick, R., Goluguri, R., Udgaonkar, J. B. 2019; 431 (4): 807-824

  Abstract

  Experimental determination of the key features of the free energy landscapes of proteins, which dictate their adeptness to fold correctly, or propensity to misfold and aggregate and which are modulated upon a change from physiological to aggregation-prone conditions, is a difficult challenge. In this study, sub-millisecond kinetic measurements of the folding and unfolding of the mouse prion protein reveal how the free energy landscape becomes more complex upon a shift from physiological (pH 7) to aggregation-prone (pH 4) conditions. Folding and unfolding utilize the same single pathway at pH 7, but at pH 4, folding occurs on a pathway distinct from the unfolding pathway. Moreover, the kinetics of both folding and unfolding at pH 4 depend not only on the final conditions but also on the conditions under which the processes are initiated. Unfolding can be made to switch to occur on the folding pathway by varying the initial conditions. Folding and unfolding pathways appear to occupy different regions of the free energy landscape, which are separated by large free energy barriers that change with a change in the initial conditions. These barriers direct unfolding of the native protein to proceed via an aggregation-prone intermediate previously identified to initiate the misfolding of the mouse prion protein at low pH, thus identifying a plausible mechanism by which the ruggedness of the free energy landscape of a protein may modulate its aggregation propensity.

  View details for DOI 10.1016/j.jmb.2018.12.009

  View details for Web of Science ID 000459949500012

  View details for PubMedID 30611749

• A Dry Transition State More Compact Than the Native State Is Stabilized by Non-Native Interactions during the Unfolding of a Small Protein BIOCHEMISTRY Sen, S., Goluguri, R., Udgaonkar, J. B. 2017; 56 (29): 3699-3703

  Abstract

  Defining the role of non-native interactions in directing the course of protein folding or unfolding reactions has been a difficult challenge. In particular, the extent to which such interactions play a productive role by stabilizing the structures of transition states (TSs) found on the folding and unfolding pathways of proteins is not known. On the contrary, it is thought that the TSs are expanded forms of the N state stabilized by native interactions, and it is not known whether non-native interactions can modulate TS structure. In this study of the unfolding of the SH3 domain of PI3 kinase using a microsecond mixing methodology, partial non-native structure formation is shown to occur initially during unfolding. The TS of this partial "folding during unfolding" reaction is more compact than the N state: the apparent rate constant of Trp53 burial during this reaction decreases with an increase in denaturant concentration. Kinetic studies of the unfolding of mutant variants suggest that the unusually compact TS is stabilized by interactions not present in N and that these non-native interactions are hydrophobic in nature. It was determined that mutation could be used to tune the degree of compaction in the TS.

  View details for DOI 10.1021/acs.biochem.7b00388

  View details for Web of Science ID 000406573100002

  View details for PubMedID 28682056

• Microsecond Rearrangements of Hydrophobic Clusters in an Initially Collapsed Globule Prime Structure Formation during the Folding of a Small Protein JOURNAL OF MOLECULAR BIOLOGY Goluguri, R., Udgaonkar, J. B. 2016; 428 (15): 3102-3117

  Abstract

  Determining how polypeptide chain collapse initiates structure formation during protein folding is a long standing goal. It has been challenging to characterize experimentally the dynamics of the polypeptide chain, which lead to the formation of a compact kinetic molten globule (MG) in about a millisecond. In this study, the sub-millisecond events that occur early during the folding of monellin from the guanidine hydrochloride-unfolded state have been characterized using multiple fluorescence and fluorescence resonance energy transfer probes. The kinetic MG is shown to form in a noncooperative manner from the unfolded (U) state as a result of at least three different processes happening during the first millisecond of folding. Initial chain compaction completes within the first 37μs, and further compaction occurs only after structure formation commences at a few milliseconds of folding. The transient nonnative and native-like hydrophobic clusters with side chains of certain residues buried form during the initial chain collapse and the nonnative clusters quickly disassemble. Subsequently, partial chain desolvation occurs, leading to the formation of a kinetic MG. The initial chain compaction and subsequent chain rearrangement appear to be barrierless processes. The two structural rearrangements within the collapsed globule appear to prime the protein for the actual folding transition.

  View details for DOI 10.1016/j.jmb.2016.06.015

  View details for Web of Science ID 000381953100013

  View details for PubMedID 27370109

• Rise of the Helix from a Collapsed Globule during the Folding of Monellin BIOCHEMISTRY Goluguri, R., Udgaonkar, J. B. 2015; 54 (34): 5356-5365

  Abstract

  Early kinetic intermediates observed during the folding of many proteins are invariably compact and appear to possess some secondary structure. Consequently, it has been difficult to understand whether compaction drives secondary structure formation or secondary structure formation facilitates compaction during folding. In this study of the folding of single-chain monellin, it is shown that a kinetic molten globule (MG) is populated at 2 ms of folding. Far-UV circular dichroism (CD) measurements show that the kinetic MG is devoid of any helical structure even under the most stabilizing folding conditions. Multisite fluorescence resonance energy transfer (FRET) measurements show that the kinetic MG is compact with different segments having contracted to different extents. It is shown that the sequence segment that goes on to form the sole helix in the native protein is fully collapsed in the kinetic MG. This segment expands to accommodate the helix as the kinetic MG folds further to the native state, while other segments of the protein contract. Helix formation starting from the kinetic MG is shown to occur in multiple kinetic steps, whether measured by far-UV CD or by FRET.

  View details for DOI 10.1021/acs.biochem.5b00730

  View details for Web of Science ID 000360773400013

  View details for PubMedID 26258844